Sample records for naphthalene diimide ligands

  1. Divalent Naphthalene Diimide Ligands Display High Selectivity for the Human Telomeric G‐quadruplex in K+ Buffer

    PubMed Central

    Street, Steven T. G.; Chin, Donovan N.; Hollingworth, Gregory J.; Berry, Monica

    2017-01-01

    Abstract Selective G‐quadruplex ligands offer great promise for the development of anti‐cancer therapies. A novel series of divalent cationic naphthalene diimide ligands that selectively bind to the hybrid form of the human telomeric G‐quadruplex in K+ buffer are described herein. We demonstrate that an imidazolium‐bearing mannoside‐conjugate is the most selective ligand to date for this quadruplex against several other quadruplex and duplex structures. We also show that a similarly selective methylpiperazine‐bearing ligand was more toxic to HeLa cancer cells than doxorubicin, whilst exhibiting three times less toxicity towards fetal lung fibroblasts WI‐38. PMID:28257554

  2. Modified naphthalene diimide as a suitable tetraplex DNA ligand: application to cancer diagnosis and anti-cancer drug

    NASA Astrophysics Data System (ADS)

    Takenaka, Shigeori

    2017-07-01

    It is known that naphthalene diimide carrying two substituents binds to DNA duplex with threading intercalation. Naphthalene diimide carrying ferrocene moieties, ferrocenylnaphthalene diimide (FND), formed a stable complex with DNA duplex and an electrochemical gene detection was achieved with current signal generated from FND bound to the DNA duplex between target DNA and DNA probe immobilized electrode. FND couldn't bind to the mismatched and its surrounding region of DNA duplex and thus FND was applied to the precision detection of single nucleotide polymorphisms (SNPs) using the improved discrimination ability between fully matched and mismatched DNA hybrids and multi-electrode chip. Some of FND derivatives bound to telomere DNA tetraplex stronger than to DNA duplex and was applied to cancer diagnosis as a measure of the elongated telomere DNA with telomerase as a suitable maker of cancer. Furthermore, cyclic naphthalene diimides realized the extremely high preference for DNA tetraplex over DNA duplex. Such molecules will open an effective anti-cancer drug based on telomerase specific inhibitor.

  3. A core-substituted naphthalene diimide fluoride sensor.

    PubMed

    Bhosale, Sheshanath V; Bhosale, Sidhanath V; Kalyankar, Mohan B; Langford, Steven J

    2009-12-03

    The synthesis and characterization of a highly fluorescent core-substituted naphthalene diimide sensor (varphi = 0.34) bearing a bis-sulfonamide group is described. The compound shows a unique selectivity and reactivity for the fluoride ion over other anions in CHCl(3) by a two-stage deprotonation process leading to a colorimetric response. In DMSO solution, the sensor is shown to be highly selective for fluoride (K(a) approximately 10(6) M(-1)) over other anions with more pronounced changes in absorption characteristics.

  4. The reductive aromatization of naphthalene diimide: a versatile platform for 2,7-diazapyrenes.

    PubMed

    Nakazato, Takumi; Kamatsuka, Takuto; Inoue, Junichi; Sakurai, Tsuneaki; Seki, Shu; Shinokubo, Hiroshi; Miyake, Yoshihiro

    2018-05-17

    The reductive aromatization of naphthalene diimide provides tetrapivaloxy-2,7-diazapyrene, which serves as a versatile platform toward peripherally substituted 2,7-diazapyrenes. Time-resolved microwave conductivity measurements demonstrated that the intrinsic electron mobility of 2,7-diazapyrene is significantly higher than that of the corresponding pyrene.

  5. Poly(naphthalene diimide) vinylene: solid state red emission and semiconducting properties for transistors

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

    Liang, Xianfeng; Tan, Luxi; Liu, Zitong

    Here in this work, a conjugated polymer PNV is developed, linking naphthalene diimide with a vinyl linkage. Owing to the C-H ∙∙∙O hydrogen bond between the carbonyl and the vinyl, PNV exhibits a high red emission with a quantum yield of 33.4% in the solid state while it shows n-type properties with an electron mobility up to 1.5 x 10 -3 cm 2 V -1 s -1 in organic field effect transistors, simultaneously.

  6. Poly(naphthalene diimide) vinylene: solid state red emission and semiconducting properties for transistors

    DOE PAGES

    Liang, Xianfeng; Tan, Luxi; Liu, Zitong; ...

    2017-04-06

    Here in this work, a conjugated polymer PNV is developed, linking naphthalene diimide with a vinyl linkage. Owing to the C-H ∙∙∙O hydrogen bond between the carbonyl and the vinyl, PNV exhibits a high red emission with a quantum yield of 33.4% in the solid state while it shows n-type properties with an electron mobility up to 1.5 x 10 -3 cm 2 V -1 s -1 in organic field effect transistors, simultaneously.

  7. Molecular recognition of naphthalene diimide ligands by telomeric quadruplex-DNA: the importance of the protonation state and mediated hydrogen bonds.

    PubMed

    Spinello, A; Barone, G; Grunenberg, J

    2016-01-28

    In depth Monte Carlo conformational scans in combination with molecular dynamics (MD) simulations and electronic structure calculations were applied in order to study the molecular recognition process between tetrasubstituted naphthalene diimide (ND) guests and G-quadruplex (G4) DNA receptors. ND guests are a promising class of telomere stabilizers due to which they are used in novel anticancer therapeutics. Though several ND guests have been studied experimentally in the past, the protonation state under physiological conditions is still unclear. Based on chemical intuition, in the case of N-methyl-piperazine substitution, different protonation states are possible and might play a crucial role in the molecular recognition process by G4-DNA. Depending on the proton concentration, different nitrogen atoms of the N-methyl-piperazine might (or might not) be protonated. This fact was considered in our simulation in terms of a case by case analysis, since the process of molecular recognition is determined by possible donor or acceptor positions. The results of our simulations show that the electrostatic interactions between the ND ligands and the G4 receptor are maximized in the case of the protonation of the terminal nitrogen atoms, forming compact ND G4 complexes inside the grooves. The influence of different protonation states in terms of the ability to form hydrogen bonds with the sugar-phosphate backbone, as well as the importance of mediated vs. direct hydrogen bonding, was analyzed in detail by MD and relaxed force constant (compliance constant) simulations.

  8. Effects of p-(Trifluoromethoxy)benzyl and p-(Trifluoromethoxy)phenyl Molecular Architecture on the Performance of Naphthalene Tetracarboxylic Diimide-Based Air-Stable n-Type Semiconductors.

    PubMed

    Zhang, Dongwei; Zhao, Liang; Zhu, Yanan; Li, Aiyuan; He, Chao; Yu, Hongtao; He, Yaowu; Yan, Chaoyi; Goto, Osamu; Meng, Hong

    2016-07-20

    N,N'-Bis(4-trifluoromethoxyphenyl) naphthalene-1,4,5,8-tetracarboxylic acid diimide (NDI-POCF3) and N,N'-bis(4-trifluoromethoxybenzyl) naphthalene-1,4,5,8-tetracarboxylic acid diimide (NDI-BOCF3) have similar optical and electrochemical properties with a deep LUMO level of approximately 4.2 eV, but exhibit significant differences in electron mobility and molecular packing. NDI-POCF3 exhibits nondetectable charge mobility. Interestingly, NDI-BOCF3 shows air-stable electron transfer performance with enhanced mobility by increasing the deposition temperature onto the octadecyltrichlorosilane (OTS)-modified SiO2/Si substrates and achieves electron mobility as high as 0.7 cm(2) V(-1) s(-1) in air. The different mobilities of those two materials can be explained by several factors including thin-film morphology and crystallinity. In contrast to the poor thin-film morphology and crystallinity of NDI-POCF3, NDI-BOCF3 exhibits larger grain sizes and improved crystallinities due to the higher deposition temperature. In addition, the theoretical calculated transfer integrals of the intermolecular lowest unoccupied molecular orbital (LUMO) of the two materials further show that a large intermolecular orbital overlap of NDI-BOCF3 can transfer electron more efficiently than NDI-POCF3 in thin-film transistors. On the basis of fact that the theoretical calculations are consistent with the experimental results, it can be concluded that the p-(trifluoromethoxy) benzyl (BOCF3) molecular architecture on the former position of the naphthalene tetracarboxylic diimides (NDI) core provides a more effective way to enhance the intermolecular electron transfer property than the p-(trifluoromethoxy) phenyl (POCF3) group for the future design of NDI-related air-stable n-channel semiconductor.

  9. Rylene and related diimides for organic electronics.

    PubMed

    Zhan, Xiaowei; Facchetti, Antonio; Barlow, Stephen; Marks, Tobin J; Ratner, Mark A; Wasielewski, Michael R; Marder, Seth R

    2011-01-11

    Organic electron-transporting materials are essential for the fabrication of organic p-n junctions, photovoltaic cells, n-channel field-effect transistors, and complementary logic circuits. Rylene diimides are a robust, versatile class of polycyclic aromatic electron-transport materials with excellent thermal and oxidative stability, high electron affinities, and, in many cases, high electron mobilities; they are, therefore, promising candidates for a variety of organic electronics applications. In this review, recent developments in the area of high-electron-mobility diimides based on rylenes and related aromatic cores, particularly perylene- and naphthalene-diimide-based small molecules and polymers, for application in high-performance organic field-effect transistors and photovoltaic cells are summarized and analyzed.

  10. Azomethine diimides end-capped with anthracene moieties: Experimental and theoretical investigations

    NASA Astrophysics Data System (ADS)

    Schab-Balcerzak, Ewa; Grucela, Marzena; Malecki, Grzegorz; Kotowicz, Sonia; Siwy, Mariola; Janeczek, Henryk; Golba, Sylwia; Praski, Aleksander

    2017-01-01

    New arylene bisimide derivatives containing imine linkages and anthracene units were synthesized. Azomethine diimides were prepared via condensation reaction of 9-anthracenecarboxaldehyde and diamines with phthalic diimide or naphthalene diimide core and Schiff base linkers. They were characterized by FTIR spectroscopy, elemental analysis and mass spectrometry (MALDI-TOF-MS). The synthesized compounds exhibited high resistance against thermal decomposition up to 400 °C. Investigated compounds are electrochemically active and undergo reversible electrochemical reduction and irreversible oxidation processes as was found in cyclic voltammetry studies. The photoluminescence measurements of synthesized compounds in solid state as thin film on glass substrate revealed their ability to emission of the blue light with quantum yield efficiency about 2%. The electronic structure and spectroscopic properties of prepared azomethine diimides were also calculated by the density functional theory (DFT). The electrical properties of the diimide derivatives were preliminary investigated by current-voltage measurements.

  11. Synthesis of 3-alkyl naphthalenes as novel estrogen receptor ligands

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

    Fang, Jing; Akwabi-Ameyaw, Adwoa; Britton, Jonathan E.

    2009-06-24

    A series of estrogen receptor ligands based on a 3-alkyl naphthalene scaffold was synthesized using an intramolecular enolate-alkyne cycloaromatization as the key step. Several of these compounds bearing a C6-OH group were shown to be high affinity ligands. All compounds had similar ER{alpha} and ER{beta} binding affinity ranging from micromolar to low nanomolar.

  12. High-Performance Visible-Blind UV Phototransistors Based on n-Type Naphthalene Diimide Nanomaterials.

    PubMed

    Song, Inho; Lee, Seung-Chul; Shang, Xiaobo; Ahn, Jaeyong; Jung, Hoon-Joo; Jeong, Chan-Uk; Kim, Sang-Wook; Yoon, Woojin; Yun, Hoseop; Kwon, O-Pil; Oh, Joon Hak

    2018-04-11

    This study investigates the performance of single-crystalline nanomaterials of wide-band gap naphthalene diimide (NDI) derivatives with methylene-bridged aromatic side chains. Such materials are found to be easily used as high-performance, visible-blind near-UV light detectors. NDI single-crystalline nanoribbons are assembled using a simple solution-based process (without solvent-inclusion problems), which is then applied to organic phototransistors (OPTs). Such OPTs exhibit excellent n-channel transistor characteristics, including an average electron mobility of 1.7 cm 2 V -1 s -1 , sensitive UV detection properties with a detection limit of ∼1 μW cm -2 , millisecond-level responses, and detectivity as high as 10 15 Jones, demonstrating the highly sensitive organic visible-blind UV detectors. The high performance of our OPTs originates from the large face-to-face π-π stacking area between the NDI semiconducting cores, which is facilitated by methylene-bridged aromatic side chains. Interestingly, NDI-based nanoribbon OPTs exhibit a distinct visible-blind near-UV detection with an identical detection limit, even under intense visible light illumination (for example, 10 4 times higher intensity than UV light intensity). Our findings demonstrate that wide-band gap NDI-based nanomaterials are highly promising for developing high-performance visible-blind UV photodetectors. Such photodetectors could potentially be used for various applications including environmental and health-monitoring systems.

  13. N,N′-Dicyclo­hexyl­naphthalene-1,8;4:5-dicarboximide

    PubMed Central

    Shukla, Deepak; Rajeswaran, Manju

    2008-01-01

    The title compound, C26H26N2O4, synthesized by the reaction of naphthalene-1,4,5,8-tetra­carboxylic acid anhydride and cyclo­hexyl­amine, exhibits good n-type semiconducting properties. Accordingly, thin-film transistor devices comprising this compound show n-type behavior with high field-effect electron moblity ca 6 cm2/Vs [Shukla, Nelson, Freeman, Rajeswaran, Ahearn, Meyer & Carey(2008 ▶). Chem. Mater. Submitted]. The asymmetric unit comprises one-quarter of the centrosymmetric mol­ecule in which all but two methyl­ene C atoms of the cyclo­hexane ring lie on a mirror plane; the point-group symmetry is 2/m. The naphthalene­diimide unit is strictly planar, and the cyclo­hexane rings adopt chair conformations with the diimide unit in an equatorial position on each ring. PMID:21201718

  14. Functionality-Oriented Derivatization of Naphthalene Diimide: A Molecular Gel Strategy-Based Fluorescent Film for Aniline Vapor Detection.

    PubMed

    Fan, Jiayun; Chang, Xingmao; He, Meixia; Shang, Congdi; Wang, Gang; Yin, Shiwei; Peng, Haonan; Fang, Yu

    2016-07-20

    Modification of naphthalene diimide (NDI) resulted in a photochemically stable, fluorescent 3,4,5-tris(dodecyloxy)benzamide derivative of NDI (TDBNDI), and introduction of the long alkyl chains endowed the compound with good compatibility with commonly found organic solvents and in particular superior self-assembly in the solution state. Further studies revealed that TDBNDI forms gels with nine of the 18 solvents tested at a concentration of 2.0% (w/v), and the critical gelation concentrations of five of the eight gels are lower than 1.0% (w/v), indicating the high efficiency of the compound as a low-molecular mass gelator (LMMG). Transmission electron microscopy, scanning electron microscopy, and confocal laser scanning microscopy studies revealed the networked fibrillar structure of the TDBNDI/methylcyclohexane (MCH) gel. On the basis of these findings, a fluorescent film was developed via simple spin-coating of the TDBNDI/MCH gel on a glass substrate surface. Fluorescence behavior and sensing performance studies demonstrated that this film is photochemically stable, and sensitive and selective to the presence of aniline vapor. Notably, the response is instantaneous, and the sensing process is fully and quickly reversible. This case study demonstrates that derivatization of photochemically stable fluorophores into LMMGs is a good strategy for developing high-performance fluorescent sensing films.

  15. Asymmetric Alkyl Side-Chain Engineering of Naphthalene Diimide-Based n-Type Polymers for Efficient All-Polymer Solar Cells.

    PubMed

    Jia, Tao; Li, Zhenye; Ying, Lei; Jia, Jianchao; Fan, Baobing; Zhong, Wenkai; Pan, Feilong; He, Penghui; Chen, Junwu; Huang, Fei; Cao, Yong

    2018-02-13

    The design and synthesis of three n-type conjugated polymers based on a naphthalene diimide-thiophene skeleton are presented. The control polymer, PNDI-2HD, has two identical 2-hexyldecyl side chains, and the other polymers have different alkyl side chains; PNDI-EHDT has a 2-ethylhexyl and a 2-decyltetradecyl side chain, and PNDI-BOOD has a 2-butyloctyl and a 2-octyldodecyl side chain. These copolymers with different alkyl side chains exhibit higher melting and crystallization temperatures, and stronger aggregation in solution, than the control copolymer PNDI-2HD that has the same side chain. Polymer solar cells based on the electron-donating copolymer PTB7-Th and these novel copolymers exhibit nearly the same open-circuit voltage of 0.77 V. Devices based on the copolymer PNDI-BOOD with different side chains have a power-conversion efficiency of up to 6.89%, which is much higher than the 4.30% obtained with the symmetric PNDI-2HD. This improvement can be attributed to the improved charge-carrier mobility and the formation of favorable film morphology. These observations suggest that the molecular design strategy of incorporating different side chains can provide a new and promising approach to developing n-type conjugated polymers. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Hybrid ligand-alkylating agents targeting telomeric G-quadruplex structures.

    PubMed

    Doria, Filippo; Nadai, Matteo; Folini, Marco; Di Antonio, Marco; Germani, Luca; Percivalle, Claudia; Sissi, Claudia; Zaffaroni, Nadia; Alcaro, Stefano; Artese, Anna; Richter, Sara N; Freccero, Mauro

    2012-04-14

    The synthesis, physico-chemical properties and biological effects of a new class of naphthalene diimides (NDIs) capable of reversibly binding telomeric DNA and alkylate it through an electrophilic quinone methide moiety (QM), are reported. FRET and circular dichroism assays showed a marked stabilization and selectivity towards telomeric G4 DNA folded in a hybrid topology. NDI-QMs' alkylating properties revealed a good reactivity on single nucleosides and selectivity towards telomeric G4. A selected NDI was able to significantly impair the growth of melanoma cells by causing telomere dysfunction and down-regulation of telomerase expression. These findings points to our hybrid ligand-alkylating NDIs as possible tools for the development of novel targeted anticancer therapies. This journal is © The Royal Society of Chemistry 2012

  17. Induction of protein oxidation in human low density lipoprotein by the photosensitive organic hydroperoxide, N,N'-bis(2-hydroxyperoxy-2-methoxyethyl)-1,4,5,8-naphthalene-tetra-carb oxylic- diimide.

    PubMed

    Matsugo, S; Yan, L J; Han, D; Packer, L

    1995-01-05

    We have developed a new molecular probe, N,N'-bis(2-hydroxyperoxy-2-methyoxyethyl)-1,4,5,8-naphthalen e-tetra-carboxylic- diimide (NP-III), that specifically generates hydroxyl radical upon irradiation with longer wavelength ultraviolet light (UVA). Hydroxyl radicals are generated only upon irradiation, thus NP-III is a new controllable hydroxyl radical source. Apolipoprotein (apo-B) of human low density lipoprotein (LDL), and bovine serum alubumin (BSA), were irradiated with UVA in the presence of NP-III and their oxidation was evaluated by two independent methods: assay of protein carbonyl groups and gel electrophoresis. NP-III oxidized apo-B and BSA in a time- and concentration-dependent manner. The results demonstrate that NP-III is a controllable, precise, and potentially tagetable source of hydroxyl radicals with which to induce protein oxidation.

  18. n-Type Water/Alcohol-Soluble Naphthalene Diimide-Based Conjugated Polymers for High-Performance Polymer Solar Cells.

    PubMed

    Wu, Zhihong; Sun, Chen; Dong, Sheng; Jiang, Xiao-Fang; Wu, Siping; Wu, Hongbin; Yip, Hin-Lap; Huang, Fei; Cao, Yong

    2016-02-17

    With the demonstration of small-area, single-junction polymer solar cells (PSCs) with power conversion efficiencies (PCEs) over the 10% performance milestone, the manufacturing of high-performance large-area PSC modules is becoming the most critical issue for commercial applications. However, materials and processes that are optimized for fabricating small-area devices may not be applicable for the production of high-performance large-area PSC modules. One of the challenges is to develop new conductive interfacial materials that can be easily processed with a wide range of thicknesses without significantly affecting the performance of the PSCs. Toward this goal, we report two novel naphthalene diimide-based, self-doped, n-type water/alcohol-soluble conjugated polymers (WSCPs) that can be processed with a broad thickness range of 5 to 100 nm as efficient electron transporting layers (ETLs) for high-performance PSCs. Space charge limited current and electron spin resonance spectroscopy studies confirm that the presence of amine or ammonium bromide groups on the side chains of the WSCP can n-dope PC71BM at the bulk heterojunction (BHJ)/ETL interface, which improves the electron extraction properties at the cathode. In addition, both amino functional groups can induce self-doping to the WSCPs, although by different doping mechanisms, which leads to highly conductive ETLs with reduced ohmic loss for electron transport and extraction. Ultimately, PSCs based on the self-doped WSCP ETLs exhibit significantly improved device performance, yielding PCEs as high as 9.7% and 10.11% for PTB7-Th/PC71BM and PffBT4T-2OD/PC71BM systems, respectively. More importantly, with PffBT4T-2OD/PC71BM BHJ as an active layer, a prominent PCE of over 8% was achieved even when a thick ETL of 100 nm was used. To the best of our knowledge, this is the highest efficiency demonstrated for PSCs with a thick interlayer and light-harvesting layer, which are important criteria for eventually making

  19. Bis(azido) compounds of Pd and Pt with bulky phosphine ligands (dppn=1,8-bis(diphenylphosphino)naphthalene, dppf=1,1‧-bis(diphenylphosphino)ferrocene, 1-dpn=1-diphenylphosphino-naphthalene): Preparation, structures, and reactivity toward isocyanides

    NASA Astrophysics Data System (ADS)

    Huh, Hyun Sue; Lee, Yeon Kyoung; Lee, Soon W.

    2006-05-01

    Pd-bis(azido) compounds [Pd(dppn)(N 3) 2] and [Pd(dppf)(N 3) 2], which contain bulky chelating bis(phosphine) ligands (dppn=1,8-bis(diphenylphosphino)naphthalene, dppf=1,1'-bis(diphenylphosphino)ferrocene), were prepared from the corresponding chlorides and NaN 3. We also prepared the Pt-bis(azido) compound [Pt(1-dpn)(SMe 2)(N 3) 2] containing a bulky monodentate phosphine (1-dpn=1-diphenylphosphino-naphthalene). All these compounds underwent [2+3] cycloaddition with isocyanides (R-NC, R=cyclohexyl, tert-butyl, 2,6-dimethylphenyl) to convert azido ligands to five-membered, C-coordinated tetrazolate rings. In addition, we observed the [Pd(dppn)Cl 2]-mediated C-C coupling of PhC tbnd6 CH to generate the η 2-PhC tbnd6 C-C tbnd6 CPh ligand. All compounds have been structurally characterized by X-ray diffraction.

  20. Naphthalene Diimide Based n-Type Conjugated Polymers as Efficient Cathode Interfacial Materials for Polymer and Perovskite Solar Cells.

    PubMed

    Jia, Tao; Sun, Chen; Xu, Rongguo; Chen, Zhiming; Yin, Qingwu; Jin, Yaocheng; Yip, Hin-Lap; Huang, Fei; Cao, Yong

    2017-10-18

    A series of naphthalene diimide (NDI) based n-type conjugated polymers with amino-functionalized side groups and backbones were synthesized and used as cathode interlayers (CILs) in polymer and perovskite solar cells. Because of controllable amine side groups, all the resulting polymers exhibited distinct electronic properties such as oxidation potential of side chains, charge carrier mobilities, self-doping behaviors, and interfacial dipoles. The influences of the chemical variation of amine groups on the cathode interfacial effects were further investigated in both polymer and perovskite solar cells. We found that the decreased electron-donating property and enhanced steric hindrance of amine side groups substantially weaken the capacities of altering the work function of the cathode and trap passivation of the perovskite film, which induced ineffective interfacial modifications and declining device performance. Moreover, with further improvement of the backbone design through the incorporation of a rigid acetylene spacer, the resulting polymers substantially exhibited an enhanced electron-transporting property. Upon use as CILs, high power conversion efficiencies (PCEs) of 10.1% and 15.2% were, respectively, achieved in polymer and perovskite solar cells. Importantly, these newly developed n-type polymers were allowed to be processed over a broad thickness range of CILs in photovoltaic devices, and a prominent PCE of over 8% for polymer solar cells and 13.5% for perovskite solar cells can be achieved with the thick interlayers over 100 nm, which is beneficial for roll-to-roll coating processes. Our findings contribute toward a better understanding of the structure-performance relationship between CIL material design and solar cell performance, and provide important insights and guidelines for the design of high-performance n-type CIL materials for organic and perovskite optoelectronic devices.

  1. Hydration of a Large Anionic Charge Distribution - Naphthalene-Water Cluster Anions

    NASA Astrophysics Data System (ADS)

    Weber, J. Mathias; Adams, Christopher L.

    2010-06-01

    We report the infrared spectra of anionic clusters of naphthalene with up to three water molecules. Comparison of the experimental infrared spectra with theoretically predicted spectra from quantum chemistry calculations allow conclusions regarding the structures of the clusters under study. The first water molecule forms two hydrogen bonds with the π electron system of the naphthalene moiety. Subsequent water ligands interact with both the naphthalene and the other water ligands to form hydrogen bonded networks, similar to other hydrated anion clusters. Naphthalene-water anion clusters illustrate how water interacts with negative charge delocalized over a large π electron system. The clusters are interesting model systems that are discussed in the context of wetting of graphene surfaces and polyaromatic hydrocarbons.

  2. Ligand-controlled assembly of Cd(II) coordination polymers based on mixed ligands of naphthalene-dicarboxylate and dipyrido[3,2-d:2',3'-f]quinoxaline: From 0D+1D cocrystal, 2D rectangular network (4,4), to 3D PtS-type architecture

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

    Liu Guocheng; Chen Yongqiang; Wang Xiuli

    Three novel Cd(II) coordination polymers, namely, [Cd(Dpq)(1,8-NDC)(H{sub 2}O){sub 2}][Cd(Dpq)(1,8-NDC)].2H{sub 2}O (1), [Cd(Dpq)(1,4-NDC)(H{sub 2}O)] (2), and [Cd(Dpq)(2,6-NDC)] (3) have been obtained from hydrothermal reactions of cadmium(II) nitrate with the mixed ligands dipyrido [3,2-d:2',3'-f]quinoxaline (Dpq) and three structurally related naphthalene-dicarboxylate ligands [1,8-naphthalene-dicarboxylic acid (1,8-H{sub 2}NDC), 1,4-naphthalene-dicarboxylic acid (1,4-H{sub 2}NDC), and 2,6-naphthalene-dicarboxylic acid (2,6-H{sub 2}NDC)]. Single-crystal X-ray diffraction analysis reveals that the three polymers exhibit novel structures due to different naphthalene-dicarboxylic acid. Compound 1 is a novel cocrystal of left- and right-handed helical chains and binuclear complexes and ultimately packed into a 3D supramolecular structure through hydrogen bonds and {pi}-{pi} stacking interactions. Compoundmore » 2 shows a 2D rectangular network (4,4) bridged by 1,4-NDC with two kinds of coordination modes and ultimately packed into a 3D supramolecular structure through inter-layer {pi}-{pi} stacking interactions. Compound 3 is a new 3D coordination polymer with distorted PtS-type network. In addition, the title compounds exhibit blue/green emission in solid state at room temperature. - Graphical abstract: Three novel Cd(II) compounds have been synthesized under hydrothermal conditions exhibiting a systematic variation of architecture by the employment of three structurally related naphthalene-dicarboxylate ligands.« less

  3. Ligand-controlled assembly of Cd(II) coordination polymers based on mixed ligands of naphthalene-dicarboxylate and dipyrido[3,2-d:2‧,3‧-f]quinoxaline: From 0D+1D cocrystal, 2D rectangular network (4,4), to 3D PtS-type architecture

    NASA Astrophysics Data System (ADS)

    Liu, Guocheng; Chen, Yongqiang; Wang, Xiuli; Chen, Baokuan; Lin, Hongyan

    2009-03-01

    Three novel Cd(II) coordination polymers, namely, [Cd(Dpq)(1,8-NDC)(H 2O) 2][Cd(Dpq)(1,8-NDC)]·2H 2O ( 1), [Cd(Dpq)(1,4-NDC)(H 2O)] ( 2), and [Cd(Dpq)(2,6-NDC)] ( 3) have been obtained from hydrothermal reactions of cadmium(II) nitrate with the mixed ligands dipyrido [3,2-d:2',3'-f]quinoxaline (Dpq) and three structurally related naphthalene-dicarboxylate ligands [1,8-naphthalene-dicarboxylic acid (1,8-H 2NDC), 1,4-naphthalene-dicarboxylic acid (1,4-H 2NDC), and 2,6-naphthalene-dicarboxylic acid (2,6-H 2NDC)]. Single-crystal X-ray diffraction analysis reveals that the three polymers exhibit novel structures due to different naphthalene-dicarboxylic acid. Compound 1 is a novel cocrystal of left- and right-handed helical chains and binuclear complexes and ultimately packed into a 3D supramolecular structure through hydrogen bonds and π- π stacking interactions. Compound 2 shows a 2D rectangular network (4,4) bridged by 1,4-NDC with two kinds of coordination modes and ultimately packed into a 3D supramolecular structure through inter-layer π- π stacking interactions. Compound 3 is a new 3D coordination polymer with distorted PtS-type network. In addition, the title compounds exhibit blue/green emission in solid state at room temperature.

  4. Cyclic perylene diimide: Selective ligand for tetraplex DNA binding over double stranded DNA.

    PubMed

    Vasimalla, Suresh; Sato, Shinobu; Takenaka, Fuminori; Kurose, Yui; Takenaka, Shigeori

    2017-12-15

    Synthesized cyclic perylene diimide, cPDI, showed the binding constant of 6.3 × 10 6  M -1 with binding number of n = 2 with TA-core as a tetraplex DNA in 50 mM Tris-HCl buffer (pH = 7.4) containing 100 mM KCl using Schatchard analysis and showed a higher preference for tetraplex DNA than for double stranded DNA with over 10 3 times. CD spectra showed that TA-core induced its antiparallel conformation upon addition of cPDI in the absence or presence of K + or Na + ions. The cPDI inhibits the telomerase activity with IC 50 of 0.3 µM using TRAP assay which is potential anti-cancer drug with low side effect. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Investigation on Fluorescence Quenching Mechanism of Perylene Diimide Dyes by Graphene Oxide.

    PubMed

    Zhao, Yuzhen; Li, Kexuan; He, Zemin; Zhang, Yongming; Zhao, Yang; Zhang, Haiquan; Miao, Zongcheng

    2016-11-30

    Perylene diimide derivatives were used as probes to investigate the effect of the molecular structures on the fluorescence quenching mechanism in a perylene diimide/graphene oxide system. The electrons transferred from the excited state of dyes to the conductive band of graphene oxide with different concentrations were determined by fluorescence spectra. The results indicated that the quenching efficiency of perylene diimides by graphene oxide was not only dependent on the difference between the lowest unoccupied molecular orbital level of dyes and the conduction band of the graphene oxide, but also mainly on the difference in the molecular structures.

  6. The electrical and dielectrical behavior of n-conducting perylene tetracarboxylic diimide derivatives

    NASA Astrophysics Data System (ADS)

    Lehmann, Daniel; Zahn, Dietrich R. T.

    2009-04-01

    A comparison of the electrical characteristics of organic field-effect transistors (OFETs) based on derivatives of the electron-conductor perylene tetracarboxylic diimide (PTCDI) in top-contact configuration is presented. The derivatives used are N,N'-dimethyl-3,4,9,10-perylene-tetracarboxylic-diimide (DiMe-PTCDI), N,N'-diphenyl-3,4,9,10-perylene-tetracarboxylic-diimide (DiPhenyl-PTCDI), N,N'-dimethoxyethyl-3,4,9,10-perylene-tetracarboxylic-diimide (DiMethoxyethyl-PTCDI), N,N'-di(3-pentyl)-3,4,9,10-perylene-tetracarboxylic-diimide (Di3Pentyl-PTCDI), and N,N'-diheptyl-3,4,9,10-perylene-tetracarboxylic-diimide (DiHeptyl-PTCDI). Current/voltage measurements were first performed in situ and later ex situ. Additionally, the effect of annealing and bias stress was probed in situ. A strong influence of the different side groups on the order of magnitude of the electron mobility is revealed, ranging from 4×10-6 cm2/V s for DiMethoxyethyl-PTCDI to 5×10-2 cm2/V s for DiHeptyl-PTCDI. While none of the devices was stable in air after exposition to air, only the DiMe-PTCDI one resumed its functionality after restoring vacuum conditions. The dielectric functions of the derivatives was derived, additionally revealing optical isotropy for all films and varying surface roughness. While DiHeptyl-PTCDI and Di3Pentyl-PTCDI, yielding also the highest electron mobilities, form smooth layers with negligible surface roughness, strong island formation was be observed for DiPhenyl-PTCDI and DiMethoxyethyl-PTCDI, yielding low mobilities. This island growth was also confirmed by atomic force microscopy measurements. Ageing of the samples for several months under ambient conditions leads to increased roughness for the very rough samples. Layers with smooth surface, on the other hand, showed no significant change in the dielectric behavior of the sample.

  7. Designed synthesis and supramolecular architectures of furan-substituted perylene diimide.

    PubMed

    Yu, Yanwen; Li, Yongjun; Qin, Zhihong; Jiang, Runsheng; Liu, Huibiao; Li, Yuliang

    2013-06-01

    Novel furan-substituted perylene diimides are successfully synthesized and an efficient supramolecular architecture approach to construct zero/one-dimensional nano- and micro-structures by controlling solvents has been demonstrated. The aggregate structure conversion in different molecular structures can be controlled in the form of sphere-like, rod-like, and vesicle-like structures. As expected, these solid supramolecular rod-like architectures displayed interesting optical waveguide behavior, which indicates the aggregate structure materials of furan-substituted perylene diimides have the potential application as micro-scale photonic elements. Copyright © 2013 Elsevier Inc. All rights reserved.

  8. (Photo)physical Properties of New Molecular Glasses End-Capped with Thiophene Rings Composed of Diimide and Imine Units

    PubMed Central

    2014-01-01

    New symmetrical arylene bisimide derivatives formed by using electron-donating–electron-accepting systems were synthesized. They consist of a phthalic diimide or naphthalenediimide core and imine linkages and are end-capped with thiophene, bithiophene, and (ethylenedioxy)thiophene units. Moreover, polymers were obtained from a new diamine, N,N′-bis(5-aminonaphthalenyl)naphthalene-1,4,5,8-dicarboximide and 2,5-thiophenedicarboxaldehyde or 2,2′-bithiophene-5,5′-dicarboxaldehyde. The prepared azomethine diimides exhibited glass-forming properties. The obtained compounds emitted blue light with the emission maximum at 470 nm. The value of the absorption coefficient was determined as a function of the photon energy using spectroscopic ellipsometry. All compounds are electrochemically active and undergo reversible electrochemical reduction and irreversible oxidation processes as was found in cyclic voltammetry and differential pulse voltammetry (DPV) studies. They exhibited a low electrochemically (DPV) calculated energy band gap (Eg) from 1.14 to 1.70 eV. The highest occupied molecular orbital and lowest unoccupied molecular orbital levels and Eg were additionally calculated theoretically by density functional theory at the B3LYP/6-31G(d,p) level. The photovoltaic properties of two model compounds as the active layer in organic solar cells in the configuration indium tin oxide/poly(3,4-(ethylenedioxy)thiophene):poly(styrenesulfonate)/active layer/Al under an illumination of 1.3 mW/cm2 were studied. The device comprising poly(3-hexylthiophene) with the compound end-capped with bithiophene rings showed the highest value of Voc (above 1 V). The conversion efficiency of the fabricated solar cell was in the range of 0.69–0.90%. PMID:24966893

  9. Interaction of albumin with perylene-diimides with aromatic substituents

    NASA Astrophysics Data System (ADS)

    Farooqi, Mohammed; Penick, Mark; Burch, Jessica; Negrete, George; Brancaleon, Lorenzo

    2015-03-01

    Polyaromatic hydrocarbons (PAH) binding to proteins remains one of the fundamental aspects of research in biophysics. Ligand binding can regulate the function of proteins. Binding to small ligands remains a very important aspect in the study of the function of many proteins. Perylene diimide or PDI derivatives have attracted initial interest as industrial dyes and pigments. Recently, much attention has been focused on their strong π - π stacks resulting from the large PDI aromatic core. These PDI stacks have distinct optical properties, and provide informative models that mimic the light-harvesting system and initial charge separation and charge transfer in the photosynthetic system. The absorption property of PDI derivatives may be largely tuned from visible to near-infrared region by chemical modifications at the bay-positions. We are currently studying a new class of PDI derivatives with substituents made of the side chains of aromatic amino acids (Tyrosine, Tryptophan and Phenylalanine). We have looked at the fluorescence absorption and emission of these PDIs in water and other organic solvents. PDIs show evidence of dimerization and possible aggregation. We also present binding studies of these PDIs with Human Serum Albumin (HSA). The binding was studied using fluorescence emission quenching of the HSA Tryptophan residue. Stern-Volmer equation is used to derive the quenching constants. PDI binding to HSA also has an effect on the fluorescence emission of the PDIs themselves by red shifting the spectra. Funded by RCMI grant.

  10. Infrared spectroscopy of hydrated naphthalene cluster anions.

    PubMed

    Knurr, Benjamin J; Adams, Christopher L; Weber, J Mathias

    2012-09-14

    We present infrared spectra of mass-selected C(10)H(8)(-)·(H(2)O)(n)·Ar(m) cluster anions (n = 1-6) obtained by Ar predissociation spectroscopy. The experimental spectra are compared with predicted spectra from density functional theory calculations. The OH groups of the water ligands are involved in H-bonds to other water molecules or to the π system of the naphthalene anion, which accommodates the excess electron. The interactions in the water network are generally found to be more important than those between water molecules and the ion. For 2 ≤ n ≤ 4 the water molecules form single layer water networks on one side of the naphthalene anion, while for n = 5 and 6, cage and multilayer structures become more energetically favorable. For cluster sizes with more than 3 water molecules, multiple conformers are likely to be responsible for the experimental spectra.

  11. Aromatic Diimides - Potential Dyes for Use in Smart Films and Fibers

    NASA Technical Reports Server (NTRS)

    Meador, Michael A.; Tyson, Daniel S.; Ilhan, Faysal; Carbaugh, Ashley

    2008-01-01

    New aromatic diimide fluorescent dyes have been prepared with potential for use as chemical sensors and in chromogenic polymers. These dyes have been designed to utilize excited state electron transfer reactions as the means for sensing chemical species. For example, an aniline en-dcapped anthryl diimides functions effectively as an "on-off" sensor for pH and the detection of phosphoryl halide based chemical warfare agents, such as Sarin. In the absence of analytes, fluorescence from this dye is completely quenched by excited state electron transfer from the terminal amines. Reaction of these amines inhibits electron transfer and activates the fluorescence of the dye. Another substituted anthryl diimide is presented with the capability to detect pH and nitroaromatic compounds, such as TNT. Films prepared by doping small amounts (less than 0.1 weight percent) of several of these dyes in polymers such as linear low density polyethylene exhibit thermochromism. At room temperature, these films fluoresce reddish-orange. Upon heating, the fluorescence turns green. This process is reversible cooling the films to room temperature restores the orange emission.

  12. Naphthalene poisoning

    MedlinePlus

    Naphthalene is a white solid substance with a strong smell. Poisoning from naphthalene destroys or changes red blood cells so they cannot carry oxygen. This can cause organ damage. This article is for information only. DO NOT use it ...

  13. Spectroscopic, electrochemical and photovoltaic properties of Pt(ii) and Pd(ii) complexes of a chelating 1,10-phenanthroline appended perylene diimide.

    PubMed

    Işık Büyükekşi, Sebile; Şengül, Abdurrahman; Erdönmez, Seda; Altındal, Ahmet; Orman, Efe Baturhan; Özkaya, Ali Rıza

    2018-02-20

    In this study, a bis-chelating bridging perylene diimide ditopic ligand, namely N,N'-di(1,10-phenanthroline)-1,6,7,12-tetrakis-(4-methoxyphenoxy)perylene tetracarboxylic acid diimide (1), was synthesized and characterized. Further reactions of 1 with d 8 metal ions such as Pt(ii) and Pd(ii) having preferential square-planar geometry afforded the novel triads [(Cl 2 )M(ii)-(1)-M(ii)(Cl 2 )] where M(ii) = Pt(ii) (2), and Pd(ii) (3), respectively. The isolated triads and the key precursor were fully characterized by FT-IR, 1D-NMR ( 1 H NMR and 13 C DEPT NMR), 2D-NMR ( 1 H- 1 H COSY, 1 H- 13 C HSQC, 1 H- 13 C HMBC), MALDI-TOF mass and UV/Vis spectroscopy. The electrochemical properties of 1, 2 and 3 were investigated by cyclic voltammetry as well as in situ spectroelectrochemistry and also in situ electrocolorimetric measurements. These compounds were shown to exhibit net colour changes suitable for electrochromic applications. The compounds exhibited remarkably narrow HOMO-LUMO gaps, leading to their ease of reduction at low negative potentials. More importantly, dye-sensitized solar cells (DSSCs) were also fabricated using 1-3 to clarify the potential use of these complexes as a sensitizer. Analysis of the experimental data indicated that 2 has good potential as a sensitizer material for DSSCs.

  14. New naphthalene whole-cell bioreporter for measuring and assessing naphthalene in polycyclic aromatic hydrocarbons contaminated site.

    PubMed

    Sun, Yujiao; Zhao, Xiaohui; Zhang, Dayi; Ding, Aizhong; Chen, Cheng; Huang, Wei E; Zhang, Huichun

    2017-11-01

    A new naphthalene bioreporter was designed and constructed in this work. A new vector, pWH1274_Nah, was constructed by the Gibson isothermal assembly fused with a 9 kb naphthalene-degrading gene nahAD (nahAa nahAb nahAc nahAd nahB nahF nahC nahQ nahE nahD) and cloned into Acinetobacter ADPWH_lux as the host, capable of responding to salicylate (the central metabolite of naphthalene). The ADPWH_Nah bioreporter could effectively metabolize naphthalene and evaluate the naphthalene in natural water and soil samples. This whole-cell bioreporter did not respond to other polycyclic aromatic hydrocarbons (PAHs; pyrene, anthracene, and phenanthrene) and demonstrated a positive response in the presence of 0.01 μM naphthalene, showing high specificity and sensitivity. The bioluminescent response was quantitatively measured after a 4 h exposure to naphthalene, and the model simulation further proved the naphthalene metabolism dynamics and the salicylate-activation mechanisms. The ADPWH_Nah bioreporter also achieved a rapid evaluation of the naphthalene in the PAH-contaminated site after chemical spill accidents, showing high consistency with chemical analysis. The engineered Acinetobacter variant had significant advantages in rapid naphthalene detection in the laboratory and potential in situ detection. The state-of-the-art concept of cloning PAHs-degrading pathway in salicylate bioreporter hosts led to the construction and assembly of high-throughput PAH bioreporter array, capable of crude oil contamination assessment and risk management. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. 40 CFR 704.43 - Chlorinated naphthalenes.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Chlorinated naphthalenes. 704.43... § 704.43 Chlorinated naphthalenes. (a) Definitions. (1) Extent of chlorination means the percent by... means the relative amounts of each isomeric chlorinated naphthalene that composes the chemical substance...

  16. 40 CFR 704.43 - Chlorinated naphthalenes.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Chlorinated naphthalenes. 704.43... § 704.43 Chlorinated naphthalenes. (a) Definitions. (1) Extent of chlorination means the percent by... means the relative amounts of each isomeric chlorinated naphthalene that composes the chemical substance...

  17. Sulfate-Reducing Naphthalene Degraders Are Picky Eaters.

    PubMed

    Wolfson, Sarah J; Porter, Abigail W; Kerkhof, Lee J; McGuinness, Lora M; Prince, Roger C; Young, Lily Y

    2018-06-25

    Polycyclic aromatic hydrocarbons (PAHs) are common organic contaminants found in anoxic environments. The capacity for PAH biodegradation in unimpacted environments, however, has been understudied. Here we investigate the enrichment, selection, and sustainability of a microbial community from a pristine environment on naphthalene as the only amended carbon source. Pristine coastal sediments were obtained from the Jacques Cousteau National Estuarine Research Reserve in Tuckerton, New Jersey, an ecological reserve which has no direct input or source of hydrocarbons. After an initial exposure to naphthalene, primary anaerobic transfer cultures completely degraded 500 µM naphthalene within 139 days. Subsequent transfer cultures mineralized naphthalene within 21 days with stoichiometric sulfate loss. Enriched cultures efficiently utilized only naphthalene and 2-methylnaphthalene from the hydrocarbon mixtures in crude oil. To determine the microorganisms responsible for naphthalene degradation, stable isotope probing was utilized on cultures amended with fully labeled 13 C-naphthalene as substrate. Three organisms were found to unambiguously synthesize 13 C-DNA from 13 C-naphthalene within 7 days. Phylogenetic analysis revealed that 16S rRNA genes from two of these organisms are closely related to the known naphthalene degrading isolates NaphS2 and NaphS3 from PAH-contaminated sites. A third 16S rRNA gene was only distantly related to its closest relative and may represent a novel naphthalene degrading microbe from this environment.

  18. Naphthalene distributions and human exposure in Southern California

    NASA Astrophysics Data System (ADS)

    Lu, Rong; Wu, Jun; Turco, Richard P.; Winer, Arthur M.; Atkinson, Roger; Arey, Janet; Paulson, Suzanne E.; Lurmann, Fred W.; Miguel, Antonio H.; Eiguren-Fernandez, Arantzazu

    The regional distribution of, and human exposure to, naphthalene are investigated for Southern California. A comprehensive approach is taken in which advanced models are linked for the first time to quantify population exposure to the emissions of naphthalene throughout Southern California. Naphthalene is the simplest and most abundant of the polycyclic aromatic hydrocarbons found in polluted urban environments, and has been detected in both outdoor and indoor air samples. Exposure to high concentrations of naphthalene may have adverse health effects, possibly causing cancer in humans. Among the significant emission sources are volatilization from naphthalene-containing products, petroleum refining, and combustion of fossil fuels and wood. Gasoline and diesel engine exhaust, with related vaporization from fuels, are found to contribute roughly half of the daily total naphthalene burden in Southern California. As part of this study, the emission inventory for naphthalene has been verified against new field measurements of the naphthalene-to-benzene ratio in a busy traffic tunnel in Los Angeles, supporting the modeling work carried out here. The Surface Meteorology and Ozone Generation (SMOG) airshed model is used to compute the spatial and temporal distributions of naphthalene and its photooxidation products in Southern California. The present simulations reveal a high degree of spatial variability in the concentrations of naphthalene-related species, with large diurnal and seasonal variations as well. Peak naphthalene concentrations are estimated to occur in the early morning hours in the winter season. The naphthalene concentration estimates obtained from the SMOG model are employed in the Regional Human Exposure (REHEX) model to calculate population exposure statistics. Results show average hourly naphthalene exposures in Southern California under summer and winter conditions of 270 and 430 ng m -3, respectively. Exposure to significantly higher concentrations

  19. Conformational diversity of flexible ligand in metal-organic frameworks controlled by size-matching mixed ligands

    NASA Astrophysics Data System (ADS)

    Hua, Xiu-Ni; Qin, Lan; Yan, Xiao-Zhi; Yu, Lei; Xie, Yi-Xin; Han, Lei

    2015-12-01

    Hydrothermal reactions of N-auxiliary flexible exo-bidentate ligand 1,3-bis(4-pyridyl)propane (bpp) and carboxylates ligands naphthalene-2,6-dicarboxylic acid (2,6-H2ndc) or 4,4‧-(hydroxymethylene)dibenzoic acid (H2hmdb), in the presence of cadmium(II) salts have given rise to two novel metal-organic frameworks based on flexible ligands (FL-MOFs), namely, [Cd2(2,6-ndc)2(bpp)(DMF)]·2DMF (1) and [Cd3(hmdb)3(bpp)]·2DMF·2EtOH (2) (DMF=N,N-Dimethylformamide). Single-crystal X-ray diffraction analyses revealed that compound 1 exhibits a three-dimensional self-penetrating 6-connected framework based on dinuclear cluster second building unit. Compound 2 displays an infinite three-dimensional 'Lucky Clover' shape (2,10)-connected network based on the trinuclear cluster and V-shaped organic linkers. The flexible bpp ligand displays different conformations in 1 and 2, which are successfully controlled by size-matching mixed ligands during the self-assembly process.

  20. Mechanism for Clastogenic Activity of Naphthalene

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

    Buchholz, Bruce A.

    2016-06-24

    Naphthalene incubations form DNA adducts in vitro in a dose dependent manner in both mouse and rat tissues. Rodent tissue incubations with naphthalene indicate that naphthalene forms as many DNA adducts as Benzo(a)pyrene, a known DNA binding carcinogen. The mouse airway has the greatest number of DNA adducts, corresponding to the higher metabolic activation of naphthalene in this location. Both rat tissues, the rat olfactory (tumor target) and the airways (non-tumor target), have similar levels of NA-DNA adducts, indicating that short term measures of initial adduct formation do not directly correlate with sites of tumor formation in the NTP bioassays.

  1. Naphthalene

    Integrated Risk Information System (IRIS)

    Naphthalene ; CASRN 91 - 20 - 3 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Effect

  2. Advances of naphthalene degradation in Pseudomonas putida ND6

    NASA Astrophysics Data System (ADS)

    Song, Fu; Shi, Yifei; Jia, Shiru; Tan, Zhilei; Zhao, Huabing

    2018-03-01

    Naphthalene is one of the most common and simple polycyclic aromatic hydrocarbons. Degradation of naphthalene has been greatly concerned due to its economic, free-pollution and its fine effect in Pseudomonas putida ND6. This review summarizes the development history of naphthalene degradation, the research progress of naphthalene degrading gene and naphthalene degradation pathway of Pseudomonas putida ND6, and the researching path of this strain. Although the study of naphthalene degradation is not consummate in Pseudomonas putida ND6, there is a potential capability for Pseudomonas putida ND6 to degrade the naphthalene in the further research.

  3. New organic semiconductors with imide/amide-containing molecular systems.

    PubMed

    Liu, Zitong; Zhang, Guanxin; Cai, Zhengxu; Chen, Xin; Luo, Hewei; Li, Yonghai; Wang, Jianguo; Zhang, Deqing

    2014-10-29

    Due to their high electron affinities, chemical and thermal stabilities, π-conjugated molecules with imide/amide frameworks have received considerable attentions as promising candidates for high-performance optoelectronic materials, particularly for organic semiconductors with high carrier mobilities. The purpose of this Research News is to give an overview of recent advances in development of high performance imide/amide based organic semiconductors for field-effect transistors. It covers naphthalene diimide-, perylene diimide- and amide-based conjugated molecules and polymers for organic semiconductors. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Selective Nitrate Recognition by a Halogen‐Bonding Four‐Station [3]Rotaxane Molecular Shuttle

    PubMed Central

    Barendt, Timothy A.; Docker, Andrew; Marques, Igor; Félix, Vítor

    2016-01-01

    Abstract The synthesis of the first halogen bonding [3]rotaxane host system containing a bis‐iodo triazolium‐bis‐naphthalene diimide four station axle component is reported. Proton NMR anion binding titration experiments revealed the halogen bonding rotaxane is selective for nitrate over the more basic acetate, hydrogen carbonate and dihydrogen phosphate oxoanions and chloride, and exhibits enhanced recognition of anions relative to a hydrogen bonding analogue. This elaborate interlocked anion receptor functions via a novel dynamic pincer mechanism where upon nitrate anion binding, both macrocycles shuttle from the naphthalene diimide stations at the periphery of the axle to the central halogen bonding iodo‐triazolium station anion recognition sites to form a unique 1:1 stoichiometric nitrate anion–rotaxane sandwich complex. Molecular dynamics simulations carried out on the nitrate and chloride halogen bonding [3]rotaxane complexes corroborate the 1H NMR anion binding results. PMID:27436297

  5. Mechanisms for naphthalene removal during electrolytic aeration.

    PubMed

    Goel, Ramesh K; Flora, Joseph R V; Ferry, John

    2003-02-01

    Batch tests were performed to investigate chemical and physical processes that may result during electrolytic aeration of a contaminated aquifer using naphthalene as a model contaminant. Naphthalene degradation of 58-66% took place electrolytically and occurred at the same rates at a pH of 4 and 7. 1,4-naphthoquinone was identified as a product of the electrolysis. Stripping due to gases produced at the electrodes did not result in any naphthalene loss. Hydrogen peroxide (which may be produced at the cathode) did not have any effect on naphthalene, but the addition of ferrous iron (which may be present in aquifers) resulted in 67-99% disappearance of naphthalene. Chlorine (which may be produced from the anodic oxidation of chloride) can effectively degrade naphthalene at pH of 4, but not at a pH of 7. Mono-, di- and poly chloronaphthalenes were identified as oxidation products. Ferric iron coagulation (due to the oxidation of ferrous iron) did not significantly contribute to naphthalene loss. Overall, electrolytic oxidation and chemical oxidation due to the electrolytic by-products formed are significant abiotic processes that could occur and should be accounted for if bioremediation of PAH-contaminated sites via electrolytic aeration is considered. Possible undesirable products such as chlorinated compounds may be formed when significant amounts of chlorides are present.

  6. Synthesis and photophysical characterizations of thermal-stable naphthalene benzimidazoles.

    PubMed

    Erten-Ela, Sule; Ozcelik, Serdar; Eren, Esin

    2011-07-01

    Microwave-assisted synthesis, photophysical and electrochemical properties of thermal-stable naphthalene benzimidazoles and naphthalimides are studied in this paper. Microwave-assisted synthesis of naphthalene benzimidazoles provide higher yields than the conventional thermal synthesis. Comparative photophysical properties of naphthalene benzimidazoles and naphthalimides are revealed that conjugation of electron-donating group onto naphthalimide moiety increases fluorescence quantum yields. Fluorophore-solvent interactions are also investigated using Lippert-Mataga equation for naphthalimides and naphthalene benzimidazoles. Thermal stabilities of naphthalene benzimidazoles are better than naphthalimides due to increased aromaticity. The experimental E(LUMO) levels of naphthalene benzimidazoles are found to be between 3.15 and 3.28 eV. Therefore, naphthalene benzimidazole derivatives consisting of anchoring groups are promising materials in organic dye sensitized solar cells. © Springer Science+Business Media, LLC 2011

  7. Experimental Electronic Spectroscopy of Two PAHs: Naphthalene and 2-METHYL Naphthalene

    NASA Astrophysics Data System (ADS)

    Friha, H.; Feraud, G.; Pino, T.; Brechignac, Ph.; Parneix, P.; Dhaoudi, Z.; Jaidane, N.; Galila, H.; Troy, T.; Schmidt, T.

    2011-06-01

    The presence of polycyclic aromatic hydrocarbons (PAHs) in the interstellar medium (ISM) was suggested in the mid-80's. Since then, their important role in the physico-chemical evolution of the ISM has been confirmed. Interstellar PAHs have been in particular proposed as possible carriers of some Diffuse Interstellar Bands (DIBs). These absorption bands are seen in the spectra of reddened stars from the visible to the near infrared and constitute a major astrophysical issue. Our purpose is to obtain electronic spectra of gas phase PAHs which will be used to probe their participation to the interstellar extinction curve from the visible (DIBs) to the UV (bump). For this goal PAHs cations represent an excellent set of target species. A new way of forming PAH+-Ar_n clusters cations has been implemented in the experimental set-up 'ICARE' at ISMO (Orsay) giving us the capability to measure the electronic spectra of cold PAH cations in the gas phase through the "Ar tagging" trick. Two molecules have been investigated in this way: naphthalene (C_1_0H_8) and 2- methyl naphthalene (C_1_1H_1_0). Clusters of naphthalene and (or 2-methyl-naphthalene) with Ar atoms are first formed in a supersonic jet, before being hit by a 281 nm laser beam which photo-ionizes the clusters which are then injected in a molecular beam through a skimmer. A tunable laser beam crossing downstream photo-dissociates the cations. The bare PAH fragments are detected using a Time-Of-Flight spectrometer while scanning the visible laser wavelength from 470 to 690 nm.

  8. 2-(Naphthalen-1-yl)-4-(naphthalen-1-yl­methyl­idene)-1,3-oxazol-5(4H)-one

    PubMed Central

    Gündoğdu, Cevher; Alp, Serap; Ergün, Yavuz; Tercan, Barış; Hökelek, Tuncer

    2011-01-01

    In the title compound, C24H15NO2, the oxazole ring is oriented at dihedral angles of 10.09 (4) and 6.04 (4)° with respect to the mean planes of the naphthalene ring systems, while the two naphthalene ring systems make a dihedral angle of 4.32 (3)°. Intra­molecular C—H⋯N hydrogen bonds link the oxazole N atom to the naphthalene ring systems. In the crystal, inter­molecular weak C—H⋯O hydrogen bonds link the mol­ecules into centrosymmetric dimers. π–π contacts between the oxazole and naphthalene rings and between the naphthalene ring systems [centroid–centroid distances = 3.5947 (9) and 3.7981 (9) Å] may further stabilize the crystal structure. Three weak C—H⋯π inter­actions also occur. PMID:21754548

  9. Acute intravascular hemolysis and methemoglobinemia following naphthalene ball poisoning.

    PubMed

    Kapoor, Rajan; Suresh, P; Barki, Satish; Mishra, Mayank; Garg, M K

    2014-09-01

    Naphthalene (C10H8) is a natural component of fossil fuels such as petroleum, diesel and coal. The common consumer products made from naphthalene are moth repellents, in the form of mothballs or crystals, and toilet deodorant blocks. Major toxic effects of naphthalene are due to precipitation of acute intravascular hemolysis. Very few cases of naphthalene poisoning and its effects have been reported from India. We report a case of accidental naphthalene poisoning, who presented with intravascular hemolysis and methemoglobinemia.

  10. Selective Nitrate Recognition by a Halogen-Bonding Four-Station [3]Rotaxane Molecular Shuttle.

    PubMed

    Barendt, Timothy A; Docker, Andrew; Marques, Igor; Félix, Vítor; Beer, Paul D

    2016-09-05

    The synthesis of the first halogen bonding [3]rotaxane host system containing a bis-iodo triazolium-bis-naphthalene diimide four station axle component is reported. Proton NMR anion binding titration experiments revealed the halogen bonding rotaxane is selective for nitrate over the more basic acetate, hydrogen carbonate and dihydrogen phosphate oxoanions and chloride, and exhibits enhanced recognition of anions relative to a hydrogen bonding analogue. This elaborate interlocked anion receptor functions via a novel dynamic pincer mechanism where upon nitrate anion binding, both macrocycles shuttle from the naphthalene diimide stations at the periphery of the axle to the central halogen bonding iodo-triazolium station anion recognition sites to form a unique 1:1 stoichiometric nitrate anion-rotaxane sandwich complex. Molecular dynamics simulations carried out on the nitrate and chloride halogen bonding [3]rotaxane complexes corroborate the (1) H NMR anion binding results. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  11. A Helicene Nanoribbon with Greatly Amplified Chirality.

    PubMed

    Schuster, Nathaniel J; Hernández Sánchez, Raúl; Bukharina, Daria; Kotov, Nicholas A; Berova, Nina; Ng, Fay; Steigerwald, Michael L; Nuckolls, Colin

    2018-05-14

    We report the synthesis and characterization of a chiral, shape-persistent, perylene-diimide-based nanoribbon. Specifically, the fusion of three perylene-diimide monomers with intervening naphthalene subunits resulted in a helical superstructure with two [6]helicene subcomponents. This π-helix-of-helicenes exhibits very intense electronic circular dichroism, including one of the largest Cotton effects ever observed in the visible range. It also displays more than an order of magnitude increase in circular dichroism for select wavelengths relative to its smaller homologue. These impressive chiroptical properties underscore the potential of this new nanoribbon architecture in the context of chiral electronic materials.

  12. Isomeric N-Annulated Perylene Diimide Dimers for Organic Solar Cells.

    PubMed

    Ma, Zetong; Fu, Huiting; Meng, Dong; Jiang, Wei; Sun, Yanming; Wang, Zhaohui

    2018-04-16

    Two isomeric N-annulated perylene diimide dimers, namely, p-BDNP and m-BDNP were designed and synthesized via geometric tuning. The distinct molecular geometry and packing arrangements of isomers with almost identical optical and electrochemical properties rendered us an in-depth understanding of the molecular structure-aggregation state-photovoltaic performance relationship. Blended with the commercially available donor PCE-10, p-BDNP and m-BDNP showed distinct differences in photovoltaic performance with power conversion efficiencies (PCEs) of 5.01 % and 4.15 %, respectively. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. IRIS Toxicological Review of Naphthalene (1998 Final)

    EPA Science Inventory

    EPA announced the release of the final report, Toxicological Review of Naphthalene: in support of the Integrated Risk Information System (IRIS). The updated Summary for Naphthalene and accompanying toxicological review have been added to the IRIS Database.

  14. Enrichment and identification of naphthalene-degrading bacteria from the Persian Gulf.

    PubMed

    Hassanshahian, Mehdi; Boroujeni, Negar Amini

    2016-06-15

    Naphthalene is a ubiquitous pollutant of the marine environment, and naphthalene biodegradation has been receiving constant scientific consideration. For cleanup of aromatic contaminated sites, bioremediation methods are considered as economical and safe approaches for the marine environment. The aims of this research are isolation and characterization of naphthalene-degrading bacteria from some marine samples of the Persian Gulf. Fifty four naphthalene-degrading bacteria were isolated from marine samples (sediment and seawater) that are enriched in ONR7a medium with naphthalene as the only carbon source. Some screening tests such as growth at high concentration of naphthalene, bioemulsifier production and surface hydrophobicity were done to select the best and prevalent strains for naphthalene degradation. Determination of the nucleotide sequence of the gene encoding for 16S rRNA shows that these isolated strains belong to these genera: Shewanella, Salegentibacter, Halomonas, Marinobacter, Oceanicola, Idiomarina and Thalassospira. These strains can degrade half of the percentage of naphthalene in 10days of incubation. This research is the first report on isolation of these genera from the Persian Gulf as naphthalene-degrader. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Exploring High-Performance n-Type Thermoelectric Composites Using Amino-Substituted Rylene Dimides and Carbon Nanotubes.

    PubMed

    Wu, Guangbao; Zhang, Zhi-Guo; Li, Yongfang; Gao, Caiyan; Wang, Xin; Chen, Guangming

    2017-06-27

    Taking advantage of the high electrical conductivity of a single-walled carbon nanotube (SWCNT) and the large Seebeck coefficient of rylene diimide, a convenient strategy is proposed to achieve high-performance n-type thermoelectric (TE) composites containing a SWCNT and amino-substituted perylene diimide (PDINE) or naphthalene diimide (NDINE). The obtained n-type composites display greatly enhanced TE performance with maximum power factors of 112 ± 8 (PDINE/SWCNT) and 135 ± 14 (NDINE/SWCNT) μW m -1 K -2 . A short doping time of 0.5 h can ensure high TE performance. The corresponding TE module consisting of five p-n junctions reaches a large output power of 3.3 μW under a 50 °C temperature gradient. In addition, the n-type composites exhibit high air stability and excellent thermal stability. This design strategy benefits the future fabricating of high-performance n-type TE materials and devices.

  16. Determination of the Rotational Barrier for Kinetically Stable Conformational Isomers via NMR and 2D TLC: An Introductory Organic Chemistry Experiment

    ERIC Educational Resources Information Center

    Rushton, Gregory T.; Burns, William G.; Lavin, Judi M.; Chong, Yong S.; Pellechia, Perry; Shimizu, Ken D.

    2007-01-01

    An experiment to determine the rotational barrier about a C[subscript aryl]-N[subscript imide] single bond that is suitable for first-semester organic chemistry students is presented. The investigation begins with the one-step synthesis of a N,N'-diaryl naphthalene diimide, which exists as two room temperature-stable atropisomers (syn and anti).…

  17. Communication: Ion mobility of the radical cation dimers: (Naphthalene)2+• and naphthalene+•-benzene: Evidence for stacked sandwich and T-shape structures

    NASA Astrophysics Data System (ADS)

    Platt, Sean P.; Attah, Isaac K.; Aziz, Saadullah; El-Shall, M. Samy

    2015-05-01

    Dimer radical cations of aromatic and polycyclic aromatic molecules are good model systems for a fundamental understanding of photoconductivity and ferromagnetism in organic materials which depend on the degree of charge delocalization. The structures of the dimer radical cations are difficult to determine theoretically since the potential energy surface is often very flat with multiple shallow minima representing two major classes of isomers adopting the stacked parallel or the T-shape structure. We present experimental results, based on mass-selected ion mobility measurements, on the gas phase structures of the naphthalene+ṡ ṡ naphthalene homodimer and the naphthalene+ṡ ṡ benzene heterodimer radical cations at different temperatures. Ion mobility studies reveal a persistence of the stacked parallel structure of the naphthalene+ṡ ṡ naphthalene homodimer in the temperature range 230-300 K. On the other hand, the results reveal that the naphthalene+ṡ ṡ benzene heterodimer is able to exhibit both the stacked parallel and T-shape structural isomers depending on the experimental conditions. Exploitation of the unique structural motifs among charged homo- and heteroaromatic-aromatic interactions may lead to new opportunities for molecular design and recognition involving charged aromatic systems.

  18. 21 CFR 172.824 - Sodium mono- and dimethyl naphthalene sulfonates.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Sodium mono- and dimethyl naphthalene sulfonates... sulfonates. The food additive sodium mono- and dimethyl naphthalene sulfonates may be safely used in... statement declaring the presence of sodium mono- and dimethyl naphthalene sulfonates. [42 FR 14491, Mar. 15...

  19. Naphthalene biodegradation in temperate and arctic marine microcosms.

    PubMed

    Bagi, Andrea; Pampanin, Daniela M; Lanzén, Anders; Bilstad, Torleiv; Kommedal, Roald

    2014-02-01

    Naphthalene, the smallest polycyclic aromatic hydrocarbon (PAH), is found in abundance in crude oil, its major source in marine environments. PAH removal occurs via biodegradation, a key process determining their fate in the sea. Adequate estimation of PAH biodegradation rates is essential for environmental risk assessment and response planning using numerical models such as the oil spill contingency and response (OSCAR) model. Using naphthalene as a model compound, biodegradation rate, temperature response and bacterial community composition of seawaters from two climatically different areas (North Sea and Arctic Ocean) were studied and compared. Naphthalene degradation was followed by measuring oxygen consumption in closed bottles using the OxiTop(®) system. Microbial communities of untreated and naphthalene exposed samples were analysed by polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and pyrosequencing. Three times higher naphthalene degradation rate coefficients were observed in arctic seawater samples compared to temperate, at all incubation temperatures. Rate coefficients at in situ temperatures were however, similar (0.048 day(-1) for temperate and 0.068 day(-1) for arctic). Naphthalene biodegradation rates decreased with similar Q10 ratios (3.3 and 3.5) in both seawaters. Using the temperature compensation method implemented in the OSCAR model, Q10 = 2, biodegradation in arctic seawater was underestimated when calculated from the measured temperate k1 value, showing that temperature difference alone could not predict biodegradation rates adequately. Temperate and arctic untreated seawater communities were different as revealed by pyrosequencing. Geographic origin of seawater affected the community composition of exposed samples.

  20. Naphthalene and Naphthoquinone: Distributions and Human Exposure in the Los Angeles Basin

    NASA Astrophysics Data System (ADS)

    Lu, R.; Wu, J.; Turco, R.; Winer, A. M.; Atkinson, R.; Paulson, S.; Arey, J.; Lurmann, F.

    2003-12-01

    Naphthalene is the simplest and most abundant of the polycyclic aromatic hydrocarbons (PAHs). Naphthalene is found primarily in the gas-phase and has been detected in both outdoor and indoor samples. Evaporation from naphthalene-containing products (including gasoline), and during refining operations, are important sources of naphthalene in air. Naphthalene is also emitted during the combustion of fossil fuels and wood, and is a component of vehicle exhaust. Exposure to high concentrations of naphthalene can damage or destroy red blood cells, causing hemolytic anemia. If inhaled over a long period of time, naphthalene may cause kidney and liver damage, skin allergy and dermatitis, cataracts and retinal damage, as well as attack the central nervous system. Naphthalene has been found to cause cancer as a result of inhalation in animal tests. Naphthoquinones are photooxidation products of naphthalene and the potential health effects of exposure to these quinones are a current focus of research. We are developing and applying models that can be used to assess human exposure to naphthalene and its photooxidation products in major air basins such as California South Coast Air Basin (SoCAB). The work utilizes the Surface Meteorology and Ozone Generation (SMOG) airshed model, and the REgional Human EXposure (REHEX) model, including an analysis of individual exposure. We will present and discuss simulations of basin-wide distributions of, and human exposures to, naphthalene and naphthoquinone, with emphasis on the uncertainties in these estimates of atmospheric concentrations and human exposure. Regional modeling of pollutant sources and exposures can lead to cost-effective and optimally health-protective emission control strategies.

  1. Degradation of naphthalene-2,6- and naphthalene-1,6-disulfonic acid by a Moraxella sp

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

    Wittich, R.M.; Tast, H.G.; Knackmuss, H.J.

    1988-07-01

    A naphthalene-2,6-disulfonic acid (2,6NDS)-degrading Moraxella strain was isolated from an industrial sewage plant. This culture could also be adapted to naphthalene-1,6-disulfonic acid as growth substrate. Regioselective 1,2-dioxygenation effected desulfonation and catabolism to 5-sulfosalicylic acid (5SS), which also could be used a the sole carbon source. 5SS-grown cells exhibited high gentisate 1,2-dioxygenase activity. Neither 5SS- nor gentisate-grown cells oxidized 2,6NDS; therefore, 2,6NDS or an early metabolite must serve as an inducer of the initial catabolic enzymes(s).

  2. Biochemical and genotoxic response of naphthalene to fingerlings of milkfish Chanos chanos.

    PubMed

    Palanikumar, L; Kumaraguru, A K; Ramakritinan, C M

    2013-09-01

    The present study investigated the acute toxicity, sub-lethal toxicity and biochemical response of naphthalene in fingerlings of milkfish Chanos chanos. The 96 h acute toxicity LC50 values for C. chanos exposed to naphthalene was 5.18 μg l(-1). The estimated no observed effect concentration and lowest observed effect concentration values for naphthalene in C. chanos were 0.42 and 0.69 μg l(-1) respectively for 30 days. The estimated maximum allowable toxicant concentration for naphthalene was 0.53 μg l(-1). Biochemical enzyme markers such as lipid peroxidation, catalase, glutathione S transferase and reduced glutathione were measured in gills and liver tissues of C. chanos exposed to sub-lethal concentrations of naphthalene. Fluctuation in lipid peroxidation and catalase level suggests that naphthalene concentrations play a vital role in induction of oxidative stress in fish. Induction of reduced glutathione level and inhibition of glutathione S-transferase level was observed in naphthalene exposed C. chanos suggesting that there may be enhanced oxidative damage due to free radicals. Increasing concentration increases in number of nuclear abnormalities. The formation of micronuclei and binucleated micronuclei induction by naphthalene confirm its genotoxic potential. The highest levels of DNA damage (% tail length) were observed at 1.24 μg l(-1) of naphthalene. The study suggests that biochemical enzymes, nuclear abnormalities and DNA damage index can serve as a biological marker for naphthalene contamination.

  3. 1,4-Bis(5-(naphthalen-1-yl)thiophen-2-yl)naphthalene, a small molecule, functions as a novel anti-HIV-1 inhibitor targeting the interaction between integrase and cellular Lens epithelium-derived growth factor.

    PubMed

    Gu, Wan-gang; Ip, Denis Tsz-Ming; Liu, Si-jie; Chan, Joseph H; Wang, Yan; Zhang, Xuan; Zheng, Yong-tang; Wan, David Chi-Cheong

    2014-04-25

    Translocation of viral integrase (IN) into the nucleus is a critical precondition of integration during the life cycle of HIV, a causative agent of Acquired Immunodeficiency Syndromes (AIDS). As the first discovered cellular factor to interact with IN, Lens epithelium-derived growth factor (LEDGF/p75) plays an important role in the process of integration. Disruption of the LEDGF/p75-IN interaction has provided a great interest for anti-HIV agent discovery. In this work, we reported that one small molecular compound, 1,4-bis(5-(naphthalen-1-yl)thiophen-2-yl)naphthalene(Compound 15), potently inhibit the IN-LEDGF/p75 interaction and affect the HIV-1 IN nuclear distribution at 1 μM. The putative binding mode of Compound 15 was constructed by a molecular docking simulation to provide structural insights into the ligand-binding mechanism. Compound 15 suppressed viral replication by measuring p24 antigen production in HIV-1IIIB acute infected C8166 cells with EC50 value of 11.19 μM. Compound 15 might supply useful structural information for further anti-HIV agent discovery. Copyright © 2014. Published by Elsevier Ireland Ltd.

  4. Perylene Diimide as a Precise Graphene-like Superoxide Dismutase Mimetic

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

    Jalilov, Almaz S.; Nilewski, Lizanne G.; Berka, Vladimir

    Here we show that the active portion of a graphitic nanoparticle can be mimicked by a perylene diimide (PDI) to explain the otherwise elusive biological and electrocatalytic activity of the nanoparticle construct. Development of molecular analogues that mimic the antioxidant properties of oxidized graphenes, in this case the poly(ethylene glycolated) hydrophilic carbon clusters (PEG–HCCs), will afford important insights into the highly efficient activity of PEG–HCCs and their graphitic analogues. PEGylated perylene diimides (PEGn–PDI) serve as well-defined molecular analogues of PEG–HCCs and oxidized graphenes in general, and their antioxidant and superoxide dismutase-like (SOD-like) properties were studied. PEGn–PDIs have two reversible reductionmore » peaks, which are more positive than the oxidation peak of superoxide (O2•–). This is similar to the reduction peak of the HCCs. Thus, as with PEG–HCCs, PEGn–PDIs are also strong single-electron oxidants of O2•–. Furthermore, reduced PEGn–PDI, PEGn–PDI•–, in the presence of protons, was shown to reduce O2•– to H2O2 to complete the catalytic cycle in this SOD analogue. The kinetics of the conversion of O2•– to O2 and H2O2 by PEG8–PDI was measured using freeze-trap EPR experiments to provide a turnover number of 133 s–1; the similarity in kinetics further supports that PEG8–PDI is a true SOD mimetic. Finally, PDIs can be used as catalysts in the electrochemical oxygen reduction reaction in water, which proceeds by a two-electron process with the production of H2O2, mimicking graphene oxide nanoparticles that are otherwise difficult to study spectroscopically.« less

  5. [Risk analysis of naphthalene pollution in soils of Tianjin].

    PubMed

    Yang, Yu; Shi, Xuan; Xu, Fu-liu; Tao, Shu

    2004-03-01

    Three approaches were applied and evaluated for probabilistic risk assessment of naphthalene in soils of Tianjin, China, based on the observed naphthalene concentration of 188 top soil samples from the area and LC50 of naphthalene to ten typical soil fauna species from the literature. It was found that the overlapping area of the two probability density functions of concentration and LC50 was 6.4%, the joint probability curve bend towards and very close to the bottom and left axis, and the calculated probability that exposure concentration exceeds LC50 of various species was as low as 1.67%, all indicating a very much acceptable risk of naphthalene to the soil fauna ecosystem and only some of very sensitive species or individual animals are threaten by localized extremely high concentration. The three approaches revealed similar results from different viewpoints.

  6. 1-anilino-8-naphthalene sulfonate as a protein conformational tightening agent.

    PubMed

    Matulis, D; Baumann, C G; Bloomfield, V A; Lovrien, R E

    1999-05-01

    1-Anilino-8-naphthalene sulfonate (ANS) anion is conventionally considered to bind to preexisting hydrophobic (nonpolar) surfaces of proteins, primarily through its nonpolar anilino-naphthalene group. Such binding is followed by an increase in ANS fluorescence intensity, similar to that occurring when ANS is dissolved in organic solvents. It is generally assumed that neither the negative sulfonate charge on the ANS, nor charges on the protein, participate significantly in ANS-protein interaction. However, titration calorimetry has demonstrated that most ANS binding to a number of proteins occurs through electrostatic forces, in which ion pairs are formed between ANS sulfonate groups and cationic groups on the proteins (D. Matulis and R. E. Lovrien, Biophys. J., 1998, Vol. 74, pp. 1-8). Here we show by viscometry and diffusion coefficient measurements that bovine serum albumin and gamma-globulin, starting from their acid-expanded, most hydrated conformations, undergo extensive molecular compaction upon ANS binding. As the cationic protein binds negatively charged ANS anion it also takes up positively charged protons from water to compensate the effect of the negative charge, and leaves the free hydroxide anions in solution thus shifting pH upward (the Scatchard-Black effect). These results indicate that ANS is not always a definitive reporter of protein molecular conformation that existed before ANS binding. Instead, ANS reports on a conformationally tightened state produced by the interplay of ionic and hydrophobic characters of both protein and ligand.

  7. Air-stable n-channel organic thin-film transistors with high field-effect mobility based on N ,N'-bis(heptafluorobutyl)-3,4:9,10-perylene diimide

    NASA Astrophysics Data System (ADS)

    Oh, Joon Hak; Liu, Shuhong; Bao, Zhenan; Schmidt, Rüdiger; Würthner, Frank

    2007-11-01

    The thin-film transistor characteristics of n-channel organic semiconductor, N ,N'-bis(2,2,3,3,4,4,4-heptafluorobutyl)-perylene tetracarboxylic diimide, are described. The slip-stacked face-to-face molecular packing allows a very dense parallel arrangement of the molecules, leading to field-effect mobility as high as 0.72cm2V-1s-1. The mobility only slightly decreased after exposure to air and remained stable for more than 50days. Our results reveal that molecular packing effects such as close stacking of perylene diimide units and segregation effects imparted by the fluorinated side chains are crucial for the air stability.

  8. Extended Hansen solubility approach: naphthalene in individual solvents.

    PubMed

    Martin, A; Wu, P L; Adjei, A; Beerbower, A; Prausnitz, J M

    1981-11-01

    A multiple regression method using Hansen partial solubility parameters, delta D, delta p, and delta H, was used to reproduce the solubilities of naphthalene in pure polar and nonpolar solvents and to predict its solubility in untested solvents. The method, called the extended Hansen approach, was compared with the extended Hildebrand solubility approach and the universal-functional-group-activity-coefficient (UNIFAC) method. The Hildebrand regular solution theory was also used to calculate naphthalene solubility. Naphthalene, an aromatic molecule having no side chains or functional groups, is "well-behaved', i.e., its solubility in active solvents known to interact with drug molecules is fairly regular. Because of its simplicity, naphthalene is a suitable solute with which to initiate the difficult study of solubility phenomena. The three methods tested (Hildebrand regular solution theory was introduced only for comparison of solubilities in regular solution) yielded similar results, reproducing naphthalene solubilities within approximately 30% of literature values. In some cases, however, the error was considerably greater. The UNIFAC calculation is superior in that it requires only the solute's heat of fusion, the melting point, and a knowledge of chemical structures of solute and solvent. The extended Hansen and extended Hildebrand methods need experimental solubility data on which to carry out regression analysis. The extended Hansen approach was the method of second choice because of its adaptability to solutes and solvents from various classes. Sample calculations are included to illustrate methods of predicting solubilities in untested solvents at various temperatures. The UNIFAC method was successful in this regard.

  9. 4-(Naphthalene-2-carboxamido)­pyridin-1-ium thio­cyanate–N-(pyridin-4-yl)naphthalene-2-carboxamide (1/1)

    PubMed Central

    Saeed, Sohail; Rashid, Naghmana; Butcher, Ray J.; Öztürk Yildirim, Sema; Hussain, Rizwan

    2012-01-01

    The asymmetric unit of the title compound, C16H13N2O+·NCS−·C16H12N2O, contains two N-(pyridin-4-yl)naphthalene-2-carboxamide mol­ecules, both are partially protonated in the pyridine moiety, i.e. the H atom attached to the pyridine N atom is partially occupied with an occupancy factor of 0.61 (3) and 0.39 (3), respectively. In the crystal, protonated and neutral N-(pyridin-4-yl)naphthalene-2-carboxamide mol­ecules are linked by N—H⋯N hydrogen bonding; the thio­cyanate counter-ion links with both protonated and neutral N-(pyridin-4-yl)naphthalene-2-carboxamide mol­ecules via N—H⋯S and N—H⋯N hydrogen bonding. The dihedral angles between the pyridine ring and naphthalene ring systems are 11.33 (6) and 9.51 (6)°, respectively. π–π stacking is observed in the crystal structure, the shortest centroid–centroid distance being 3.5929 (8) Å. The crystal structure was determined from a nonmerohedral twin {ratio of the twin components = 0.357 (1):0.643 (1) and twin law [-100 0-10 -101]}. PMID:23125774

  10. Comparative Biochemistry and Metabolism. Part 2. Naphthalene Lung Toxicity.

    DTIC Science & Technology

    1985-11-01

    Metabolites to Intra- and Extracellular Proteins .............. ........ 18 Thiol Status in Isolated Hepatocytes Incubated with Naphthalene or Menadione ...Viabilities of isolated hepatocytes incubated with menadione and varying concentrations of n aphthalene...23 15 Intracellular reduced glutathione levels in hepa- tocytes incubated in the presence of menadione or varying concentrations of naphthalene

  11. Toxicity of Naphthalene and Benzene on Tribollium castaneum Herbst.

    PubMed

    Pajaro-Castro, Nerlis; Caballero-Gallardo, Karina; Olivero-Verbel, Jesus

    2017-06-21

    Naphthalene and benzene are widely-used volatile organic compounds. The aim of this research was to examine the toxicological effects of naphthalene and benzene against Tribolium castaneum as an animal model. Adult insects were exposed to these aromatic compounds to assess mortality after 4-48 h of exposure. The lethal concentration 50 (LC 50 ) for naphthalene, naphthalin, and benzene were 63.6 µL/L, 20.0 µL/L, and 115.9 µL/L in air, respectively. Real-time polymerase chain reaction (PCR) analysis revealed expression changes in genes related to oxidative stress and metabolism [Glutathione S-Transferase (Gst), and Cytochrome P450 6BQ8 (Cyp6bq8)]; reproduction and metamorphosis [Hormone receptor in 39-like protein (Hr39), Ecdysone receptor: (Ecr), and Chitin synthase 2 (Chs2)]; and neurotransmission [Histamine-gated chloride channel 2 (Hiscl2)] in insects exposed for 4 h to 70.2 µL/L naphthalene. Adults exposed to benzene (80 µL/L; 4 h) overexpressed genes related to neurotransmission [GABA-gated anion channel (Rdl), Hiscl2, and GABA-gated ion channel (Grd)]; reproduction and metamorphosis [Ultraspiracle nuclear receptor (USP), Ecr; and Hr39]; and development (Chs2). The data presented here provides evidence that naphthalene and benzene inhalation are able to induce alterations on reproduction, development, metamorphosis, oxidative stress, metabolism, neurotransmission, and death of the insect.

  12. Biodegradation of naphthalene and phenanthren by Bacillus subtilis 3KP

    NASA Astrophysics Data System (ADS)

    Ni'matuzahroh, Trikurniadewi, N.; Pramadita, A. R. A.; Pratiwi, I. A.; Salamun, Fatimah, Sumarsih, Sri

    2017-06-01

    The purposes of this research were to know growth response, degradation ability, and uptake mechanism of naphthalene and phenanthrene by Bacillus subtilis 3KP. Bacillus subtilis 3KP was grown on Mineral Synthetic (MS) medium with addition of 1% yeast extract and naphthalene and phenanthrene respectively 200 ppm in different cultures. Bacillus subtilis 3KP growth response was monitored by Total Plate Count (TPC) method, the degradation ability was monitored by UV-Vis spectrophotometer, and the uptake mechanism of hydrocarbon was monitored by emulsification activity, decrease of surface tension, and activity of Bacterial Adherence to Hydrocarbon (BATH). Bacillus subtilis 3KP was able to grow and show biphasic growth pattern on both of substrates. Naphthalene and phenanthrene were used as a carbon source for Bacillus subtilis 3KP growth that indicated by the reduction of substrate concomitant with the growth. At room temperature conditions (± 30°C) and 90 rpm of agitation for 7 days, Bacillus subtilis 3KP could degrade naphthalene in the amount of 70.5% and phenanthrene in the amount of 24.8%. Based on the analysis of UV-Vis spectrophotometer, three metabolites, 1-hydroxy-2-naphthoic acid, salicylic acid, and pyrocatechol were found in both cultures. The metabolite identification became basis of propose degradation pathway of naphthalene and phenanthrene by Bacillus subtilis 3KP. The results of hydrocarbon uptake mechanism test show that Bacillus subtilis 3KP used all of the mechanism to degrade naphthalene and phenanthrene.

  13. Combination of degradation pathways for naphthalene utilization in Rhodococcus sp. strain TFB

    PubMed Central

    Tomás-Gallardo, Laura; Gómez-Álvarez, Helena; Santero, Eduardo; Floriano, Belén

    2014-01-01

    Rhodococcus sp. strain TFB is a metabolic versatile bacterium able to grow on naphthalene as the only carbon and energy source. Applying proteomic, genetic and biochemical approaches, we propose in this paper that, at least, three coordinated but independently regulated set of genes are combined to degrade naphthalene in TFB. First, proteins involved in tetralin degradation are also induced by naphthalene and may carry out its conversion to salicylaldehyde. This is the only part of the naphthalene degradation pathway showing glucose catabolite repression. Second, a salicylaldehyde dehydrogenase activity that converts salicylaldehyde to salicylate is detected in naphthalene-grown cells but not in tetralin-or salicylate-grown cells. Finally, we describe the chromosomally located nag genes, encoding the gentisate pathway for salicylate conversion into fumarate and pyruvate, which are only induced by salicylate and not by naphthalene. This work shows how biodegradation pathways in Rhodococcus sp. strain TFB could be assembled using elements from different pathways mainly because of the laxity of the regulatory systems and the broad specificity of the catabolic enzymes. PMID:24325207

  14. Bacterial chemotaxis along vapor-phase gradients of naphthalene.

    PubMed

    Hanzel, Joanna; Harms, Hauke; Wick, Lukas Y

    2010-12-15

    The role of bacterial growth and translocation for the bioremediation of organic contaminants in the vadose zone is poorly understood. Whereas air-filled pores restrict the mobility of bacteria, diffusion of volatile organic compounds in air is more efficient than in water. Past research, however, has focused on chemotactic swimming of bacteria along gradients of water-dissolved chemicals. In this study we tested if and to what extent Pseudomonas putida PpG7 (NAH7) chemotactically reacts to vapor-phase gradients forming above their swimming medium by the volatilization from a spot source of solid naphthalene. The development of an aqueous naphthalene gradient by air-water partitioning was largely suppressed by means of activated carbon in the agar. Surprisingly, strain PpG7 was repelled by vapor-phase naphthalene although the steady state gaseous concentrations were 50-100 times lower than the aqueous concentrations that result in positive chemotaxis of the same strain. It is thus assumed that the efficient gas-phase diffusion resulting in a steady, and possibly toxic, naphthalene flux to the cells controlled the chemotactic reaction rather than the concentration to which the cells were exposed. To our knowledge this is the first demonstration of apparent chemotactic behavior of bacteria in response to vapor-phase effector gradients.

  15. A helical perylene diimide-based acceptor for non-fullerene organic solar cells: synthesis, morphology and exciton dynamics

    NASA Astrophysics Data System (ADS)

    Chen, Li; Wu, Mingliang; Shao, Guangwei; Hu, Jiahua; He, Guiying; Bu, Tongle; Yi, Jian-Peng; Xia, Jianlong

    2018-05-01

    Helical perylene diimide-based (hPDI) acceptors have been established as one of the most promising candidates for non-fullerene organic solar cells (OSCs). In this work, we report a novel hPDI-based molecule, hPDI2-CN2, as an electron acceptor for OSCs. Combining the hPDI2-CN2 with a low-bandgap polymeric donor (PTB7-Th), the blending film morphology exhibited high sensitivity to various treatments (such as thermal annealing and addition of solvent additives), as evidenced by atomic force microscope studies. The power conversion efficiency (PCE) was improved from 1.42% (as-cast device) to 2.76% after thermal annealing, and a PCE of 3.25% was achieved by further addition of 1,8-diiodooctane (DIO). Femtosecond transient absorption (TA) spectroscopy studies revealed that the improved thin-film morphology was highly beneficial for the charge carrier transport and collection. And a combination of fast exciton diffusion rate and the lowest recombination rate contributed to the best performance of the DIO-treated device. This result further suggests that the molecular conformation needs to be taken into account in the design of perylene diimide-based acceptors for OSCs.

  16. 21 CFR 172.824 - Sodium mono- and dimethyl naphthalene sulfonates.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... SERVICES (CONTINUED) FOOD FOR HUMAN CONSUMPTION (CONTINUED) FOOD ADDITIVES PERMITTED FOR DIRECT ADDITION TO FOOD FOR HUMAN CONSUMPTION Multipurpose Additives § 172.824 Sodium mono- and dimethyl naphthalene sulfonates. The food additive sodium mono- and dimethyl naphthalene sulfonates may be safely used in...

  17. Comparative Biochemistry and Metabolism: Part 2. Naphthalene Lung Toxicity

    DTIC Science & Technology

    1984-10-14

    naphthalene, produces a highly selective lesion of the pulmonary bronchiolar epithelium in mice. This lesion appears to depend upon the cytochrome P450...predominating. The rates of metabolism were lower than in rodent lung and there were marked interindividual differences. Pulmonary microsome...54 Effect of Cobalt Protoporphyrin on Naphthalene and 2-Methylnaphthalene-Induced Pulmonary Bronchiolar Necrosis

  18. Sources, concentrations, and risks of naphthalene in indoor and outdoor air.

    PubMed

    Batterman, S; Chin, J-Y; Jia, C; Godwin, C; Parker, E; Robins, T; Max, P; Lewis, T

    2012-08-01

    Naphthalene is a ubiquitous pollutant, and very high concentrations are sometimes encountered indoors when this chemical is used as a pest repellent or deodorant. This study describes the distribution and sources of vapor-phase naphthalene concentrations in four communities in southeast Michigan, USA. Outdoors, naphthalene was measured in the communities and at a near-road site. Indoors, naphthalene levels were characterized in 288 suburban and urban homes. The median outdoor concentration was 0.15 μg/m(3), and a modest contribution from rush-hour traffic was noted. The median indoor long-term concentration was 0.89 μg/m(3), but concentrations were extremely skewed and 14% of homes exceeded 3 μg/m(3), the chronic reference concentration for non-cancer effects, 8% exceeded 10 μg/m(3), and levels reached 200 μg/m(3). The typical excess individual lifetime cancer risk was about 10(-4) and reached 10(-2) in some homes. Important sources include naphthalene's use as a pest repellent and deodorant, migration from attached garages and, to lesser extents, cigarette smoke and vehicle emissions. Excessive use as a repellent caused the highest concentrations. Naphthalene presents high risks in a subset of homes, and policies and actions to reduce exposures, for example, sales bans or restrictions, improved labeling, and consumer education, should be considered. Long-term average concentrations of naphthalene in most homes fell into the 0.2-1.7 μg/m(3) range reported as representative in earlier studies. The highly skewed distribution of concentrations results in a subset of homes with elevated concentrations and health risks that greatly exceed US EPA and World Health Organization (WHO) guidelines. The most important indoor source is the use of naphthalene as a pest repellant or deodorant; secondary sources include presence of an attached garage, cigarette smoking, and outdoor sources. House-to-house variation was large, reflecting differences among the residences and

  19. Does a concomitant exposure to lead influence unfavorably the naphthalene subchronic toxicity and toxicokinetics?

    PubMed

    Katsnelson, Boris A; Minigaliyeva, Ilzira A; Degtyareva, Tamara D; Privalova, Larisa I; Beresneva, Tatyana A

    2014-01-01

    Rats were given 20 times during 40 d either naphthalene per gavage or the same and lead acetate intraperitoneally in single doses corresponding to 5% of the respective 50% lethal doses. The concomitant exposure to lead not only added some typical indicators of lead toxicity to the moderate naphthalene intoxication picture but also exaggerated some less specific indices for intoxication. However, a number of such indices testified to attenuation of naphthalene's adverse effects under the impact of lead. Lead also lowered urinary excretion of both total and conjugated naphthalene, while the free- to total naphthalene ratio in urine sharply increased. These results corroborate implicitly the initial hypothesis that lead, being an inhibitor of cytochrome P450, hinders phase I of the naphthalene biotransformation and, thus, the formation of derivates which can be more toxic but are capable of entering into reactions of conjugation with resulting detoxication and elimination of naphthalene from the body. © 2013 SETAC.

  20. Characterization of naphthalene degradation by Streptomyces sp. QWE-5 isolated from active sludge.

    PubMed

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

    2014-01-01

    A bacterial strain, QWE-5, which utilized naphthalene as its sole carbon and energy source, was isolated and identified as Streptomyces sp. It was a Gram-positive, spore-forming bacterium with a flagellum, with whole, smooth, convex and wet colonies. The optimal temperature and pH for QWE-5 were 35 °C and 7.0, respectively. The QWE-5 strain was capable of completely degrading naphthalene at a concentration as high as 100 mg/L. At initial naphthalene concentrations of 10, 20, 50, 80 and 100 mg/L, complete degradation was achieved within 32, 56, 96, 120 and 144 h, respectively. Kinetics of naphthalene degradation was described using the Andrews equation. The kinetic parameters were as follows: qmax (maximum specific degradation rate) = 1.56 h⁻¹, Ks (half-rate constant) = 60.34 mg/L, and KI (substrate-inhibition constant) = 81.76 mg/L. Metabolic intermediates were identified by gas chromatography and mass spectrometry, allowing a new degradation pathway for naphthalene to be proposed. In this pathway, monooxygenation of naphthalene yielded naphthalen-1-ol. Further degradation by Streptomyces sp. QWE-5 produced acetophenone, followed by adipic acid, which was produced as a combination of decarboxylation and hydroxylation processes.

  1. Tethered tertiary amines as solid-state n-type dopants for solution-processable organic semiconductors

    DOE PAGES

    Russ, Boris; Robb, Maxwell J.; Popere, Bhooshan C.; ...

    2015-12-09

    A scarcity of stable n-type doping strategies compatible with facile processing has been a major impediment to the advancement of organic electronic devices. Localizing dopants near the cores of conductive molecules can lead to improved efficacy of doping. We and others recently showed the effectiveness of tethering dopants covalently to an electron-deficient aromatic molecule using trimethylammonium functionalization with hydroxide counterions linked to a perylene diimide core by alkyl spacers. In this work, we demonstrate that, contrary to previous hypotheses, the main driver responsible for the highly effective doping observed in thin films is the formation of tethered tertiary amine moietiesmore » during thin film processing. Furthermore, we demonstrate that tethered tertiary amine groups are powerful and general n-doping motifs for the successful generation of free electron carriers in the solid-state, not only when coupled to the perylene diimide molecular core, but also when linked with other small molecule systems including naphthalene diimide, diketopyrrolopyrrole, and fullerene derivatives. Our findings help expand a promising molecular design strategy for future enhancements of n-type organic electronic materials.« less

  2. Tethered tertiary amines as solid-state n-type dopants for solution-processable organic semiconductors

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

    Russ, Boris; Robb, Maxwell J.; Popere, Bhooshan C.

    A scarcity of stable n-type doping strategies compatible with facile processing has been a major impediment to the advancement of organic electronic devices. Localizing dopants near the cores of conductive molecules can lead to improved efficacy of doping. We and others recently showed the effectiveness of tethering dopants covalently to an electron-deficient aromatic molecule using trimethylammonium functionalization with hydroxide counterions linked to a perylene diimide core by alkyl spacers. In this work, we demonstrate that, contrary to previous hypotheses, the main driver responsible for the highly effective doping observed in thin films is the formation of tethered tertiary amine moietiesmore » during thin film processing. Furthermore, we demonstrate that tethered tertiary amine groups are powerful and general n-doping motifs for the successful generation of free electron carriers in the solid-state, not only when coupled to the perylene diimide molecular core, but also when linked with other small molecule systems including naphthalene diimide, diketopyrrolopyrrole, and fullerene derivatives. Our findings help expand a promising molecular design strategy for future enhancements of n-type organic electronic materials.« less

  3. Sources, Concentrations and Risks of Naphthalene in Indoor and Outdoor Air

    PubMed Central

    Batterman, Stuart; Chin, Jo-Yu; Jia, Chunrong; Godwin, Christopher; Parker, Edith; Robins, Thomas; Max, Paul; Lewis, Toby

    2011-01-01

    Naphthalene is a ubiquitous pollutant, and very high concentrations are sometimes encountered indoors when this chemical is used as a pest repellent or deodorant. This study describes the distribution and sources of vapor phase naphthalene concentrations in four communities in southeast Michigan, USA. Outdoors, naphthalene was measured in the communities and at a near-road site. Indoors, naphthalene levels were characterized in 288 suburban and urban homes. The median outdoor concentration was 0.15 µg m−3, and a modest contribution from rush-hour traffic was noted. The median indoor long-term concentration was 0.89 µg m−3, but concentrations were extremely skewed and 14% of homes exceeded 3 µg m−3, the chronic reference concentration for non-cancer effects, 8% exceeded 10 µg m−3, and levels reached 200 µg m−3. The typical individual lifetime cancer risk was about 10−4, and reached 10−2 in some homes. Important sources include naphthalene's use as a pest repellent and deodorant, migration from attached garages, and to lesser extents, cigarette smoke and vehicle emissions. Excessive use as a repellent caused the highest concentrations. Naphthalene presents high risks in a subset of homes, and policies and actions to reduce exposures, e.g., sales bans or restrictions, improved labeling and consumer education, should be considered. PMID:22145682

  4. Characterization of New Materials for Photovoltaic Thin Films: Aggregation Phenomena in Self-Assembled Perylene-Based Diimides

    DTIC Science & Technology

    2005-07-21

    or solution-based methods such as spin casting or drop casting,’ 1ś󈧖 self-assembly,1922 Langmuir - Blodgett techniques,23 or electrochemical methods...and Langmuir - exist. Molecules containing a perylene diimide core have Blodgett techniques.’ 8 In many situations, the molecules also been proposed for...remain soluble in the W. J. Langmuir 1996, 12, 2169. absence of other ionic species. These systems represent (35) Antonietti, M.; Conrad, J. Angew

  5. Solubility prediction of naphthalene in carbon dioxide from crystal microstructure

    NASA Astrophysics Data System (ADS)

    Sang, Jiarong; Jin, Junsu; Mi, Jianguo

    2018-03-01

    Crystals dissolved in solvents are ubiquitous in both natural and artificial systems. Due to the complicated structures and asymmetric interactions between the crystal and solvent, it is difficult to interpret the dissolution mechanism and predict solubility using traditional theories and models. Here we use the classical density functional theory (DFT) to describe the crystal dissolution behavior. As an example, naphthalene dissolved in carbon dioxide (CO2) is considered within the DFT framework. The unit cell dimensions and microstructure of crystalline naphthalene are determined by minimizing the free-energy of the crystal. According to the microstructure, the solubilities of naphthalene in CO2 are predicted based on the equality of naphthalene's chemical potential in crystal and solution phases, and the interfacial structures and free-energies between different crystal planes and solution are determined to investigate the dissolution mechanism at the molecular level. The theoretical predictions are in general agreement with the available experimental data, implying that the present model is quantitatively reliable in describing crystal dissolution.

  6. Comparative Biochemistry and Metabolism. Part 2. Naphthalene Lung Toxicity

    DTIC Science & Technology

    1983-08-01

    Amounts of Supernatant Enzyme Protein on the Rates of Formation of a Polar Metabolite and NapY-’ halene - Glutathione Adducts...demonstrating the regio- and stereospecific formation of glutathione adducts from aromatic and aliphatic epoxides (Yagen et al., 1981; Van Bladeren et al...butylated hydroxyanisole, Cancer Res. 41:4309-4315. Bock, K.W., Van Ackeren, G., Lorch, "L., Birke, F., (1976), Metabolism of naphthalene to naphthalene

  7. Cometabolic Degradation of Dibenzofuran and Dibenzothiophene by a Naphthalene-Degrading Comamonas sp. JB.

    PubMed

    Ji, Xiangyu; Xu, Jing; Ning, Shuxiang; Li, Nan; Tan, Liang; Shi, Shengnan

    2017-12-01

    Comamonas sp. JB was used to investigate the cometabolic degradation of dibenzofuran (DBF) and dibenzothiophene (DBT) with naphthalene as the primary substrate. Dehydrogenase and ATPase activity of the growing system with the presence of DBF and DBT were decreased when compared to only naphthalene in the growing system, indicating that the presence of DBF and DBT inhibited the metabolic activity of strain JB. The pathways and enzymes involved in the cometabolic degradation were tested. Examination of metabolites elucidated that strain JB cometabolically degraded DBF to 1,2-dihydroxydibenzofuran, subsequently to 2-hydroxy-4-(3'-oxo-3'H-benzofuran-2'-yliden)but-2-enoic acid, and finally to catechol. Meanwhile, strain JB cometabolically degraded DBT to 1,2-dihydroxydibenzothiophene and subsequently to the ring cleavage product. A series of naphthalene-degrading enzymes including naphthalene dioxygenase, 1,2-dihydroxynaphthalene dioxygenase, salicylaldehyde dehydrogenase, salicylate hydroxylase, and catechol 2,3-oxygenase have been detected, confirming that naphthalene was the real inducer of expression the degradation enzymes and metabolic pathways were controlled by naphthalene-degrading enzymes.

  8. Infrared Spectroscopy of Naphthalene Aggregation and Cluster Formation in Argon Matrices

    NASA Technical Reports Server (NTRS)

    Roser, J. E.; Allamondola, L. J.

    2011-01-01

    Fourier-transform mid-infrared absorption spectra of mixed argon/naphthalene matrices at 5 K are shown with ratios of argon-to-naphthalene that vary from 1000 to 0. These spectra show the changes as naphthalene clustering and aggregation occurs, with moderate spectral shifts affecting the C-H vibrational modes and relatively small or no shifts to the C-C and C-C-C vibrational modes. The possible contribution of homogeneous naphthalene clusters to the interstellar unidentified infrared bands is discussed. The contribution of polycyclic aromatic hydrocarbon (PAH) clusters to the 7.7 micron emission plateau and the blue shading of the 12.7 micron emission band are identified as promising candidates for future research. In addition, since PAH clusters are model components of Jupiter and Titan's atmospheres, the information presented here may also be applicable to the spectroscopy of these objects.

  9. Secondary Organic Aerosol Formation from the Photooxidation of Naphthalene

    NASA Astrophysics Data System (ADS)

    Zhou, S.; Chen, Y.; Wenger, J.

    2009-04-01

    Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous air pollutants that are released into the atmosphere as a by-product of combustion processes. The gas-phase PAHs can be chemically transformed via reaction with the hydroxyl radical to produce a range of oxidised organic compounds and other pollutants such as ozone and secondary organic aerosol (SOA). Epidemiological studies have established that exposure to this type of air pollution is associated with damaging effects on the respiratory and cardiovascular systems, and can lead to asthma, oxidative stress, health deterioration and even death. The major anthropogenic source of SOA in urban areas is believed to be aromatic hydrocarbons, which are present in automobile fuels and are used as solvents. As a result, research is currently being performed on the characterisation of SOA produced from aromatic hydrocarbons such as toluene, the xylenes and trimethylbenzenes. However, significant amounts of PAHs are also released into urban areas from automobile emissions and the combustion of fossil fuels for home heating. Naphthalene is regularly cited as the most abundant PAH in polluted urban air, with typical ambient air concentrations of 0.05 - 0.20 parts per billion (ppbV) in European cities, comparable to the xylenes. Since naphthalene reacts in an analogous manner to monocyclic aromatic compounds then it is also expected to make a significant contribution to ambient SOA. However, the yield and chemical composition of SOA produced from the atmospheric degradation of naphthalene is not well known. In this presentation, the effects of NOx level and relative humidity on the SOA formation from the phootooixdation of naphthalene will be presented. A series of experiments has been performed in a large atmospheric simulation chamber equipped with a gas chromatograph and analyzers for monitoring nitrogen oxides (NOx) and ozone. SOA formation from the photooxidation of naphthalene was measured using a scanning mobility

  10. Effects of secondary carbon supplement on biofilm-mediated biodegradation of naphthalene by mutated naphthalene 1, 2-dioxygenase encoded by Pseudomonas putida strain KD9.

    PubMed

    Dutta, Kunal; Shityakov, Sergey; Khalifa, Ibrahim; Mal, Arpan; Moulik, Satya Priya; Panda, Amiya Kumar; Ghosh, Chandradipa

    2018-05-18

    Polycyclic aromatic hydrocarbons (PAHs) belong to a diverse group of environmental pollutants distributed ubiquitously in the environment. The carcinogenic properties of PAHs are the main causes of harm to human health. The green technology, biodegradation have become convenient options to address the environmental pollution. In this study, we analyzed the biodegradation potential of naphthalene with secondary carbon supplements (SCSs) in carbon deficient media (CSM) by Pseudomonas putida strain KD9 isolated from oil refinerary waste. The rigid-flexible molecular docking method revealed that the mutated naphthalene 1,2-dioxygenase had lower affinity for naphthalene than that found in wild type strain. Moreover, analytical methods (HPLC, qRT-PCR) and soft agar chemotaxis suggest sucrose (0.5 wt%) to be the best chemo-attractant and it unequivocally caused enhanced biodegradation of naphthalene (500 mg L -1 ) in both biofilm-mediated and shake-flask biodegradation methods. In addition, the morphological analysis detected from microscopy clearly showed KD9 to change its size and shape (rod to pointed) during biodegradation of naphthalene in CSM as sole source of carbon and energy. The forward versus side light scatter plot of the singlet cells obtained from flow cytometry suggests smaller cell size in CSM and lower florescence intensity of the total DNA content of cells. This study concludes that sucrose may be used as potential bio-stimulation agent. Copyright © 2018 Elsevier B.V. All rights reserved.

  11. MEASUREMENT OF HEMOGLOBIN AND ALBUMIN ADDUCTS OF NAPHTHALENE-1,2-OXIDE, 1,2-NAPHTHOQUINONE AND 1,4-NAPHTHOQUINONE AFTER ADMINISTRATION OF NAPHTHALENE TO F344 RATS

    EPA Science Inventory

    Naphthalene-1,2-oxide (NPO), 1,2-naphthoquinone (1,2-NPQ) and 1,4-naphthoquinone (1,4-NPQ) are the major metabolites of naphthalene that are thought to be responsible for the cytotoxicity and genotoxicity of this chemical. We measured cysteinyl adducts of these metabolites in ...

  12. Visualization of Capsule Reentry Vehicle Heat Shield Ablation Using Naphthalene PLIF

    NASA Technical Reports Server (NTRS)

    Combs, Christopher S.; Clemens, Noel T.; Danehy, Paul M.

    2014-01-01

    The Orion Multi-Purpose Crew Vehicle (MPCV) will use an ablative heat shield and improved understanding of the ablation process would be beneficial for design purposes. Given that ablation is a multi-physics process involving heat and mass transfer, codes aiming to predict heat shield ablation are in need of experimental data pertaining to the turbulent transport of ablation products for validation. At The University of Texas at Austin, a technique is being developed that uses planar laser-induced fluorescence (PLIF) of a low-temperature sublimating ablator (naphthalene) to visualize the transport of ablation products in a supersonic flow. Since ablation at reentry temperatures can be difficult to recreate in a laboratory setting it is desirable to create a limited physics problem and simulate the ablation process at relatively low temperature conditions using naphthalene. A scaled Orion MPCV model with a solid naphthalene heat shield has been tested in a Mach 5 wind tunnel at various angles of attack in the current work. PLIF imaging reveals the distribution of the ablation products as they are transported into the heat-shield boundary layer and over the capsule shoulders into the separated shear layer and backshell recirculation region. Visualizations of the capsule shear layer using both naphthalene PLIF and Schlieren imaging compared favorably. High concentrations of naphthalene in the capsule separated flow region, intermittent turbulent structures on the heat shield surface, and interesting details of the capsule shear layer structure were observed using the naphthalene PLIF technique. The capsule shear layer was also shown to generally appear to be more turbulent at lower angles of attack. Furthermore, the PLIF signal increased steadily over the course of a run indicating that during a wind tunnel run the model heated up and the rate of naphthalene ablation increased. The shear layer showed increasing signs of turbulence over the course of a wind tunnel run

  13. Organic Semiconductors based on Dyes and Color Pigments.

    PubMed

    Gsänger, Marcel; Bialas, David; Huang, Lizhen; Stolte, Matthias; Würthner, Frank

    2016-05-01

    Organic dyes and pigments constitute a large class of industrial products. The utilization of these compounds in the field of organic electronics is reviewed with particular emphasis on organic field-effect transistors. It is shown that for most major classes of industrial dyes and pigments, i.e., phthalocyanines, perylene and naphthalene diimides, diketopyrrolopyrroles, indigos and isoindigos, squaraines, and merocyanines, charge-carrier mobilities exceeding 1 cm(2) V(-1) s(-1) have been achieved. The most widely investigated molecules due to their n-channel operation are perylene and naphthalene diimides, for which even values close to 10 cm(2) V(-1) s(-1) have been demonstrated. The fact that all of these π-conjugated colorants contain polar substituents leading to strongly quadrupolar or even dipolar molecules suggests that indeed a much larger structural space shows promise for the design of organic semiconductor molecules than was considered in this field traditionally. In particular, because many of these dye and pigment chromophores demonstrate excellent thermal and (photo-)chemical stability in their original applications in dyeing and printing, and are accessible by straightforward synthetic protocols, they bear a particularly high potential for commercial applications in the area of organic electronics. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Simultaneous Quantification of Multiple Urinary Naphthalene Metabolites by Liquid Chromatography Tandem Mass Spectrometry

    PubMed Central

    Ayala, Daniel C.; Morin, Dexter; Buckpitt, Alan R.

    2015-01-01

    Naphthalene is an environmental toxicant to which humans are exposed. Naphthalene causes dose-dependent cytotoxicity to murine airway epithelial cells but a link between exposure and human pulmonary disease has not been established. Naphthalene toxicity in rodents depends on P450 metabolism. Subsequent biotransformation results in urinary elimination of several conjugated metabolites. Glucuronide and sulfate conjugates of naphthols have been used as markers of naphthalene exposure but, as the current studies demonstrate, these assays provide a limited view of the range of metabolites generated from the parent hydrocarbon. Here, we present a liquid chromatography tandem mass spectrometry method for measurement of the glucuronide and sulfate conjugates of 1-naphthol as well as the mercapturic acids and N-acetyl glutathione conjugates from naphthalene epoxide. Standard curves were linear over 2 log orders. On column detection limits varied from 0.91 to 3.4 ng; limits of quantitation from 1.8 to 6.4 ng. The accuracy of measurement of spiked urine standards was -13.1 to + 5.2% of target and intra-day and inter-day variability averaged 7.2 (± 4.5) and 6.8 (± 5.0) %, respectively. Application of the method to urine collected from mice exposed to naphthalene at 15 ppm (4 hrs) showed that glutathione-derived metabolites accounted for 60-70% of the total measured metabolites and sulfate and glucuronide conjugates were eliminated in equal amounts. The method is robust and directly measures several major naphthalene metabolites including those derived from glutathione conjugation of naphthalene epoxide. The assays do not require enzymatic deconjugation, extraction or derivatization thus simplifying sample work up. PMID:25853821

  15. KINETICS OF CHROMATE REDUCTION DURING NAPHTHALENE DEGRADATION IN A MIXED CULTURE

    EPA Science Inventory

    A mixed culture of Bacillus sp. K1 and Sphingomonas paucimobilis EPA 505 was exposed to chromate and naphthalene. Batch experiments showed that chromate was reduced and naphthalene was degraded by the mixed culture. Chromate reduction occurred initially at a high rate followed by...

  16. Assessment of ligand binding at a site relevant to SOD1 oxidation and aggregation.

    PubMed

    Manjula, Ramu; Wright, Gareth S A; Strange, Richard W; Padmanabhan, Balasundaram

    2018-05-01

    Cu/Zn superoxide dismutase-1 (SOD1) mutations are causative for a subset of amyotrophic lateral sclerosis (ALS) cases. These mutations lead to structural instability, aggregation and ultimately motor neuron death. We have determined crystal structures of SOD1 in complex with a naphthalene-catechol-linked compound which binds with low micro-molar affinity to a site important for oxidative damage-induced aggregation. SOD1 Trp32 oxidation is indeed significantly inhibited by ligand binding. Our work shows how compound linking can be applied successfully to ligand interactions on the SOD1 surface to generate relatively good binding strength. The ligand, positioned in a region important for SOD1 fibrillation, offers the possibility that it, or a similar compound, could prevent the abnormal self-association that drives SOD1 toxicity in ALS. © 2018 Federation of European Biochemical Societies.

  17. Polyaniline nanotubes and their dendrites doped with different naphthalene sulfonic acids

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

    Zhang Zhiming; Chemistry and Chemical Engineering College, Ocean University of China, Qingdao 266003; Wei Zhixiang

    2005-03-01

    Polyaniline (PANI) nanotubes (130-250 nm in average diameter) doped with {alpha}-naphthalene sulfonic acid ({alpha}-NSA), {beta}-naphthalene sulfonic acid ({beta}-NSA) and 1,5-naphthalene disulfonic acid were synthesized via a self-assembly process. It was found that the formation yield, morphology (hollow or solid), size, crystalline and electrical properties of the nanostructures are affected by the position and number of -SO{sub 3}H groups attached to the naphthalene ring of NSA as well as the synthesis conditions. Moreover, these nanotubes aggregate to form a dendritic morphology when the polymerization is performed at a static state. The micelles composed of dopant or dopant/anilinium cations might act inmore » a template-like fashion in forming self-assembled PANI nanotubes, which was further confirmed by X-ray diffraction measurements, while the aggregated morphology of the nanotubes might result from polymer chain interactions including {pi}-{pi} interactions, hydrogen and ionic bonds.« less

  18. [Effects of naphthalene on soil respiration, nutrients and enzyme activities in the subalpine forest of western Sichuan, China].

    PubMed

    Yang, Fan; Yang, Wan Qin; Wu, Fu Zhong; Wang, Hui; Lan, Li Ying; Liu, Yu Wei; Guo, Cai Hong; Tan, Bo

    2017-06-18

    As a biocide to reduce soil and litter faunal populations in field experiments, naphthalene has been widely used in the study of ecological functions of soil fauna, but the non-target effects of naphthalene bring about enormous uncertainty to its application. In order to understand whether there were non-target effects of naphthalene in subalpine forest soil, soil in the subalpine forests of west Qinghai-Tibet Plateau was taken as study object. The short-term responses of soil respiration rate, nutrient content and enzyme activity to naphthalene were studied in microcosms. The results showed that soil respiration rate was significantly suppressed by application of naphthalene within 0-10 days, and then showed a significant promotion effect. Naphthalene significantly affected the dynamics of soil NH 4 + -N and NO 3 - -N contents. With application of naphthalene, the highest contents of NH 4 + -N and NO 3 - -N occurred at the 3rd and 7th day, respectively. But they were observed at the 45th and 52nd day with no-naphthalene, respectively. Moreover, soil dissolved carbon content in the naphthalene microcosms showed a sharp increase and then decrease dynamic at the 3rd day, while small change was detected in the no-naphthalene microcosms. Dissolved nitrogen content in both the naphthalene and no-naphthalene microcosms showed an increase at first and then decreased subsequently during the study period. Similar dynamics were found for the soil enzyme activities in both the naphthalene and no-naphthalene microcosms. The highest activities of urease, nitrate reductase and nitrite reductase in both the naphthalene and no-naphthalene microcosms were at the 45th, 38th and 10th day, respectively. In addition, the interaction of naphthalene treatment and sampling time had significant effects on soil respiration rate, the contents of NH 4 + -N, NO 3 - -N and dissolved nitrogen, but had no significant effects on soil dissolved carbon content, and the activities of invertase

  19. Influence of the presence of PAHs and coal tar on naphthalene sorption in soils

    NASA Astrophysics Data System (ADS)

    Bayard, Rémy; Barna, Ligia; Mahjoub, Borhane; Gourdon, Rémy

    2000-11-01

    The mobility of the most water-soluble polynuclear aromatic hydrocarbons (PAHs) such as naphthalene in contaminated soils from manufactured gas plant (MGP) sites or other similar sites is influenced not only by the naturally occurring soil organic matter (SOM) but also, and in many cases mostly, by the nature and concentration of coal tar xenobiotic organic matter (XOM) and other PAH molecules present in the medium under various physical states. The objective of the present study was to quantify the effects of these factors using batch experiments, in order to simulate naphthalene transport in soil-tar-water systems using column experiments. Naphthalene sorption was studied in the presence of (i) solid coal tar particles, (ii) phenanthrene supplied as pure crystals, in the aqueous solution or already sorbed onto the soil, (iii) fluoranthene as pure crystals, and (iv) an aqueous solution of organic molecules extracted from a liquid tar. All experiments were conducted under abiotic conditions using short naphthalene/sorbent contact times of 24-60 h. Although these tests do not reflect true equilibrium conditions which usually take more time to establish, they were used to segregate relatively rapid sorption phenomena ("pseudo equilibrium") from slow sorption and other aging phenomena. For longer contact times, published data have shown that experimental biases due to progressive changes in the characteristics of the soil and the solution may drastically modify the affinity of the solutes for the soil. Slow diffusion in the microporosity and in dense organic phases may also become significant over the long term, along with some irreversible aging phenomena which have not been addressed in this work. Results showed that PAHs had no effect on naphthalene sorption when present in the aqueous solution or as pure crystals, due to their low solubility in water. Adsorbed phenanthrene was found to reduce naphthalene adsorption only when present at relatively high

  20. Synthesis, spectroscopic and DNA binding ability of CoII, NiII, CuII and ZnII complexes of Schiff base ligand (E)-1-(((1H-benzo[d]imidazol-2-yl)methylimino)methyl)naphthalen-2-ol. X-ray crystal structure determination of cobalt (II) complex.

    PubMed

    Yarkandi, Naeema H; El-Ghamry, Hoda A; Gaber, Mohamed

    2017-06-01

    A novel Schiff base ligand, (E)-1-(((1H-benzo[d]imidazol-2-yl)methylimino)methyl)naphthalen-2-ol (HL), has been designed and synthesized in addition to its metal chelates [Co(L) 2 ]·l2H 2 O, [Ni(L)Cl·(H 2 O) 2 ].5H 2 O, [Cu(L)Cl] and [Zn(L)(CH 3 COO)]. The structures of the isolated compounds have been confirmed and identified by means of different spectral and physicochemical techniques including CHN analysis, 1 H & 13 C NMR, mass spectral analysis, molar conductivity measurement, UV-Vis, infrared, magnetic moment in addition to TGA technique. The infrared spectral results ascertained that the ligand acts as monobasic tridentate binding to the metal centers via deprotonated hydroxyl oxygen, azomethine and imidazole nitrogen atoms. The UV-Vis, magnetic susceptibility and molar conductivity data implied octahedral geometry for Co(II) & Ni(II) complexes, tetrahedral for Zn(II) complex and square planar for Cu(II) complex. X-ray structural analysis of Co(II) complex 1 has been reported and discussed. Moreover, the type of interaction between the ligand & its complexes towards salmon sperm DNA (SS-DNA) has been examined by the measurement of absorption spectra and viscosity which confirmed that the ligand and its complexes interact with DNA via intercalation interaction as concluded from the values of binding constants (K b ). Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Self-assembled copper(II) metallacycles derived from asymmetric Schiff base ligands: efficient hosts for ADP/ATP in phosphate buffer.

    PubMed

    Kumar, Amit; Pandey, Rampal; Kumar, Ashish; Gupta, Rakesh Kumar; Dubey, Mrigendra; Mohammed, Akbar; Mobin, Shaikh M; Pandey, Daya Shankar

    2015-10-21

    Novel asymmetric Schiff base ligands 2-{[3-(3-hydroxy-1-methyl-but-2-enylideneamino)-2,4,6-trimethylphenylimino]-methyl}-phenol (H2L(1)) and 1-{[3-(3-hydroxy-1-methyl-but-2-enylideneamino)-2,4,6-trimethylphenylimino]-methyl}-naphthalen-2-ol (H2L(2)) possessing dissimilar N,O-chelating sites and copper(ii) metallacycles (CuL(1))4 (1) and (CuL(2))4 (2) based on these ligands have been described. The ligands and complexes have been thoroughly characterized by satisfactory elemental analyses, and spectral (IR, (1)H, (13)C NMR, ESI-MS, UV/vis) and electrochemical studies. Structures of H2L(2) and 1 have been unambiguously determined by X-ray single crystal analyses. The crystal structure of H2L(2) revealed the presence of two distinct N,O-chelating sites on dissimilar cores (naphthalene and β-ketoaminato groups) offering a diverse coordination environment. Metallacycles 1 and 2 having a cavity created by four Cu(ii) centres coordinated in a homo- and heteroleptic fashion with respective ligands act as efficient hosts for adenosine-5'-diphosphate (ADP) and adenosine-5'-triphosphate (ATP) respectively, over other nucleoside polyphosphates (NPPs). The disparate sensitivity of these metallacycles toward ADP and ATP has been attributed to the size of the ligands assuming diverse dimensions and spatial orientations. These are attuned for π-π stacking and electrostatic interactions suitable for different guest molecules under analogous conditions, metallacycle 1 offers better orientation for ADP, while 2 for ATP. The mechanism of the host-guest interaction has been investigated by spectral and electrochemical studies and supported by molecular docking studies.

  2. Rigidifying Nonplanar Perylene Diimides by Ring Fusion Toward Geometry-Tunable Acceptors for High-Performance Fullerene-Free Solar Cells.

    PubMed

    Zhong, Hongliang; Wu, Chen-Hao; Li, Chang-Zhi; Carpenter, Joshua; Chueh, Chu-Chen; Chen, Jung-Yao; Ade, Harald; Jen, Alex K-Y

    2016-02-03

    Rigid fused perylene diimide (PDI) dimers bridged with heterocycles exhibit superior photovoltaic performance compared to their unfused semiflexible analogues. Changing the chalcogen atoms in the aromatic bridges gradually increases the twist angles between the two PDI planes, leading to a varied morphology in which the one bridged by thiophene achieves a balance and shows the best efficiency of 6.72%. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. [Degradation characteristics of naphthalene with a Pseudomonas aeruginosa strain isolated from soil contaminated by diesel].

    PubMed

    Liu, Wen-Chao; Wu, Bin-Bin; Li, Xiao-Sen; Lu, Dian-Nan; Liu, Yong-Min

    2015-02-01

    Abstract: A naphthalene-degrading bacterium (referred as HD-5) was isolated from the diesel-contaminated soil and was assigned to Pseudomonas aeruginosa according to 16S rDNA sequences analysis. Gene nah, which encodes naphthalene dioxygenase, was identified from strain HD-5 by PCR amplification. Different bioremediation approaches, including nature attenuation, bioaugmentation with strain Pseudomonas aeruginosa, biostimulation, and an integrated degradation by bioaugmentation and biostimulation, were evaluated for their effectiveness in the remediating soil containing 5% naphthalene. The degradation rates of naphthalene in the soil were compared among the different bioremediation approaches, the FDA and dehydrogenase activity in bioremediation process were measured, and the gene copy number of 16S rRNA and nah in soil were dynamically monitored using real-time PCR. It was shown that the naphthalene removal rate reached 71.94%, 62.22% and 83.14% in approaches of bioaugmentation (B), biostimulation(S) and integrated degradation composed of bioaugmentation and biostimulation (BS), respectively. The highest removal rate of naphthalene was achieved by using BS protocol, which also gives the highest FDA and dehydrogenase activity. The gene copy number of 16S rRNA and nah in soil increased by about 2.67 x 10(11) g(-1) and 8.67 x 10(8) g(-1) after 31 days treatment using BS protocol. Above-mentioned results also demonstrated that the screened bacterium, Pseudomonas aeruginosa, could grow well in naphthalene-contaminated soil and effectively degrade naphthalene, which is of fundamental importance for bioremediation of naphthalene-contaminated soil.

  4. Simplified MPN method for enumeration of soil naphthalene degraders using gaseous substrate.

    PubMed

    Wallenius, Kaisa; Lappi, Kaisa; Mikkonen, Anu; Wickström, Annika; Vaalama, Anu; Lehtinen, Taru; Suominen, Leena

    2012-02-01

    We describe a simplified microplate most-probable-number (MPN) procedure to quantify the bacterial naphthalene degrader population in soil samples. In this method, the sole substrate naphthalene is dosed passively via gaseous phase to liquid medium and the detection of growth is based on the automated measurement of turbidity using an absorbance reader. The performance of the new method was evaluated by comparison with a recently introduced method in which the substrate is dissolved in inert silicone oil and added individually to each well, and the results are scored visually using a respiration indicator dye. Oil-contaminated industrial soil showed slightly but significantly higher MPN estimate with our method than with the reference method. This suggests that gaseous naphthalene was dissolved in an adequate concentration to support the growth of naphthalene degraders without being too toxic. The dosing of substrate via gaseous phase notably reduced the work load and risk of contamination. The result scoring by absorbance measurement was objective and more reliable than measurement with indicator dye, and it also enabled further analysis of cultures. Several bacterial genera were identified by cloning and sequencing of 16S rRNA genes from the MPN wells incubated in the presence of gaseous naphthalene. In addition, the applicability of the simplified MPN method was demonstrated by a significant positive correlation between the level of oil contamination and the number of naphthalene degraders detected in soil.

  5. A novel Pseudomonas gessardii strain LZ-E simultaneously degrades naphthalene and reduces hexavalent chromium.

    PubMed

    Huang, Haiying; Wu, Kejia; Khan, Aman; Jiang, Yiming; Ling, Zhenmin; Liu, Pu; Chen, Yong; Tao, Xuanyu; Li, Xiangkai

    2016-05-01

    Combined pollutants with polycyclic aromatic hydrocarbons (PAHs) and heavy metals have been identified as toxic and unmanageable contaminates. In this work, Pseudomonas gessardii strain LZ-E isolated from wastewater discharge site of a petrochemical company degrades naphthalene and reduces Cr(VI) simultaneously. 95% of 10mgL(-1) Cr(VI) was reduced to Cr(III) while 77% of 800mgL(-1) naphthalene was degraded when strain LZ-E was incubated in BH medium for 48h. Furthermore, naphthalene promotes Cr(VI) reduction in strain LZ-E as catechol and phthalic acid produced in naphthalene degradation are able to reduce Cr(VI) abiotically. An aerated bioreactor system was setup to test strain LZ-E's remediation ability. Strain LZ-E continuously remediated naphthalene and Cr(VI) at rates of 15mgL(-1)h(-1) and 0.20mgL(-1)h(-1) of 800mgL(-1) naphthalene and 10mgL(-1) Cr(VI) addition with eight batches in 16days. In summary, strain LZ-E is a potential applicant for combined pollution remediation. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  6. Photoelectrochemical processes in organic semiconductor: Ambipolar perylene diimide thin film

    NASA Astrophysics Data System (ADS)

    Kim, Jung Yong; Chung, In Jae

    2018-03-01

    A thin film of N,N‧-dioctadecyl-3,4,9,10-perylene tetracarboxylic diimide (PTCDI-C18) is spin-coated on indium tin oxide (ITO) glass. Using the PTCDI-C18/ITO electrode, we fabricate a photoelectrochemical cell with the ITO/PTCDI-C18/Redox Electrolyte/Pt configuration. The electrochemical properties of this device are investigated as a function of hydroquinone (HQ) concentration, bias voltage, and wavelength of light. Anodic photocurrent is observed at V ≥ -0.2 V vs. Ag/AgCl, indicating that the PTCDI-C18 film acts as an n-type semiconductor as usual. However, when benzoquinone (BQ) is inserted into the electrolyte system instead of HQ, cathodic photocurrent is observed at V ≤ 0.0 V, displaying that PTCDI-C18 abnormally serves as a p-type semiconductor. Hence the overall results reveal that the PTCDI-C18 film can be an ambipolar functional semiconductor depending on the redox couple in the appropriate voltage.

  7. Naphthalene metabolism in relation to target tissue anatomy, physiology, cytotoxicity and tumorigenic mechanism of action

    PubMed Central

    Bogen, Kenneth T.; Benson, Janet M.; Yost, Garold S.; Morris, John B.; Dahl, Alan R.; Clewell, Harvey J.; Krishnan, Kannan; Omiecinski, Curtis J.

    2014-01-01

    This report provides a summary of deliberations conducted under the charge for members of Module C Panel participating in the Naphthalene State-of-the-Science Symposium (NS3), Monterey, CA, October 9–12, 2006. The panel was charged with reviewing the current state of knowledge and uncertainty about naphthalene metabolism in relation to anatomy, physiology and cytotoxicity in tissues observed to have elevated tumor incidence in these rodent bioassays. Major conclusions reached concerning scientific claims of high confidence were that: (1) rat nasal tumor occurrence was greatly enhanced, if not enabled, by adjacent, histologically related focal cellular proliferation; (2) elevated incidence of mouse lung tumors occurred at a concentration (30 ppm) cytotoxic to the same lung region at which tumors occurred, but not at a lower and less cytotoxic concentration (tumorigenesis NOAEL = 10 ppm); (3) naphthalene cytotoxicity requires metabolic activation (unmetabolized naphthalene is not a proximate cause of observed toxicity or tumors); (4) there are clear regional and species differences in naphthalene bioactivation; and (5) target tissue anatomy and physiology is sufficiently well understood for rodents, non-human primates and humans to parameterize species-specific physiologically based pharmacokinetic (PBPK) models for nasal and lung effects. Critical areas of uncertainty requiring resolution to enable improved human cancer risk assessment were considered to be that: (1) cytotoxic naphthalene metabolites, their modes of cytotoxic action, and detailed low-dose dose–response need to be clarified, including in primate and human tissues, and neonatal tissues; (2) mouse, rat, and monkey inhalation studies are needed to better define in vivo naphthalene uptake and metabolism in the upper respiratory tract; (3) in vivo validation studies are needed for a PBPK model for monkeys exposed to naphthalene by inhalation, coupled to cytotoxicity studies referred to above; and (4

  8. Hydrogenation of liquid natural rubber via diimide reduction in hydrazine hydrate/hydrogen peroxide system

    NASA Astrophysics Data System (ADS)

    Yusof, Muhammad Jefri Mohd; Jamaluddin, Naharullah; Abdullah, Ibrahim; Yusoff, Siti Fairus M.

    2015-09-01

    Liquid natural rubber (LNR) with molecular weight of lower than 105 and shorter polymeric chain than natural rubber was prepared. LNR was then hydrogenated via diimide reduction by oxidation of hydrazine hydrate with hydrogen peroxide. The unsaturated units of the rubber were converted into saturated hydrocarbon to strengthen the backbone of the polymer so it was able to resist thermal degradation. The results indicated that hydrogenation degree of the product (HLNR) could be extended to 91.2% conversion under appropriate conditions. The hydrogenated LNR (HLNR) was characterized using Fourier-Transform Infrared (FTIR) and Nuclear Magnetic Resonance (NMR) spectroscopy. The physical characteristics of HLNR were analyzed with Termogravimetric Analysis (TGA).

  9. Differentiation of naphthalene and paradichlorobenzene mothballs based on their difference in specific gravity.

    PubMed

    Fukuda, T; Koyama, K; Yamashita, M; Koichi, N; Takeda, M

    1991-08-01

    The present study was conducted to measure the specific gravities of paradichlorobenzene and naphthalene mothballs and compare them with the specific gravity of a saturated aqueous solution of sodium chloride (1.197). The specific gravities of 450 paradichlorobenzene mothballs from 5 manufactures and 150 naphthalene mothballs from 2 manufactures were measured with a specific gravity meter. The mean specific gravities of paradichlorobenzene mothballs were between 1.429 and 1.437 (p = 0.99). On the other hand, the mean specific gravities of naphthalene mothballs were between 1.094 and 1.100 (p = 0.99). Based on the fact that paradichlorobenzene mothballs sink in a saturated solution of salt whereas naphthalene mothballs float on it, these 2 kinds of mothballs ought to be rapidly and accurately distinguished in clinical settings.

  10. Interrelation of nonequivalent Csbnd C bonds of naphthalene frame and spatial orientation of substituents: Beta-naphthalene sulfonyl fluoride and beta-naphthalene sulfonyl chloride

    NASA Astrophysics Data System (ADS)

    Giricheva, Nina I.; Petrov, Vjacheslav M.; Oberhammer, Heinz; Petrova, Valentina N.; Dakkouri, Marwan; Ivanov, Sergey N.; Girichev, Georgiy V.

    2013-06-01

    β-naphthalene sulfonyl fluoride, β-NaphSF, and β-naphthalene sulfonyl chloride, β-NaphSCl, were studied by gas-phase electron diffraction (GED) and quantum chemical calculations (B3LYP and MP2 in combination with cc-pVDZ, aug-cc-pVDZ and cc-pVTZ basis sets). For each compound the calculations predicted the existence of two conformers which are enantiomers. On the basis of the experimental data it was found that the gas phase over β-NaphSF and NaphSCl at 357(5) K and 395(5) K, respectively, consists of molecular species of C1 symmetry in which the Cβsbnd Ssbnd Hal plane deviates from the perpendicular orientation relative to the naphthalene skeleton plane. The following geometrical parameters (Å and degrees) were obtained from the experiment (uncertainties are in parentheses): rh1(Csbnd H)aver. = 1.097(7), rh1(Csbnd C)aver. = 1.410(3), rh1(Csbnd S) = 1.753(6), rh1(Ssbnd O)aver. = 1.414(4), rh1(Ssbnd F) = 1.559(5), ∠Csbnd Cβsbnd C = 122.8(3), ∠Cβsbnd Ssbnd F = 103.3(30); Φ(Cαsbnd Cβsbnd Ssbnd F) = 104(6) for β-NaphSF, and rh1(Csbnd H)aver. = 1.089(4), rh1(Csbnd C)aver. = 1.411(3), rh1(Csbnd S) = 1.757(5), rh1(Ssbnd O)aver. = 1.419(3), rh1(Ssbnd Сl) = 2.053(4), ∠Csbnd Cβsbnd C = 122.8(1), ∠Cβsbnd Ssbnd Cl = 102.2(7), Φ(Cαsbnd Cβsbnd Ssbnd Cl) = 108(3) for β-NaphSCl. The calculated barriers to internal rotation of the sulfonyl halide groups exceed considerably the thermal energy values corresponding to the temperatures of the GED experiments. Natural bond orbital (NBO) analyses of the electron density distribution were applied to explain the peculiarities of the molecular structure of the studied compounds and the deviation from the structures of their benzene analogs.

  11. Carbon Nitride-Aromatic Diimide-Graphene Nanohybrids: Metal-Free Photocatalysts for Solar-to-Hydrogen Peroxide Energy Conversion with 0.2% Efficiency.

    PubMed

    Kofuji, Yusuke; Isobe, Yuki; Shiraishi, Yasuhiro; Sakamoto, Hirokatsu; Tanaka, Shunsuke; Ichikawa, Satoshi; Hirai, Takayuki

    2016-08-10

    Solar-to-chemical energy conversion is a challenging subject for renewable energy storage. In the past 40 years, overall water splitting into H2 and O2 by semiconductor photocatalysis has been studied extensively; however, they need noble metals and extreme care to avoid explosion of the mixed gases. Here we report that generating hydrogen peroxide (H2O2) from water and O2 by organic semiconductor photocatalysts could provide a new basis for clean energy storage without metal and explosion risk. We found that carbon nitride-aromatic diimide-graphene nanohybrids prepared by simple hydrothermal-calcination procedure produce H2O2 from pure water and O2 under visible light (λ > 420 nm). Photoexcitation of the semiconducting carbon nitride-aromatic diimide moiety transfers their conduction band electrons to graphene and enhances charge separation. The valence band holes on the semiconducting moiety oxidize water, while the electrons on the graphene moiety promote selective two-electron reduction of O2. This metal-free system produces H2O2 with solar-to-chemical energy conversion efficiency 0.20%, comparable to the highest levels achieved by powdered water-splitting photocatalysts.

  12. Enrichment and characterization of sulfate reducing, naphthalene degrading microorganisms

    NASA Astrophysics Data System (ADS)

    Steffen, Kümmel; Florian-Alexander, Herbst; Márcia, Duarte; Dietmar, Pieper; Jana, Seifert; Bergen Martin, von; Hans-Hermann, Richnow; Carsten, Vogt

    2014-05-01

    Polycyclic aromatic hydrocarbons (PAH) are pollutants of great concern due to their potential toxicity, mutagenicity and carcinogenicity. PAH are widely distributed in the environment by accidental discharges during the transport, use and disposal of petroleum products, and during forest and grass fires. Caused by their hydrophobic nature, PAH basically accumulate in sediments from where they are slowly released into the groundwater. Although generally limited by the low water solubility of PAH, microbial degradation is one of the major mechanisms leading to the complete clean-up of PAH-contaminated sites. Whereas organisms and biochemical pathways responsible for the aerobic breakdown of PAH are well known, anaerobic PAH biodegradation is less understood; only a few anaerobic PAH degrading cultures have been described. We studied the anaerobic PAH degradation in a microcosm approach to enrich anaerobic PAH degraders. Anoxic groundwater and sediment samples were used as inoculum. Groundwater samples were purchased from the erstwhile gas works facility and a former wood impregnation site. In contrast, sources of sediment samples were a former coal refining area and an old fuel depot. Samples were incubated in anoxic mineral salt medium with naphthalene as sole carbon source and sulfate as terminal electron acceptor. Grown cultures were characterized by feeding with 13C-labeled naphthalene, 16S rRNA gene sequencing using an Illumina® approach, and functional proteome analyses. Finally, six enrichment cultures able to degrade naphthalene under anoxic conditions were established. First results point to a dominance of identified sequences affiliated to the freshwater sulfate-reducing strain N47, which is a known anaerobic naphthalene degrader, in four out of the six enrichments. In those enrichments, peptides related to the pathway of anoxic naphthalene degradation in N47 were abundant. Overall the data underlines the importance of Desulfobacteria for natural

  13. Hypothesis-based weight-of-evidence evaluation and risk assessment for naphthalene carcinogenesis

    PubMed Central

    Bailey, Lisa A.; Nascarella, Marc A.; Kerper, Laura E.; Rhomberg, Lorenz R.

    2016-01-01

    Inhalation of naphthalene causes olfactory epithelial nasal tumors in rats (but not in mice) and benign lung adenomas in mice (but not in rats). The limited available human data have not identified an association between naphthalene exposure and increased respiratory cancer risk. Assessing naphthalene's carcinogenicity in humans, therefore, depends entirely on experimental evidence from rodents. We evaluated the respiratory carcinogenicity of naphthalene in rodents, and its potential relevance to humans, using our Hypothesis-Based Weight-of-Evidence (HBWoE) approach. We systematically and comparatively reviewed data relevant to key elements in the hypothesized modes of action (MoA) to determine which is best supported by the available data, allowing all of the data from each realm of investigation to inform interpretation of one another. Our analysis supports a mechanism that involves initial metabolism of naphthalene to the epoxide, followed by GSH depletion, cytotoxicity, chronic inflammation, regenerative hyperplasia, and tumor formation, with possible weak genotoxicity from downstream metabolites occurring only at high cytotoxic doses, strongly supporting a non-mutagenic threshold MoA in the rat nose. We also conducted a dose–response analysis, based on the likely MoA, which suggests that the rat nasal MoA is not relevant in human respiratory tissues at typical environmental exposures. Our analysis illustrates how a thorough WoE evaluation can be used to support a MoA, even when a mechanism of action cannot be fully elucidated. A non-mutagenic threshold MoA for naphthalene-induced rat nasal tumors should be considered as a basis to determine human relevance and to guide regulatory and risk-management decisions. PMID:26202831

  14. STABILITY OF HEMOGLOBIN AND ALBUMIN ADDUCTS OF NAPHTHALENE OXIDE, 1,2-NAPHTHOQUINONE, AND 1,4-NAPHTHOQUINONE

    EPA Science Inventory

    Naphthalene is an important industrial chemical, which has recently been shown to cause tumors of the respiratory tract in rodents. It is thought that one or more reactive metabolites of naphthalene, namely, naphthalene-1,2-oxide (NPO), 1,2-naphthoquinone (1,2-NPQ), and 1,4-na...

  15. Biodegradation of naphthalene and anthracene by chemo-tactically active rhizobacteria of populus deltoides

    PubMed Central

    Bisht, Sandeep; Pandey, Piyush; Sood, Anchal; Sharma, Shivesh; Bisht, N. S.

    2010-01-01

    Several naphthalene and anthracene degrading bacteria were isolated from rhizosphere of Populus deltoides, which were growing in non-contaminated soil. Among these, four isolates, i.e. Kurthia sp., Micrococcus varians, Deinococcus radiodurans and Bacillus circulans utilized chrysene, benzene, toluene and xylene, in addition to anthracene and naphthalene. Kurthia sp and B. circulans showed positive chemotactic response for naphthalene and anthracene. The mean growth rate constant (K) of isolates were found to increase with successive increase in substrate concentration (0.5 to 1.0 mg/50ml). B. circulans SBA12 and Kurthia SBA4 degraded 87.5% and 86.6% of anthracene while, Kurthia sp. SBA4, B. circulans SBA12, and M. varians SBA8 degraded 85.3 %, 95.8 % and 86.8 % of naphthalene respectively after 6 days of incubation as determined by HPLC analysis. PMID:24031572

  16. Alkylation effects on the energy transfer of highly vibrationally excited naphthalene.

    PubMed

    Hsu, Hsu Chen; Tsai, Ming-Tsang; Dyakov, Yuri A; Ni, Chi-Kung

    2011-11-04

    The energy transfer of highly vibrationally excited isomers of dimethylnaphthalene and 2-ethylnaphthalene in collisions with krypton were investigated using crossed molecular beam/time-of-flight mass spectrometer/time-sliced velocity map ion imaging techniques at a collision energy of approximately 300 cm(-1). Angular-resolved energy-transfer distribution functions were obtained directly from the images of inelastic scattering. The results show that alkyl-substituted naphthalenes transfer more vibrational energy to translational energy than unsubstituted naphthalene. Alkylation enhances the V→T energy transfer in the range -ΔE(d)=-100~-1500 cm(-1) by approximately a factor of 2. However, the maximum values of V→T energy transfer for alkyl-substituted naphthalenes are about 1500~2000 cm(-1), which is similar to that of naphthalene. The lack of rotation-like wide-angle motion of the aromatic ring and no enhancement in very large V→T energy transfer, like supercollisions, indicates that very large V→T energy transfer requires special vibrational motions. This transfer cannot be achieved by the low-frequency vibrational motions of alkyl groups. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Naphthalene SOA: redox activity and naphthoquinone gas-particle partitioning

    NASA Astrophysics Data System (ADS)

    McWhinney, R. D.; Zhou, S.; Abbatt, J. P. D.

    2013-10-01

    Chamber secondary organic aerosol (SOA) from low-NOx photooxidation of naphthalene by hydroxyl radical was examined with respect to its redox cycling behaviour using the dithiothreitol (DTT) assay. Naphthalene SOA was highly redox-active, consuming DTT at an average rate of 118 ± 14 pmol per minute per μg of SOA material. Measured particle-phase masses of the major previously identified redox active products, 1,2- and 1,4-naphthoquinone, accounted for only 21 ± 3% of the observed redox cycling activity. The redox-active 5-hydroxy-1,4-naphthoquinone was identified as a new minor product of naphthalene oxidation, and including this species in redox activity predictions increased the predicted DTT reactivity to 30 ± 5% of observations. These results suggest that there are substantial unidentified redox-active SOA constituents beyond the small quinones that may be important toxic components of these particles. A gas-to-SOA particle partitioning coefficient was calculated to be (7.0 ± 2.5) × 10-4 m3 μg-1 for 1,4-naphthoquinone at 25 °C. This value suggests that under typical warm conditions, 1,4-naphthoquinone is unlikely to contribute strongly to redox behaviour of ambient particles, although further work is needed to determine the potential impact under conditions such as low temperatures where partitioning to the particle is more favourable. Also, higher order oxidation products that likely account for a substantial fraction of the redox cycling capability of the naphthalene SOA are likely to partition much more strongly to the particle phase.

  18. Naphthalene, an insect repellent, is produced by Muscodor vitigenus, a novel endophytic fungus

    Treesearch

    Bryn H. Daisy; Gary A. Strobel; Uvidelio Castillo; David Ezra; Joe Sears; David K. Weaver; Justin B. Runyon

    2002-01-01

    Muscodor vitigenus is a recently described endophytic fungus of Paullinia paullinioides, a liana growing in the understorey of the rainforests of the Peruvian Amazon. This fungus produces naphthalene under certain cultural conditions. Naphthalene produced by M. vitigenus was identified by gas chromatography/mass...

  19. A Thermal Dehydrogenative Diels–Alder Reaction of Styrenes for the Concise Synthesis of Functionalized Naphthalenes

    PubMed Central

    Kocsis, Laura S.; Benedetti, Erica

    2012-01-01

    Functionalized naphthalenes are valuable building blocks in many important areas. A microwave-assisted, intramolecular dehydrogenative Diels-Alder reaction of styrenyl derivatives to provide cyclopenta[b]naphthalene substructures not previously accessible using existing synthetic methods is described. The synthetic utility of these uniquely functionalized naphthalenes was demonstrated by a single-step conversion of one of these cycloadducts to a fluorophore bearing a structural resemblance to Prodan. PMID:22913473

  20. A thermal dehydrogenative Diels-Alder reaction of styrenes for the concise synthesis of functionalized naphthalenes.

    PubMed

    Kocsis, Laura S; Benedetti, Erica; Brummond, Kay M

    2012-09-07

    Functionalized naphthalenes are valuable building blocks in many important areas. A microwave-assisted, intramolecular dehydrogenative Diels-Alder reaction of styrenyl derivatives to provide cyclopenta[b]naphthalene substructures not previously accessible using existing synthetic methods is described. The synthetic utility of these uniquely functionalized naphthalenes was demonstrated by a single-step conversion of one of these cycloadducts to a fluorophore bearing a structural resemblance to Prodan.

  1. Hydrogenation of liquid natural rubber via diimide reduction in hydrazine hydrate/hydrogen peroxide system

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

    Yusof, Muhammad Jefri Mohd; Jamaluddin, Naharullah; Abdullah, Ibrahim

    Liquid natural rubber (LNR) with molecular weight of lower than 10{sup 5} and shorter polymeric chain than natural rubber was prepared. LNR was then hydrogenated via diimide reduction by oxidation of hydrazine hydrate with hydrogen peroxide. The unsaturated units of the rubber were converted into saturated hydrocarbon to strengthen the backbone of the polymer so it was able to resist thermal degradation. The results indicated that hydrogenation degree of the product (HLNR) could be extended to 91.2% conversion under appropriate conditions. The hydrogenated LNR (HLNR) was characterized using Fourier-Transform Infrared (FTIR) and Nuclear Magnetic Resonance (NMR) spectroscopy. The physical characteristicsmore » of HLNR were analyzed with Termogravimetric Analysis (TGA)« less

  2. Benzene and naphthalene in air and breath as indicators of exposure to jet fuel

    PubMed Central

    Egeghy, P; Hauf-Cabalo, L; Gibson, R; Rappaport, S

    2003-01-01

    Aims: To estimate exposures to benzene and naphthalene among military personnel working with jet fuel (JP-8) and to determine whether naphthalene might serve as a surrogate for JP-8 in studies of health effects. Methods: Benzene and naphthalene were measured in air and breath of 326 personnel in the US Air Force, who had been assigned a priori into low, moderate, and high exposure categories for JP-8. Results: Median air concentrations for persons in the low, moderate, and high exposure categories were 3.1, 7.4, and 252 µg benzene/m3 air, 4.6, 9.0, and 11.4 µg benzene/m3 breath, 1.9, 10.3, and 485 µg naphthalene/m3 air, and 0.73, 0.93, and 1.83 µg naphthalene/m3 breath, respectively. In the moderate and high exposure categories, 5% and 15% of the benzene air concentrations, respectively, were above the 2002 threshold limit value (TLV) of 1.6 mg/m3. Multiple regression analyses of air and breath levels revealed prominent background sources of benzene exposure, including cigarette smoke. However, naphthalene exposure was not unduly influenced by sources other than JP-8. Among heavily exposed workers, dermal contact with JP-8 contributed to air and breath concentrations along with several physical and environmental factors. Conclusions: Personnel having regular contact with JP-8 are occasionally exposed to benzene at levels above the current TLV. Among heavily exposed workers, uptake of JP-8 components occurs via both inhalation and dermal contact. Naphthalene in air and breath can serve as useful measures of exposure to JP-8 and uptake of fuel components in the body. PMID:14634191

  3. Squamocin, an annonaceous acetogenin, enhances naphthalene degradation mediated by Bacillus atrophaeus CN4.

    PubMed

    Parellada, Eduardo A; Igarza, Mercedes; Isacc, Paula; Bardón, Alicia; Ferrero, Marcela; Ameta, Keshav Lalit; Neske, Adriana

    Squamocin belongs to a group of compounds called annonaceous acetogenins. They are secondary products of Annonaceae metabolism and can be isolated from Annona cherimolia seeds. This paper deals with the stimulation of biofilm formation of Bacillus atrophaeus CN4 by employing low squamocin concentrations to increase naphthalene degradation. Bacillus atrophaeus CN4, isolated from contaminated soil, has the ability to degrade naphthalene as the only source of carbon and energy. In the absence of additional carbon sources, the strain removed 69% of the initial concentration of naphthalene (approx. 0.2mmol/l) in the first 12h of incubation. The addition of squamocin in LB medium stimulated Bacillus atrophaeus CN4 biofilm formation and enhanced naphthalene removal. Squamocin (2.5μg/ml) does not affect planktonic growth and therefore, the observed increases are solely due to the stimulation of biofilm formation. Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

  4. Energy transfer of highly vibrationally excited naphthalene: collisions with CHF3, CF4, and Kr.

    PubMed

    Chen Hsu, Hsu; Tsai, Ming-Tsang; Dyakov, Yuri A; Ni, Chi-Kung

    2011-08-07

    Energy transfer of highly vibrationally excited naphthalene in the triplet state in collisions with CHF(3), CF(4), and Kr was studied using a crossed-beam apparatus along with time-sliced velocity map ion imaging techniques. Highly vibrationally excited naphthalene (2.0 eV vibrational energy) was formed via the rapid intersystem crossing of naphthalene initially excited to the S(2) state by 266 nm photons. The shapes of the collisional energy-transfer probability density functions were measured directly from the scattering results of highly vibrationally excited naphthalene. In comparison to Kr atoms, the energy transfer in collisions between CHF(3) and naphthalene shows more forward scatterings, larger cross section for vibrational to translational (V → T) energy transfer, smaller cross section for translational to vibrational and rotational (T → VR) energy transfer, and more energy transferred from vibration to translation, especially in the range -ΔE(d) = -100 to -800 cm(-1). On the other hand, the difference of energy transfer properties between collisional partners Kr and CF(4) is small. The enhancement of the V → T energy transfer in collisions with CHF(3) is attributed to the large attractive interaction between naphthalene and CHF(3) (1-3 kcal/mol).

  5. Development of Naphthalene PLIF for Making Quantitative Measurements of Ablation Products Transport in Supersonic Flows

    NASA Astrophysics Data System (ADS)

    Combs, Christopher; Clemens, Noel

    2014-11-01

    Ablation is a multi-physics process involving heat and mass transfer and codes aiming to predict ablation are in need of experimental data pertaining to the turbulent transport of ablation products for validation. Low-temperature sublimating ablators such as naphthalene can be used to create a limited physics problem and simulate ablation at relatively low temperature conditions. At The University of Texas at Austin, a technique is being developed that uses planar laser-induced fluorescence (PLIF) of naphthalene to visualize the transport of ablation products in a supersonic flow. In the current work, naphthalene PLIF will be used to make quantitative measurements of the concentration of ablation products in a Mach 5 turbulent boundary layer. For this technique to be used for quantitative research in supersonic wind tunnel facilities, the fluorescence properties of naphthalene must first be investigated over a wide range of state conditions and excitation wavelengths. The resulting calibration of naphthalene fluorescence will be applied to the PLIF images of ablation from a boundary layer plug, yielding 2-D fields of naphthalene mole fraction. These images may help provide data necessary to validate computational models of ablative thermal protection systems for reentry vehicles. Work supported by NASA Space Technology Research Fellowship Program under grant NNX11AN55H.

  6. Charge versus Energy Transfer Effects in High-Performance Perylene Diimide Photovoltaic Blend Films.

    PubMed

    Singh, Ranbir; Shivanna, Ravichandran; Iosifidis, Agathaggelos; Butt, Hans-Jürgen; Floudas, George; Narayan, K S; Keivanidis, Panagiotis E

    2015-11-11

    Perylene diimide (PDI)-based organic photovoltaic devices can potentially deliver high power conversion efficiency values provided the photon energy absorbed is utilized efficiently in charge transfer (CT) reactions instead of being consumed in nonradiative energy transfer (ET) steps. Hitherto, it remains unclear whether ET or CT primarily drives the photoluminescence (PL) quenching of the PDI excimer state in PDI-based blend films. Here, we affirm the key role of the thermally assisted PDI excimer diffusion and subsequent CT reaction in the process of PDI excimer PL deactivation. For our study we perform PL quenching experiments in the model PDI-based composite made of poly[4,8-bis(5-(2-ethylhexyl)thiophen-2-yl)benzo[1,2-b;4,5-b']dithiophene-2,6-diyl-alt-(4-(2-ethylhexanoyl)-thieno[3,4-b]thiophene)-2-6-diyl] (PBDTTT-CT) polymeric donor mixed with the N,N'-bis(1-ethylpropyl)-perylene-3,4,9,10-tetracarboxylic diimide (PDI) acceptor. Despite the strong spectral overlap between the PDI excimer PL emission and UV-vis absorption of PBDTTT-CT, two main observations indicate that no significant ET component operates in the overall PL quenching: the PL intensity of the PDI excimer (i) increases with decreasing temperature and (ii) remains unaffected even in the presence of 10 wt % content of the PBDTTT-CT quencher. Temperature-dependent wide-angle X-ray scattering experiments further indicate that nonradiative resonance ET is highly improbable due to the large size of PDI domains. The dominance of the CT over the ET process is verified by the high performance of devices with an optimum composition of 30:70 PBDTTT-CT:PDI. By adding 0.4 vol % of 1,8-diiodooctane we verify the plasticization of the polymer side chains that balances the charge transport properties of the PBDTTT-CT:PDI composite and results in additional improvement in the device efficiency. The temperature-dependent spectral width of the PDI excimer PL band suggests the presence of energetic disorder in the

  7. Perylene Diimide Based ``Nanofabric'' Thin Films for Organic Photovoltaic Cells

    NASA Astrophysics Data System (ADS)

    Carter, Austin; Park, June Hyoung; Min, Yong; Epstein, Arthur

    2011-03-01

    We report progress in using a perylene diimide (PDI) nanofabric as an effective electron accepting nanostructure for organic photovoltaics (OPV). A key challenge in OPV continues to be the recovery of electrons after charge separation due to the relatively poor mobility of C60 and related materials. A series of PDI compounds and complexes have been synthesized and used to fabricate nanofibers and thin films using solution and vacuum deposition techniques. Overlaping PDI-based nanofibers form a fast electron-transporting ``nanofabric'' that has been characterized (AFM, PL, UV-vis, etc.) and can be blended with electron donating materials. A solution-processible OPV configuration containing a nanofabric heterojunction (FHJ) of poly(3-hexylthiophene) and the PDI nanofabric was investigated. We observed a significant improvement in power-conversion efficiency due in part to expansion of the interfacial area and the presence of high mobility electron pathways to the LiF/Al electrode. This work is supported by the Wright Center for Photovoltaic Innovation and Commercialization, the Institute for Materials Research and the Center for Affordable Nanoengineering of Polymeric Biomedical Devices.

  8. Oxidation of Naphthenoaromatic and Methyl-Substituted Aromatic Compounds by Naphthalene 1,2-Dioxygenase

    PubMed Central

    Selifonov, S. A.; Grifoll, M.; Eaton, R. W.; Chapman, P. J.

    1996-01-01

    Oxidation of acenaphthene, acenaphthylene, and fluorene was examined with recombinant strain Pseudomonas aeruginosa PAO1(pRE695) expressing naphthalene dioxygenase genes cloned from plasmid NAH7. Acenaphthene underwent monooxygenation to 1-acenaphthenol with subsequent conversion to 1-acenaphthenone and cis- and trans-acenaphthene-1,2-diols, while acenaphthylene was dioxygenated to give cis-acenaphthene-1,2-diol. Nonspecific dehydrogenase activities present in the host strain led to the conversion of both of the acenaphthene-1,2-diols to 1,2-acenaphthoquinone. The latter was oxidized spontaneously to naphthalene-1,8-dicarboxylic acid. No aromatic ring dioxygenation products were detected from acenaphthene and acenaphthylene. Mixed monooxygenase and dioxygenase actions of naphthalene dioxygenase on fluorene yielded products of benzylic 9-monooxygenation, aromatic ring dioxygenation, or both. The action of naphthalene dioxygenase on a variety of methyl-substituted aromatic compounds, including 1,2,4-trimethylbenzene and isomers of dimethylnaphthalene, resulted in the formation of benzylic alcohols, i.e., methyl group monooxygenation products, which were subsequently converted to the corresponding carboxylic acids by dehydrogenase(s) in the host strain. Benzylic monooxygenation of methyl groups was strongly predominant over aromatic ring dioxygenation and essentially nonspecific with respect to the substitution pattern of the aromatic substrates. In addition to monooxygenating benzylic methyl and methylene groups, naphthalene dioxygenase behaved as a sulfoxygenase, catalyzing monooxygenation of the sulfur heteroatom of 3-methylbenzothiophene. PMID:16535238

  9. Naphthalene and benzene degradation under Fe(III)-reducing conditions in petroleum-contaminated aquifers

    USGS Publications Warehouse

    Anderson, Robert T.; Lovely, Derek R.

    1999-01-01

    Naphthalene was oxidized anaerobically to CO2 in sediments collected from a petroleum-contaminated aquifer in Bemidji, Minnesota in which Fe(III) reduction was the terminal electron-accepting process. Naphthalene was not oxidized in sediments from the methanogenic zone at Bemidji or in sediments from the Fe(III)-reducing zone of other petroleum-contaminated aquifers studied. In a profile across the Fe(III)-reducing zone of the Bemidji aquifer, rates of naphthalene oxidation were fastest in sediments with the highest proportion of Fe(III), which was also the zone of the most rapid degradation of benzene, toluene, and acetate. The comparative studies attempted to elucidate factors that might account for the fact that unsubstituted aromatic hydrocarbons such as benzene and naphthalene were degraded under Fe(III)-reducing conditions at Bemidji, but not at the other aquifers examined. These studies indicated that the ability of Fe(III)-reducing microorganisms to degrade benzene and naphthalene at the Bemidji site cannot be attributed to groundwater components that make Fe(III) more available for reduction or other potential factors that were evaluated. However, unlike the other aquifers evaluated, uncontaminated sediments at the Bemidji site could be adapted for anaerobic benzene degradation merely with the addition of benzene. These findings indicate that Bemidji sediments naturally contain Fe(III) reducers capable of degradation of unsubstituted aromatic hydrocarbons.

  10. 40 CFR 721.10045 - Diazotized substituted heteromonocycle coupled with naphthalene sulfonic acid derivative, nickel...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... coupled with naphthalene sulfonic acid derivative, nickel complex, alkaline salt (generic). 721.10045... derivative, nickel complex, alkaline salt (generic). (a) Chemical substance and significant new uses subject... heteromonocycle coupled with naphthalene sulfonic acid derivative, nickel complex, alkaline salt (PMN P-02-737) is...

  11. 40 CFR 721.10045 - Diazotized substituted heteromonocycle coupled with naphthalene sulfonic acid derivative, nickel...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... coupled with naphthalene sulfonic acid derivative, nickel complex, alkaline salt (generic). 721.10045... derivative, nickel complex, alkaline salt (generic). (a) Chemical substance and significant new uses subject... heteromonocycle coupled with naphthalene sulfonic acid derivative, nickel complex, alkaline salt (PMN P-02-737) is...

  12. 40 CFR 721.10045 - Diazotized substituted heteromonocycle coupled with naphthalene sulfonic acid derivative, nickel...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... coupled with naphthalene sulfonic acid derivative, nickel complex, alkaline salt (generic). 721.10045... derivative, nickel complex, alkaline salt (generic). (a) Chemical substance and significant new uses subject... heteromonocycle coupled with naphthalene sulfonic acid derivative, nickel complex, alkaline salt (PMN P-02-737) is...

  13. 40 CFR 721.10045 - Diazotized substituted heteromonocycle coupled with naphthalene sulfonic acid derivative, nickel...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... coupled with naphthalene sulfonic acid derivative, nickel complex, alkaline salt (generic). 721.10045... derivative, nickel complex, alkaline salt (generic). (a) Chemical substance and significant new uses subject... heteromonocycle coupled with naphthalene sulfonic acid derivative, nickel complex, alkaline salt (PMN P-02-737) is...

  14. 40 CFR 721.10045 - Diazotized substituted heteromonocycle coupled with naphthalene sulfonic acid derivative, nickel...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... coupled with naphthalene sulfonic acid derivative, nickel complex, alkaline salt (generic). 721.10045... derivative, nickel complex, alkaline salt (generic). (a) Chemical substance and significant new uses subject... heteromonocycle coupled with naphthalene sulfonic acid derivative, nickel complex, alkaline salt (PMN P-02-737) is...

  15. Native Fluorescence Detection Methods and Detectors for Naphthalene and/or Other Volatile Organic Compound Vapors

    NASA Technical Reports Server (NTRS)

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

    2014-01-01

    Naphthalene, benzene, toluene, xylene, and other volatile organic compounds have been identified as serious health hazards. This is especially true for personnel working with JP8 jet fuel and other fuels containing naphthalene as well as other hazardous volatile organic compounds (VOCs). Embodiments of the invention are directed to methods and apparatus for near-real-time in-situ detection and accumulated dose measurement of exposure to naphthalene vapor and other hazardous gaseous VOCs. The methods and apparatus employ excitation of fluorophors native or endogenous to compounds of interest using light sources emitting in the ultraviolet below 300 nm and measurement of native fluorescence emissions in distinct wavebands above the excitation wavelength. The apparatus of some embodiments are cell-phone-sized sensor/dosimeter "badges" to be worn by personnel potentially exposed to naphthalene or other hazardous VOCs. The badge sensor of some embodiments provides both real time detection and data logging of exposure to naphthalene or other VOCs of interest from which both instantaneous and accumulated dose can be determined. The badges employ a new native fluorescence based detection method to identify and differentiate VOCs. The particular focus of some embodiments are the detection and identification of naphthalene while other embodiments are directed to detection and identification of other VOCs like aromatic hydrocarbons such as benzene, toluene, and xylene.

  16. Green and Red Fluorescent Dyes for Translational Applications in Imaging and Sensing Analytes: A Dual‐Color Flag

    PubMed Central

    Oliveira, Elisabete; Bértolo, Emilia; Núñez, Cristina; Pilla, Viviane; Santos, Hugo M.; Fernández‐Lodeiro, Javier; Fernández‐Lodeiro, Adrian; Djafari, Jamila; Capelo, José Luis

    2017-01-01

    Abstract Red and green are two of the most‐preferred colors from the entire chromatic spectrum, and red and green dyes are widely used in biochemistry, immunohistochemistry, immune‐staining, and nanochemistry applications. Selective dyes with green and red excitable chromophores can be used in biological environments, such as tissues and cells, and can be irradiated with visible light without cell damage. This critical review, covering a period of five years, provides an overview of the most‐relevant results on the use of red and green fluorescent dyes in the fields of bio‐, chemo‐ and nanoscience. The review focuses on fluorescent dyes containing chromophores such as fluorescein, rhodamine, cyanine, boron–dipyrromethene (BODIPY), 7‐nitobenz‐2‐oxa‐1,3‐diazole‐4‐yl, naphthalimide, acridine orange, perylene diimides, coumarins, rosamine, Nile red, naphthalene diimide, distyrylpyridinium, benzophosphole P‐oxide, benzoresorufins, and tetrapyrrolic macrocycles. Metal complexes and nanomaterials with these dyes are also discussed. PMID:29318095

  17. Toxicity and metabolism of methylnaphthalenes: Comparison with naphthalene and 1-nitronaphthalene

    PubMed Central

    Lin, Ching Yu; Wheelock, Åsa M.; Morin, Dexter; Baldwin, R. Michael; Lee, Myong Gong; Taff, Aysha; Plopper, Charles; Buckpitt, Alan; Rohde, Arlean

    2009-01-01

    Naphthalene and close structural analogues have been shown to cause necrosis of bronchiolar epithelial cells in mice by both inhalation exposure and by systemic administration. Cancer bioassays of naphthalene in mice have demonstrated a slight increase in bronchiolar/alveolar adenomas in female mice, and in inflammation and metaplasia of the olfactory epithelium in the nasal cavity. Similar work in rats demonstrated a significant, and concentration-dependent increase in the incidence of respiratory epithelial adenomas and neuroblastomas in the nasal epithelium of both male and female rats. Although the studies on the acute toxicity of the methylnaphthalene derivatives are more limited, it appears that the species selective toxicity associated with naphthalene administration also is observed with methylnaphthalenes. Chronic administration of the methylnaphthalenes, however, failed to demonstrate the same oncogenic potential as that observed with naphthalene. The information available on the isopropylnaphthalene derivatives suggests that they are not cytotoxic. Like the methylnaphthalenes, 1-nitronaphthalene causes lesions in both Clara and ciliated cells. However, the species selective lung toxicity observed in the mouse with both naphthalene and the methylnaphthalenes is not seen with 1-nitronaphthalene. With 1-nitronaphthalene, the rat is far more susceptible to parenteral administration of the compound than mice. The wide-spread distribution of these compounds in the environment and the high potential for low level exposure to humans supports a need for further work on the mechanisms of toxicity in animal models with attention to whether these processes are applicable to humans. Although it is tempting to suppose that the toxicity and mechanisms of toxicity of the alkylnaphthalenes and nitronaphthalenes are similar to naphthalene, there is sufficient published literature to suggest that this may not be the case. Certainly the enzymes involved in the metabolic

  18. Development of Naphthalene PLIF for Visualizing Ablation Products From a Space Capsule Heat Shield

    NASA Technical Reports Server (NTRS)

    Combs, C. S.; Clemens, N. T.; Danehy, P. M.

    2014-01-01

    The Orion Multi-Purpose Crew Vehicle (MPCV) will use an ablative heat shield. To better design this heat shield and others that will undergo planetary entry, an improved understanding of the ablation process would be beneficial. Here, a technique developed at The University of Texas at Austin that uses planar laser-induced fluorescence (PLIF) of a low-temperature sublimating ablator (naphthalene) to enable visualization of the ablation products in a hypersonic flow is applied. Although high-temperature ablation is difficult and expensive to recreate in a laboratory environment, low-temperature sublimation creates a limited physics problem that can be used to explore ablation-product transport in a hypersonic flow-field. In the current work, a subscale capsule reentry vehicle model with a solid naphthalene heat shield has been tested in a Mach 5 wind tunnel. The PLIF technique provides images of the spatial distribution of sublimated naphthalene in the heat-shield boundary layer, separated shear layer, and backshell recirculation region. Visualizations of the capsule shear layer using both naphthalene PLIF and Schlieren imaging compared favorably. PLIF images have shown high concentrations of naphthalene in the capsule separated flow region, intermittent turbulent structures on the heat shield surface, and interesting details of the capsule shear layer structure. It was shown that, in general, the capsule shear layer appears to be more unsteady at lower angels of attack. The PLIF images demonstrated that during a wind tunnel run, as the model heated up, the rate of naphthalene ablation increased, since the PLIF signal increased steadily over the course of a run. Additionally, the shear layer became increasingly unsteady over the course of a wind tunnel run, likely because of increased surface roughness but also possibly because of the increased blowing. Regions with a relatively low concentration of naphthalene were also identified in the capsule backshell

  19. Benzene and Naphthalene Degrading Bacterial Communities in an Oil Sands Tailings Pond

    PubMed Central

    Rochman, Fauziah F.; Sheremet, Andriy; Tamas, Ivica; Saidi-Mehrabad, Alireza; Kim, Joong-Jae; Dong, Xiaoli; Sensen, Christoph W.; Gieg, Lisa M.; Dunfield, Peter F.

    2017-01-01

    Oil sands process-affected water (OSPW), produced by surface-mining of oil sands in Canada, is alkaline and contains high concentrations of salts, metals, naphthenic acids, and polycyclic aromatic compounds (PAHs). Residual hydrocarbon biodegradation occurs naturally, but little is known about the hydrocarbon-degrading microbial communities present in OSPW. In this study, aerobic oxidation of benzene and naphthalene in the surface layer of an oil sands tailings pond were measured. The potential oxidation rates were 4.3 μmol L−1 OSPW d−1 for benzene and 21.4 μmol L−1 OSPW d−1 for naphthalene. To identify benzene and naphthalene-degrading microbial communities, metagenomics was combined with stable isotope probing (SIP), high-throughput sequencing of 16S rRNA gene amplicons, and isolation of microbial strains. SIP using 13C-benzene and 13C-naphthalene detected strains of the genera Methyloversatilis and Zavarzinia as the main benzene degraders, while strains belonging to the family Chromatiaceae and the genus Thauera were the main naphthalene degraders. Metagenomic analysis revealed a diversity of genes encoding oxygenases active against aromatic compounds. Although these genes apparently belonged to many phylogenetically diverse taxa, only a few of these taxa were predominant in the SIP experiments. This suggested that many members of the community are adapted to consuming other aromatic compounds, or are active only under specific conditions. 16S rRNA gene sequence datasets have been submitted to the Sequence Read Archive (SRA) under accession number SRP109130. The Gold Study and Project submission ID number in Joint Genome Institute IMG/M for the metagenome is Gs0047444 and Gp0055765. PMID:29033909

  20. Theoretical Study of the Electronic Spectra of a Polycyclic Aromatic Hydrocarbon, Naphthalene, and its Derivatives

    NASA Technical Reports Server (NTRS)

    Du, Ping; Salama, Farid; Loew, Gilda H.

    1993-01-01

    In order to preselect possible candidates for the origin of diffuse interstellar bands observed, semiempirical quantum mechanical method INDO/S was applied to the optical spectra of neutral, cationic, and anionic states of naphthalene and its hydrogen abstraction and addition derivatives. Comparison with experiment shows that the spectra of naphthalene and its ions were reliably predicted. The configuration interaction calculations with single-electron excitations provided reasonable excited state wavefunctions compared to ab initio calculations that included higher excitations. The degree of similarity of the predicted spectra of the hydrogen abstraction and derivatives to those of naphthalene and ions depends largely on the similarity of the it electron configurations. For the hydrogen addition derivatives, very little resemblance of the predicted spectra to naphthalene was found because of the disruption of the aromatic conjugation system. The relevance of these calculations to astrophysical issues is discussed within the context of these polycyclic aromatic hydrocarbon models. Comparing the calculated electronic energies to the Diffuse Interstellar Bands (DIBs), a list of possible candidates of naphthalene derivatives is established which provides selected candidates for a definitive test through laboratory studies.

  1. Naphthalene emissions from moth repellents or toilet deodorant blocks determined using head-space and small-chamber tests.

    PubMed

    Jo, Wan-Kuen; Lee, Jong-Hyo; Lim, Ho-Jin; Jeong, Woo-Sik

    2008-01-01

    The present study investigated the emissions of naphthalene and other compounds from several different moth repellents (MRs) and one toilet deodorant block (TDB) currently sold in Korea, using a headspace analysis. The emission factors and emission rates of naphthalene were studied using a small-scale environmental chamber. Paper-type products emitted a higher concentration of the total volatile organic compounds (VOCs) (normalized to the weight of test piece) than ball-type products, which in turn emitted higher concentration than a gel-type product. In contrast, naphthalene was either the most or the second highest abundant compound for the four ball products, whereas for paper and gel products it was not detected or was detected at much lower levels. The abundance of naphthalene ranged between 18.4% and 37.3% for ball products. The results showed that the lower the air changes per hour (ACH) level was, the higher the naphthalene concentrations became. In general, a low ACH level suggests a low ventilation rate. The emission factor for naphthalene was nearly 100 times higher for a ball MR than for a gel or a paper MR. For the ball MR, the lower ACH level resulted in higher emission rate.

  2. Changes in oxygen consumption and respiratory enzymes as stress indicators in an estuarine edible crab Scylla serrata exposed to naphthalene.

    PubMed

    Vijayavel, K; Balasubramanian, M P

    2006-06-01

    The sublethal effect of naphthalene was studied on the physiology of a mud crab Scylla serrata. The 96 h acute toxicity of naphthalene was determined and found to be 28 mg 1(-1) (LC100), 18 mg 1(-1) (LC50), 10 mg 1(-1) (LC0) respectively. The 30 days sublethal effect (LC0) 9 mg 1(-1), 8 mg 1(-1), 10 mg 1(-1), of naphthalene was investigated in the crab S. serrata with reference to oxygen consumption and changes in the activity of respiratory enzymes. The results indicated that naphthalene caused disturbance in the normal physiology of the crab. The bioaccumulation of naphthalene was also investigated in gills, hepatopancreas, haemolymph and ovary. The consumption of oxygen increased in the naphthalene medium when compared with that of the crabs exposed to naphthalene free medium. A decreased trend in the activity of respiratory enzymes such as lactate dehydrogenase (LDH), isocitrate dehydrogenase (ICDH), succinate dehydrogenase (SDH), malate dehydrogenase (MDH), alpha-ketoglutarate dehydrogenase (alpha-KDH) and glutathione (GSH) were recorded in the hepatopancreas, ovary and gills of S. serrata for all the tested concentrations of naphthalene and the results were analyzed for their significance.

  3. Measurement of Biologically Available Naphthalene in Gas and Aqueous Phases by Use of a Pseudomonas putida Biosensor

    PubMed Central

    Werlen, Christoph; Jaspers, Marco C. M.; van der Meer, Jan Roelof

    2004-01-01

    Genetically constructed microbial biosensors for measuring organic pollutants are mostly applied in aqueous samples. Unfortunately, the detection limit of most biosensors is insufficient to detect pollutants at low but environmentally relevant concentrations. However, organic pollutants with low levels of water solubility often have significant gas-water partitioning coefficients, which in principle makes it possible to measure such compounds in the gas rather than the aqueous phase. Here we describe the first use of a microbial biosensor for measuring organic pollutants directly in the gas phase. For this purpose, we reconstructed a bioluminescent Pseudomonas putida naphthalene biosensor strain to carry the NAH7 plasmid and a chromosomally inserted gene fusion between the sal promoter and the luxAB genes. Specific calibration studies were performed with suspended and filter-immobilized biosensor cells, in aqueous solution and in the gas phase. Gas phase measurements with filter-immobilized biosensor cells in closed flasks, with a naphthalene-contaminated aqueous phase, showed that the biosensor cells can measure naphthalene effectively. The biosensor cells on the filter responded with increasing light output proportional to the naphthalene concentration added to the water phase, even though only a small proportion of the naphthalene was present in the gas phase. In fact, the biosensor cells could concentrate a larger proportion of naphthalene through the gas phase than in the aqueous suspension, probably due to faster transport of naphthalene to the cells in the gas phase. This led to a 10-fold lower detectable aqueous naphthalene concentration (50 nM instead of 0.5 μM). Thus, the use of bacterial biosensors for measuring organic pollutants in the gas phase is a valid method for increasing the sensitivity of these valuable biological devices. PMID:14711624

  4. Adsorption of naphthalene and ozone on atmospheric air/ice interfaces coated with surfactants: a molecular simulation study.

    PubMed

    Liyana-Arachchi, Thilanga P; Valsaraj, Kalliat T; Hung, Francisco R

    2012-03-15

    The adsorption of gas-phase naphthalene and ozone molecules onto air/ice interfaces coated with different surfactant species (1-octanol, 1-hexadecanol, or 1-octanal) was investigated using classical molecular dynamics (MD) simulations. Naphthalene and ozone exhibit a strong preference to be adsorbed at the surfactant-coated air/ice interfaces, as opposed to either being dissolved into the bulk of the quasi-liquid layer (QLL) or being incorporated into the ice crystals. The QLL becomes thinner when the air/ice interface is coated with surfactant molecules. The adsorption of both naphthalene and ozone onto surfactant-coated air/ice interfaces is enhanced when compared to bare air/ice interface. Both naphthalene and ozone tend to stay dissolved in the surfactant layer and close to the QLL, rather than adsorbing on top of the surfactant molecules and close to the air region of our systems. Surfactants prefer to orient at a tilted angle with respect to the air/ice interface; the angular distribution and the most preferred angle vary depending on the hydrophilic end group, the length of the hydrophobic tail, and the surfactant concentration at the air/ice interface. Naphthalene prefers to have a flat orientation on the surfactant coated air/ice interface, except at high concentrations of 1-hexadecanol at the air/ice interface; the angular distribution of naphthalene depends on the specific surfactant and its concentration at the air/ice interface. The dynamics of naphthalene molecules at the surfactant-coated air/ice interface slow down as compared to those observed at bare air/ice interfaces. The presence of surfactants does not seem to affect the self-association of naphthalene molecules at the air/ice interface, at least for the specific surfactants and the range of concentrations considered in this study.

  5. [Characteristics of natural strains of naphthalene-utilizing bacteria of the genus Pseudomonas].

    PubMed

    Levchuk, A A; Vasilenko, S L; Bulyga, I M; Titok, M A; Thomas, K M

    2005-01-01

    Sixty-three strains of bacteria capable of utilizing naphthalene as the sole source of carbon and energy were isolated from 137 samples of soil taken in different sites in Belarus. All isolated bacteria contained extrachromosomal genetic elements of 45 to 150 kb in length. It was found that bacteria of 31 strains contained the IncP-9 incompatibility group plasmids, bacteria of one strain carried a plasmid containing replicons IncP-9 and IncP-7, and bacteria of 31 strains contained unidentified plasmids. Primary identification showed that the hosts of plasmids of naphthalene biodegradation are fluorescent bacteria of the genus Pseudomonas (P. putida and P. aeruginosa; a total of 47 strains) and unidentified nonfluorescent microorganisms (a total of 16 strains). In addition to the ability to utilize naphthalene, some strains exhibited the ability to stimulate the growth and development of the root system of Secale cereale.

  6. Desaturation, dioxygenation, and monooxygenation reactions catalyzed by naphthalene dioxygenase from Pseudomonas sp. strain 9816-4.

    PubMed

    Gibson, D T; Resnick, S M; Lee, K; Brand, J M; Torok, D S; Wackett, L P; Schocken, M J; Haigler, B E

    1995-05-01

    The stereospecific oxidation of indan and indene was examined with mutant and recombinant strains expressing naphthalene dioxygenase of Pseudomonas sp. strain 9816-4. Pseudomonas sp. strain 9816/11 and Escherichia coli JM109(DE3)[pDTG141] oxidized indan to (+)-(1S)-indanol, (+)-cis-(1R,2S)-indandiol, (+)-(1S)-indenol, and 1-indanone. The same strains oxidized indene to (+)-cis-(1R,2S)-indandiol and (+)-(1S)-indenol. Purified naphthalene dioxygenase oxidized indan to the same four products formed by strains 9816/11 and JM109(DE3)[pDTG141]. In addition, indene was identified as an intermediate in indan oxidation. The major products formed from indene by purified naphthalene dioxygenase were (+)-(1S)-indenol and (+)-(1R,2S)-indandiol. The results show that naphthalene dioxygenase catalyzes the enantiospecific monooxygenation of indan to (+)-(1S)-indanol and the desaturation of indan to indene, which then serves as a substrate for the formation of (+)-(1R,2S)-indandiol and (+)-(1S)-indenol. The relationship of the desaturase, monooxygenase, and dioxygenase activities of naphthalene dioxygenase is discussed with reference to reactions catalyzed by toluene dioxygenase, plant desaturases, cytochrome P-450, methane monooxygenase, and other bacterial monooxygenases.

  7. Desaturation, dioxygenation, and monooxygenation reactions catalyzed by naphthalene dioxygenase from Pseudomonas sp. strain 9816-4.

    PubMed Central

    Gibson, D T; Resnick, S M; Lee, K; Brand, J M; Torok, D S; Wackett, L P; Schocken, M J; Haigler, B E

    1995-01-01

    The stereospecific oxidation of indan and indene was examined with mutant and recombinant strains expressing naphthalene dioxygenase of Pseudomonas sp. strain 9816-4. Pseudomonas sp. strain 9816/11 and Escherichia coli JM109(DE3)[pDTG141] oxidized indan to (+)-(1S)-indanol, (+)-cis-(1R,2S)-indandiol, (+)-(1S)-indenol, and 1-indanone. The same strains oxidized indene to (+)-cis-(1R,2S)-indandiol and (+)-(1S)-indenol. Purified naphthalene dioxygenase oxidized indan to the same four products formed by strains 9816/11 and JM109(DE3)[pDTG141]. In addition, indene was identified as an intermediate in indan oxidation. The major products formed from indene by purified naphthalene dioxygenase were (+)-(1S)-indenol and (+)-(1R,2S)-indandiol. The results show that naphthalene dioxygenase catalyzes the enantiospecific monooxygenation of indan to (+)-(1S)-indanol and the desaturation of indan to indene, which then serves as a substrate for the formation of (+)-(1R,2S)-indandiol and (+)-(1S)-indenol. The relationship of the desaturase, monooxygenase, and dioxygenase activities of naphthalene dioxygenase is discussed with reference to reactions catalyzed by toluene dioxygenase, plant desaturases, cytochrome P-450, methane monooxygenase, and other bacterial monooxygenases. PMID:7751268

  8. Comparative Metabolism of Hydrazine and Naphthalene.

    DTIC Science & Technology

    1980-09-01

    compounds and chemicals like those in cigarette smoke. Another question of considerable importance to the Air Force is whether animal species currently...the pulmonary cytochrome P-450 monooxygenases differ between species or that enzymes responsible for the detoxification of the "toxic" metabolite(s...metabolic steps in the activation and detoxification of a compound like naphthalene are undertaken in animal lung tissue so that such processes can be

  9. The disposition and metabolism of naphthalene in rats.

    PubMed

    Kilanowicz, A; Czerski, B; Sapota, A

    1999-01-01

    The aim of this study was to investigate the distribution, excretion and metabolism of naphthalene-[ring-U-3H] in rats. The experiments were performed on 54 male outbred IMP: Wist rats with body weight of 200-220 g. The compound was administered intraperitoneally in olive oil in a single dose of 20 mg/kg (about 540 kBq per animal). 3H radioactivity was traced in selected organs and tissues, blood, urine and faeces, 1-72 h following the administration. The main metabolites were isolated from urine and identified by the GC-MS method. Urine and faeces proved to be the main route of tritium elimination. Over 88% of the compound was excreted during the first 72 hours. Maximum level of tritium in plasma was observed at the 2nd h after administration following a biphasic decline. Half-lifes for phases I and II were 0.8 and 99 h, respectively. In erythrocytes 3H-decline was monophasic with the half-life of about 9 h. In organs and tissues, the highest concentrations during the first hours after administration were detected in the fat, liver and kidneys. Then, gradual decline of tritium was noticed in all examined tissues. In urine of rats the following substances were identified: (1) naphthalene, (2) 1-naphthol, (3) 2-naphthol, (4) 1,2-naphthalenediol-1,2-dihydro, (5) methylthionaphthalenes (two isomers). In conclusion, naphthalene has a relatively rapid turnover rate in the rat organism and does not form considerable deposits in the tissue. The metabolism encompasses ring hydroxylation, hydration and glutathione conjugation.

  10. Naphthalene degradation by bacterial consortium (DV-AL) developed from Alang-Sosiya ship breaking yard, Gujarat, India.

    PubMed

    Patel, Vilas; Jain, Siddharth; Madamwar, Datta

    2012-03-01

    Naphthalene degrading bacterial consortium (DV-AL) was developed by enrichment culture technique from sediment collected from the Alang-Sosiya ship breaking yard, Gujarat, India. The 16S rRNA gene based molecular analyzes revealed that the bacterial consortium (DV-AL) consisted of four strains namely, Achromobacter sp. BAB239, Pseudomonas sp. DV-AL2, Enterobacter sp. BAB240 and Pseudomonas sp. BAB241. Consortium DV-AL was able to degrade 1000 ppm of naphthalene in Bushnell Haas medium (BHM) containing peptone (0.1%) as co-substrate with an initial pH of 8.0 at 37°C under shaking conditions (150 rpm) within 24h. Maximum growth rate and naphthalene degradation rate were found to be 0.0389 h(-1) and 80 mg h(-1), respectively. Consortium DV-AL was able to utilize other aromatic and aliphatic hydrocarbons such as benzene, phenol, carbazole, petroleum oil, diesel fuel, and phenanthrene and 2-methyl naphthalene as sole carbon source. Consortium DV-AL was also efficient to degrade naphthalene in the presence of other pollutants such as petroleum hydrocarbons and heavy metals. Copyright © 2011 Elsevier Ltd. All rights reserved.

  11. Isolation of a naphthalene-degrading strain from activated sludge and bioaugmentation with it in a MBR treating coal gasification wastewater.

    PubMed

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

    2015-03-01

    A highly effective naphthalene-degrading bacterial strain was isolated from acclimated activated sludge from a coal gasification wastewater plant, and identified as a Streptomyces sp., designated as strain QWE-35. The optimal pH and temperature for naphthalene degradation were 7.0 and 35°C. The presence of additional glucose and methanol significantly increased the degradation efficiency of naphthalene. The strain showed tolerance to the toxicity of naphthalene at a concentration as great as 200 mg/L. The Andrews mode could be fitted to the degradation kinetics data well over a wide range of initial naphthalene concentrations (10-200 mg/L), with kinetic values q max = 0.84 h(-1), K s = 40.39 mg/L, and K i = 193.76 mg/L. Metabolic intermediates were identified by gas chromatography and mass spectrometry, allowing a new degradation pathway for naphthalene to be proposed for the first time. Strain QWE-35 was added into a membrane bioreactor (MBR) to enhance the treatment of real coal gasification wastewater. The results showed that the removal of chemical oxygen demand and total nitrogen were similar between bioaugmented and non-bioaugmented MBRs, however, significant removal of naphthalene was obtained in the bioaugmented reactor. The findings suggest a potential bioremediation role of Streptomyces sp. QWE-35 in the removal of naphthalene from wastewaters.

  12. Research Needs Related to Naphthalene Assessment (2005, Workshop)

    EPA Science Inventory

    EPA has announced the release of the final report from the 2005 peer consultation workshop which sought expert opinion on research needs related to the mode of action of the inhalation carcinogenicity of naphthalene. This report is a summary of the main points of presentations an...

  13. Near-IR MCD of the nonheme ferrous active site in naphthalene 1,2-dioxygenase: correlation to crystallography and structural insight into the mechanism of Rieske dioxygenases.

    PubMed

    Ohta, Takehiro; Chakrabarty, Sarmistha; Lipscomb, John D; Solomon, Edward I

    2008-02-06

    Near-IR MCD and variable temperature, variable field (VTVH) MCD have been applied to naphthalene 1,2-dioxygenase (NDO) to describe the coordination geometry and electronic structure of the mononuclear nonheme ferrous catalytic site in the resting and substrate-bound forms with the Rieske 2Fe2S cluster oxidized and reduced. The structural results are correlated with the crystallographic studies of NDO and other related Rieske nonheme iron oxygenases to develop molecular level insights into the structure/function correlation for this class of enzymes. The MCD data for resting NDO with the Rieske center oxidized indicate the presence of a six-coordinate high-spin ferrous site with a weak axial ligand which becomes more tightly coordinated when the Rieske center is reduced. Binding of naphthalene to resting NDO (Rieske oxidized and reduced) converts the six-coordinate sites into five-coordinate (5c) sites with elimination of a water ligand. In the Rieske oxidized form the 5c sites are square pyramidal but transform to a 1:2 mixture of trigonal bipyramial/square pyramidal sites when the Rieske center is reduced. Thus the geometric and electronic structure of the catalytic site in the presence of substrate can be significantly affected by the redox state of the Rieske center. The catalytic ferrous site is primed for the O2 reaction when substrate is bound in the active site in the presence of the reduced Rieske site. These structural changes ensure that two electrons and the substrate are present before the binding and activation of O2, which avoids the uncontrolled formation and release of reactive oxygen species.

  14. Infrared spectroscopy of polycyclic aromatic hydrocarbon cations. 1: Matrix-isolated naphthalene and perdeuterated naphthalene

    NASA Technical Reports Server (NTRS)

    Hudgins, D. M.; Sandford, S. A.; Allamandola, Louis J.

    1994-01-01

    Ionized polycyclic aromatic hydrocarbons (PAHs) are thought to constitute an important component of the interstellar medium. Despite this fact, the infrared spectroscopic properties of ionized PAHs are almost unknown. The results we present here derive from our ongoing spectroscopic study of matrix isolated PAH ions and include the spectra of the naphthalene cation, C10H8(+), and its fully deuterated analog, C10D8(+), between 4000 and 200/cm. Ions are generated by in situ Lyman-alpha photoionization of the neutral precursor. Bands of the C10H8(+) ion are observed at 1525.7, 1518.8, 1400.9, 1218.0, 1216.9, 1214.9, 1023.2, and 758.7/cm. Positions and relative intensities of these bands agree well with those in the available literature. The 758.7/cm band has not previously been reported. C10D8(+) ion bands appear at 1466.2, 1463.8, 1379.4, 1373.8, 1077.3, 1075.4, and 1063.1/cm. Compared to the analogous modes in the neutral molecule, the intensities of the cation's CC modes are enhanced by an order of magnitude, while CH modes are depressed by this same factor. Integrated absorption intensities are calculated for the strongest bands of C10H8 and for the observed bands of C10H8(+). Absolute intensities derived for the naphthalene cation differ from earlier experimental results by a factor of approximately 50, and from theoretical predictions by a factor of approximately 300. Reasons for these discrepancies and from the astronomical implications of PAH cation spectra are discussed.

  15. Rotation and diffusion of naphthalene on Pt(111)

    NASA Astrophysics Data System (ADS)

    Kolsbjerg, E. L.; Goubert, G.; McBreen, P. H.; Hammer, B.

    2018-03-01

    The behavior of naphthalene on Pt(111) surfaces is studied by combining insight from scanning tunneling microscopy (STM) and van der Waals enabled density functional theory. Adsorption, diffusion, and rotation are investigated by a series of variable temperature STM experiments revealing naphthalene ability to rotate on-site with ease with a rotational barrier of 0.69 eV. Diffusion to neighbouring sites is found to be more difficult. The experimental results are in good agreement with the theoretical investigations which confirm that the barrier for diffusion is slightly higher than the one for rotation. The theoretical barriers for rotation and translation are found to be 0.75 and 0.78 eV, respectively. An automatic mapping of the possible diffusion pathways reveals very detailed diffusion paths with many small local minima that would have been practically impossible to find manually. This automated procedure provides detailed insight into the preferred diffusion pathways that are important for our understanding of molecule-substrate interactions.

  16. Decomposition of naphthalene by dc gliding arc gas discharge.

    PubMed

    Yu, Liang; Li, Xiaodong; Tu, Xin; Wang, Yu; Lu, Shengyong; Yan, Jianhua

    2010-01-14

    Gliding arc discharge has been proved to be effective in treatment of gas and liquid contaminants. In this study, physical characteristics of dc gliding arc discharge and its application to naphthalene destruction are investigated with different external resistances and carrier gases. The decomposition rate increases with increasing of oxygen concentration and decreases with external resistance. This value can be achieved up to 92.3% at the external resistance of 50 kOmega in the oxygen discharge, while the highest destruction energy efficiency reaches 3.6 g (kW h)(-1) with the external resistance of 93 kOmega. Possible reaction pathways and degradation mechanisms in the plasma with different gases are proposed by qualitative analysis of postdestructed products. In the air and oxygen gliding arc discharges, the naphthalene degradation is mainly governed by reactions with oxygen-derived radicals.

  17. Near-saturated red emitters: four-coordinate copper(i) halide complexes containing 8-(diphenylphosphino)quinoline and 1-(diphenylphosphino)naphthalene ligands.

    PubMed

    Liu, Li-Ping; Li, Qian; Xiang, Song-Po; Liu, Li; Zhong, Xin-Xin; Liang, Chen; Li, Guang Hua; Hayat, Tasawar; Alharbi, Njud S; Li, Fa-Bao; Zhu, Nian-Yong; Wong, Wai-Yeung; Qin, Hai-Mei; Wang, Lei

    2018-06-07

    Recently, highly emissive neutral copper halide complexes have received much attention. Here, a series of four-coordinate mononuclear Cu(i) halide complexes, [CuX(dpqu)(dpna)] (dpqu = 8-(diphenylphosphino)quinoline, dpna = 1-(diphenylphosphino)naphthalene, X = I (1), Br (2) and Cl (3)), were synthesized, and their molecular structures and photophysical properties were investigated. These complexes exhibit near-saturated red emission in the solid state at room temperature and have peak emission wavelengths at 669-691 nm with microsecond lifetimes (τ = 0.46-1.80 μs). Small S1-T1 energy gaps in the solid state indicate that the emission occurs from a thermally activated excited singlet state at ambient temperature. The emission of the complexes 1-3 mainly originates from MLCT transition. The solution-processed devices of complex 1 exhibit stable red emission with a CIE(x, y) of (0.62, 0.38) for a doped device and (0.63, 0.37) for a non-doped device.

  18. Bacterial Chemotaxis to Naphthalene and Nitroarene Compounds

    DTIC Science & Technology

    2008-07-31

    Qualitative capillary assays showing chemotaxis of succinate-grown 17 (uninduced) and induced (succinate plus salicylate -grown) Acidovorax sp. JS42...succinate plus 2NT- or succinate plus salicylate -grown) wild-type Acidovorax sp. JS42 cells List of Tables Table 1. Summary of chemotaxis...mM salicylate , or naphthalene crystals. Noble agar (1.8%; Difco) was used to solidify MSB medium for plates. For plasmid selection and maintenance

  19. Photoinduced Charge Transport Spectra for Porphyrin and Naphthalene Derivative-based Dendrimers

    NASA Astrophysics Data System (ADS)

    Park, J. H.; Wu, Y.; Parquette, J. R.; Epstein, A. J.

    2006-03-01

    Dendrimers are important chemical structures for harvesting charge. We prepared model dendrimers using two porphyrin derivatives and a naphthalene derivative. Films of these porphyrin derivatives have a strong Soret band (˜430nm) and four significant Q-bands; the naphthalene derivative has strong absorption at 365 and 383nm. Two kinds of photovoltaic cell structures [ITO/BaytronP/(thick or thin) dendrimer/Al] are constructed to investigate the optical response spectra of dendrimers under electric potential(V) on the cell (range from -1V to 2V). To obtain pure optical responses, incident light is modulated with an optical chopper and a lock-in amplifier is used to measure current (IAC) and phase (θ). For the excitation of the Soret band, IAC and θ do not change substantially with change of sign and amplitude of V. For Q-bands and naphthalene absorption bands, θ nearly follows the polarity of V on the cells and IAC is linear with V. Hence, IAC is nearly ohmic for Q- band although there are shifts due to built-in-potential. IAC for Soret band is almost same for thick and thin active layer cells. In contrast, IAC increases with thickness increase for Q bands. Mechanisms of photogeneration and charge transport will be discussed.

  20. Ligands-with-Benefits”: Naphthalene-Substituted Schiff Bases Yielding New Ni II Metal Clusters with Ferromagnetic and Emissive Properties and Undergoing Exciting Transformations

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

    Perlepe, Panagiota S.; Cunha-Silva, Luis; Gagnon, Kevin J.

    The initial employment of the fluorescent bridging ligand N-naphthalidene-2-amino-5-chlorobenzoic acid (nacbH 2) in metal cluster chemistry has led to new Ni 12 (1) and Ni 5 (2) clusters with wheel-like and molecular-chain topologies, respectively. The doubly-deprotonated nacb 2- ligands were found to adopt four different coordination modes within 1 and 2. The nature of the ligand has also allowed unexpected organic transformations to occur and ferromagnetic and emission behaviors to emerge. The combined work presented here demonstrates the ability of some "ligands-with-benefits" to yield beautiful structures with exciting topologies and interesting physicochemical properties.

  1. Ligands-with-Benefits”: Naphthalene-Substituted Schiff Bases Yielding New Ni II Metal Clusters with Ferromagnetic and Emissive Properties and Undergoing Exciting Transformations

    DOE PAGES

    Perlepe, Panagiota S.; Cunha-Silva, Luis; Gagnon, Kevin J.; ...

    2016-01-20

    The initial employment of the fluorescent bridging ligand N-naphthalidene-2-amino-5-chlorobenzoic acid (nacbH 2) in metal cluster chemistry has led to new Ni 12 (1) and Ni 5 (2) clusters with wheel-like and molecular-chain topologies, respectively. The doubly-deprotonated nacb 2- ligands were found to adopt four different coordination modes within 1 and 2. The nature of the ligand has also allowed unexpected organic transformations to occur and ferromagnetic and emission behaviors to emerge. The combined work presented here demonstrates the ability of some "ligands-with-benefits" to yield beautiful structures with exciting topologies and interesting physicochemical properties.

  2. Noncovalent Interactions of DNA Bases with Naphthalene and Graphene.

    PubMed

    Cho, Yeonchoo; Min, Seung Kyu; Yun, Jeonghun; Kim, Woo Youn; Tkatchenko, Alexandre; Kim, Kwang S

    2013-04-09

    The complexes of a DNA base bound to graphitic systems are studied. Considering naphthalene as the simplest graphitic system, DNA base-naphthalene complexes are scrutinized at high levels of ab initio theory including coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] at the complete basis set (CBS) limit. The stacked configurations are the most stable, where the CCSD(T)/CBS binding energies of guanine, adenine, thymine, and cytosine are 9.31, 8.48, 8.53, 7.30 kcal/mol, respectively. The energy components are investigated using symmetry-adapted perturbation theory based on density functional theory including the dispersion energy. We compared the CCSD(T)/CBS results with several density functional methods applicable to periodic systems. Considering accuracy and availability, the optB86b nonlocal functional and the Tkatchenko-Scheffler functional are used to study the binding energies of nucleobases on graphene. The predicted values are 18-24 kcal/mol, though many-body effects on screening and energy need to be further considered.

  3. A Semi-Empirical Formula of the Dependence of the Fluorescence Intensity of Naphthalene on Temperature and the Oxygen Concentration

    NASA Astrophysics Data System (ADS)

    An, B.; Wang, Z.-G.; Yang, L.-C.; Li, X.-P.

    2017-09-01

    Two-ring aromatics, such as naphthalene, are important fluorescent components of kerosene in the planar laser-induced fluorescent (PLIF) technique. Quantifying measurements of kerosene vapor concentrations by PLIF require a prior knowledge of the fluorescence intensity of naphthalene over a wide temperature and oxygen concentration range. To promote the application of PLIF, a semi-empirical formula based on the collision theory and experimental data at the laser wavelength of 266 nm and a pressure of 0.1 MPa is established to predict the fluorescence intensity of naphthalene at different temperatures and oxygen concentrations. This formula takes vibrational states, temperature, and oxygen quenching into account. Verified by published experimental data, the formula can predict the fluorescence intensity of naphthalene with an error less than 9%.

  4. Nitration of naphthalene and remarks on the mechanism of electrophilic aromatic nitration.

    PubMed

    Olah, G A; Narang, S C; Olah, J A

    1981-06-01

    Naphthalene was nitrated with a variety of nitrating agents. Comparison of data with Perrin's electrochemical nitration [Perrin, C. L. (1977) J. Am. Chem. Soc. 99, 5516-5518] shows that nitration of naphthalene gives an alpha-nitronaphthalene to beta-nitronaphthalene ratio that varies between 9 and 29 and is thus not constant. Perrin's data, therefore, are considered to be inconclusive evidence for the proposed one-electron transfer mechanism for the nitration of naphthalene and other reactive aromatics. Moodie and Schoefield [Hoggett, J. G., Moodie, R. B., Penton, J. R. & Schoefield, K. (1971) Nitration and Aromatic Reactivity (Cambridge Univ. Press, London)], as well as Perrin, independently concluded that, in the general scheme of nitration of reactive aromatics, there is the necessity to introduce into the classical Ingold mechanism an additional step involving a distinct intermediate preceding the formation of the Wheland intermediate (sigma complexes). This view coincides with our two-step mechanistic picture [Kuhn, S. J. & Olah, G. A. (1961) J. Am. Chem. Soc. 83, 4564-4571] of the nitronium salt nitration of aromatic hydrocarbons (including benzene and toluene), in which low substrate selectivity but high positional selectivity was found, indicating the independence of substrate from positional selectivity.

  5. Nitration of naphthalene and remarks on the mechanism of electrophilic aromatic nitration*

    PubMed Central

    Olah, George A.; Narang, Subhash C.; Olah, Judith A.

    1981-01-01

    Naphthalene was nitrated with a variety of nitrating agents. Comparison of data with Perrin's electrochemical nitration [Perrin, C. L. (1977) J. Am. Chem. Soc. 99, 5516-5518] shows that nitration of naphthalene gives an α-nitronaphthalene to β-nitronaphthalene ratio that varies between 9 and 29 and is thus not constant. Perrin's data, therefore, are considered to be inconclusive evidence for the proposed one-electron transfer mechanism for the nitration of naphthalene and other reactive aromatics. Moodie and Schoefield [Hoggett, J. G., Moodie, R. B., Penton, J. R. & Schoefield, K. (1971) Nitration and Aromatic Reactivity (Cambridge Univ. Press, London)], as well as Perrin, independently concluded that, in the general scheme of nitration of reactive aromatics, there is the necessity to introduce into the classical Ingold mechanism an additional step involving a distinct intermediate preceding the formation of the Wheland intermediate (σ complexes). This view coincides with our two-step mechanistic picture [Kuhn, S. J. & Olah, G. A. (1961) J. Am. Chem. Soc. 83, 4564-4571] of the nitronium salt nitration of aromatic hydrocarbons (including benzene and toluene), in which low substrate selectivity but high positional selectivity was found, indicating the independence of substrate from positional selectivity. PMID:16593026

  6. Behavior of 2,6-bis(decyloxy)naphthalene inside lipid bilayer.

    PubMed

    Kepczynski, Mariusz; Kumorek, Marta; Stepniewski, Michał; Róg, Tomasz; Kozik, Bartłomiej; Jamróz, Dorota; Bednar, Jan; Nowakowska, Maria

    2010-12-02

    Interactions between small organic molecules and lipid or cell membranes are important because of their role in the distribution of biologically active substances inside the membrane and their permeation through the cell membranes. In the current paper, we have explored the effect of the attachment of long hydrocarbon tails on the behavior of small organic molecule inside the lipid membrane. Naphthalene with two decyloxy groups attached at the opposite sites of the ring (2,6-bis(decyloxy)naphthalene, 3) was synthesized and incorporated into phosphatidylcholine (PC) vesicles. Fluorescence methods as well as molecular dynamic (MD) simulations were used to estimate the position, orientation, and migration of compound 3 in PC bilayer. It was found that the naphthalene ring of compound 3 resides in the upper acyl chain region of the bilayer and the hydrocarbon tails are directed to the center of the bilayer. As was shown with cryotransmission electron microscopy (cryo-TEM), such lipidlike conformation enables compound 3 to be incorporated into liposomes at a very high content without their disintegration. Moreover, compound 3 can migrate from one leaflet to other. The mechanism of this process is, however, different from that characteristic of the flip-flop event of lipid molecules in the membrane. Finally, the possible application of compound 3 as a rotational molecular probe for monitoring fluidity of liposomal membrane in the acyl side chain region was checked by studies of the effect of cholesterol on the fluorescence anisotropy of 3.

  7. The Effect of Reduction Potential on the Generation of the Perylene Diimide Radical Anions

    NASA Astrophysics Data System (ADS)

    Zhao, Y. Z.; Li, K. X.; Ding, S. Y.; Zhu, M.; Ren, H. P.; Ma, Q.; Guo, Z.; Tian, S. P.; Zhang, H. Q.; Miao, Z. C.

    2018-07-01

    Perylene diimide derivatives (PDIs) with different substituents in the bay positions (Un-PDI, DFPDI and THBPDI) were chosen in this report to investigate the effect of potential on the reduction of PDIs through base (hydrazine, 1,2-ethanediamine and triethylamine)-driven keto-enol anion tautomerism. The reduction potentials (PDI/PDI•-) of these compounds determined via cyclic voltammetry are -0.51, ‒0.34, and -0.098 V for Un-PDI, DFPDI, and THBPDI, respectively. The reduction of Un-PDI, DFPDI and THBPDI by hydrazine can produce corresponding radical anions and dianions, but the volume of hydrazine added at which the radicals started to appear is different and depends on their reduction potential. The similar phenomenon was observed using 1,2-ethylenediamine and triethylamine. However, only the radical anion was obtained even in a large excess of 1,2-ethanediamine or triethylamine. Moreover, the reduction of these PDIs with different bases added in the same amount was investigated, and the correlation with their basicity was shown.

  8. Optical biosensor for environmental on-line monitoring of naphthalene and salicylate bioavailability with an immobilized bioluminescent catabolic reporter bacterium.

    PubMed Central

    Heitzer, A; Malachowsky, K; Thonnard, J E; Bienkowski, P R; White, D C; Sayler, G S

    1994-01-01

    An optical whole-cell biosensor based on a genetically engineered bioluminescent catabolic reporter bacterium was developed for continuous on-line monitoring of naphthalene and salicylate bioavailability and microbial catabolic activity potential in waste streams. The bioluminescent reporter bacterium, Pseudomonas fluorescens HK44, carries a transcriptional nahG-luxCDABE fusion for naphthalene and salicylate catabolism. Exposure to either compound resulted in inducible bioluminescence. The reporter culture was immobilized onto the surface of an optical light guide by using strontium alginate. This biosensor probe was then inserted into a measurement cell which simultaneously received the waste stream solution and a maintenance medium. Exposure under defined conditions to both naphthalene and salicylate resulted in a rapid increase in bioluminescence. The magnitude of the response and the response time were concentration dependent. Good reproducibility of the response was observed during repetitive perturbations with either naphthalene or salicylate. Exposure to other compounds, such as glucose and complex nutrient medium or toluene, resulted in either minor bioluminescence increases after significantly longer response times compared with naphthalene or no response, respectively. The environmental utility of the biosensor was tested by using real pollutant mixtures. A specific bioluminescence response was obtained after exposure to either an aqueous solution saturated with JP-4 jet fuel or an aqueous leachate from a manufactured-gas plant soil, since naphthalene was present in both pollutant mixtures. PMID:8017932

  9. Urinary and breast milk biomarkers to assess exposure to naphthalene in pregnant women: an investigation of personal and indoor air sources

    PubMed Central

    2014-01-01

    Background Naphthalene exposures for most non-occupationally exposed individuals occur primarily indoors at home. Residential indoor sources include pest control products (specifically moth balls), incomplete combustion such as cigarette smoke, woodstoves and cooking, some consumer and building products, and emissions from gasoline sources found in attached garages. The study aim was to assess naphthalene exposure in pregnant women from Canada, using air measurements and biomarkers of exposure. Methods Pregnant women residing in Ottawa, Ontario completed personal and indoor air sampling, and questionnaires. During pregnancy, pooled urine voids were collected over two 24-hour periods on a weekday and a weekend day. At 2–3 months post-birth, they provided a spot urine sample and a breast milk sample following the 24-hour air monitoring. Urines were analyzed for 1-naphthol and 2-naphthol and breast milk for naphthalene. Simple linear regression models examined associations between known naphthalene sources, air and biomarker samples. Results Study recruitment rate was 11.2% resulting in 80 eligible women being included. Weekday and weekend samples were highly correlated for both personal (r = 0.83, p < 0.0001) and indoor air naphthalene (r = 0.91, p < 0.0001). Urine specific gravity (SG)-adjusted 2-naphthol concentrations collected on weekdays and weekends (r = 0.78, p < 0.001), and between pregnancy and postpartum samples (r = 0.54, p < 0.001) were correlated. Indoor and personal air naphthalene concentrations were significantly higher post-birth than during pregnancy (p < 0.0001 for signed rank tests); concurrent urine samples were not significantly different. Naphthalene in breast milk was associated with urinary 1-naphthol: a 10% increase in 1-naphthol was associated with a 1.6% increase in breast milk naphthalene (95% CI: 0.2%-3.1%). No significant associations were observed between naphthalene sources reported in self

  10. Polymer/Polymer Blend Solar Cells Using Tetraazabenzodifluoranthene Diimide Conjugated Polymers as Electron Acceptors

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

    Li, Haiyan; Hwang, Ye-Jin; Earmme, Taeshik

    2015-03-02

    Two n-type semiconducting polymers with alternating arylene (thiophene or selenophene)–tetraazabenzodifluoranthene diimide (BFI) donor–acceptor architecture have been investigated as new electron acceptors in polymer/polymer blend solar cells. The new selenophene-linked polymer, PBFI-S, has a significantly smaller optical band gap (1.13 eV) than the thiophene-linked PBFI-T (1.38 eV); however, both polymers have similar HOMO/LUMO energy levels determined from cyclic voltammetry. Blends of PBFI-T with the thiazolothiazole–dithienylsilole donor polymer (PSEHTT) gave a 2.60% power conversion efficiency (PCE) with a 7.34 mA/cm2 short-circuit current. In contrast, PBFI-S:PSEHTT blends had a 0.75% PCE with similarly reduced photocurrent and external quantum efficiency. Reduced free energy formore » charge transfer and reduced bulk electron mobility in PBFI-S:PSEHTT blends compared to PBFI-T:PSEHTT blends as well as significant differences in bulk film morphology are among the reasons for the large loss in efficiency in PBFI-S:PSEHTT blend solar cells.« less

  11. An Overview of the Toxicity of Naphthalene, EDB and Ethanol

    EPA Science Inventory

    This presentation is a short summary of information on the toxicity and carcinogenicity of naphthalene and 1,2-dibromoethane (EDB) that is available in the EPA Integrated Risk Information System (IRIS) and information on the toxicity of ethanol available from the Health, Environm...

  12. IRIS Toxicological Review of Naphthalene (Scoping and Problem Formulation Materials)

    EPA Science Inventory

    In July 2014, EPA released scoping and problem formulation materials for new IRIS assessments of ethylbenzene and naphthalene for public comment and discussion. The scoping information was based on input from EPA's program and regional offices and was provided for informational p...

  13. Photo-driven electron transfer from the highly reducing excited state of naphthalene diimide radical anion to a CO 2 reduction catalyst within a molecular triad

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

    Martinez, Jose F.; La Porte, Nathan T.; Mauck, Catherine M.

    2017-01-01

    The naphthalene-1,4:5,8-bis(dicarboximide) radical anion (NDI -˙), which is easily produced by mild chemical or electrochemical reduction (-0.5 Vvs.SCE), can be photoexcited at wavelengths as long as 785 nm, and has an excited state (NDI -˙*) oxidation potential of -2.1 Vvs.SCE, making it a very attractive choice for artificial photosynthetic systems that require powerful photoreductants, such as CO 2 reduction catalysts. However, once an electron is transferred from NDI -˙* to an acceptor directly bound to it, a combination of strong electronic coupling and favorable free energy change frequently make the back electron transfer rapid. To mitigate this effect, we havemore » designed a molecular triad system comprising an NDI -˙ chromophoric donor, a 9,10-diphenylanthracene (DPA) intermediate acceptor, and a Re(dmb)(CO) 3carbon dioxide reduction catalyst, where dmb is 4,4'-dimethyl-2,2'-bipyridine, as the terminal acceptor. Photoexcitation of NDI -˙ to NDI -˙* is followed by ultrafast reduction of DPA to DPA -˙, which then rapidly reduces the metal complex. The overall time constant for the forward electron transfer to reduce the metal complex is τ = 20.8 ps, while the time constant for back-electron transfer is six orders of magnitude longer, τ = 43.4 μs. Achieving long-lived, highly reduced states of these metal complexes is a necessary condition for their use as catalysts. The extremely long lifetime of the reduced metal complex is attributed to careful tuning of the redox potentials of the chromophore and intermediate acceptor. The NDI -˙–DPA fragment presents many attractive features for incorporation into other photoinduced electron transfer assemblies directed at the long-lived photosensitization of difficult-to-reduce catalytic centers.« less

  14. Deposition of naphthalene and tetradecane vapors in models of the human respiratory system.

    PubMed

    Zhang, Zhe; Kleinstreuer, Clement

    2011-01-01

    Jet-propulsion fuel (particularly JP-8) is currently being used worldwide, exposing especially Air Force personnel and people living near airfields to JP-8 vapors and aerosols during aircraft fueling, maintenance operations, and/or cold starts. JP-8 is a complex mixture containing >200, mostly toxic, aliphatic and aromatic hydrocarbon compounds of which tetradecane and naphthalene were chosen as two representative chemical markers for computer simulations. Thus, transport and deposition of naphthalene and tetradecane vapors have been simulated in models of the human respiratory system. The inspiratory deposition data were analyzed in terms of regional deposition fractions (DFs) and deposition enhancement factors (DEF). The vapor depositions are affected by vapor properties (e.g. diffusivity), airway geometric features, breathing patterns, inspiratory flow rates, as well as airway-wall absorption parameter. Specifically, the respiratory uptake of vapors is greatly influenced by the degree of airway-wall absorption. For example, being an almost insoluble species in the mucus layer, the deposition of tetradecane vapor is nearly zero in the extrathoracic and tracheobronchial (TB) airways, that is, the DF is <1%. The remaining vapors may penetrate further and deposit in the alveolar airways. The DF of tetradecane vapors during inhalation in the alveolar region can range from 7% to 24%, depending on breathing waveform, inhalation rate, and thickness of the mucus layer. In contrast, naphthalene vapor almost completely deposits in the extrathoracic and TB airways and hardly moves downstream and deposits in the respiratory zone. The DFs of naphthalene vapor in the extrathoracic airways from nasal/oral to trachea under normal breathing conditions (Q = 15-60 L/min) are about 12-34%, although they are about 66-87% in the TB airways. In addition, the variation of breathing routes (say, from nasal breathing to oral breathing) may influence the vapor deposition in the

  15. Microwave-assisted intramolecular dehydrogenative Diels-Alder reactions for the synthesis of functionalized naphthalenes/solvatochromic dyes.

    PubMed

    Kocsis, Laura S; Benedetti, Erica; Brummond, Kay M

    2013-04-01

    Functionalized naphthalenes have applications in a variety of research fields ranging from the synthesis of natural or biologically active molecules to the preparation of new organic dyes. Although numerous strategies have been reported to access naphthalene scaffolds, many procedures still present limitations in terms of incorporating functionality, which in turn narrows the range of available substrates. The development of versatile methods for direct access to substituted naphthalenes is therefore highly desirable. The Diels-Alder (DA) cycloaddition reaction is a powerful and attractive method for the formation of saturated and unsaturated ring systems from readily available starting materials. A new microwave-assisted intramolecular dehydrogenative DA reaction of styrenyl derivatives described herein generates a variety of functionalized cyclopenta[b]naphthalenes that could not be prepared using existing synthetic methods. When compared to conventional heating, microwave irradiation accelerates reaction rates, enhances yields, and limits the formation of undesired byproducts. The utility of this protocol is further demonstrated by the conversion of a DA cycloadduct into a novel solvatochromic fluorescent dye via a Buchwald-Hartwig palladium-catalyzed cross-coupling reaction. Fluorescence spectroscopy, as an informative and sensitive analytical technique, plays a key role in research fields including environmental science, medicine, pharmacology, and cellular biology. Access to a variety of new organic fluorophores provided by the microwave-assisted dehydrogenative DA reaction allows for further advancement in these fields.

  16. Microwave-assisted Intramolecular Dehydrogenative Diels-Alder Reactions for the Synthesis of Functionalized Naphthalenes/Solvatochromic Dyes

    PubMed Central

    Kocsis, Laura S.; Benedetti, Erica; Brummond, Kay M.

    2013-01-01

    Functionalized naphthalenes have applications in a variety of research fields ranging from the synthesis of natural or biologically active molecules to the preparation of new organic dyes. Although numerous strategies have been reported to access naphthalene scaffolds, many procedures still present limitations in terms of incorporating functionality, which in turn narrows the range of available substrates. The development of versatile methods for direct access to substituted naphthalenes is therefore highly desirable. The Diels-Alder (DA) cycloaddition reaction is a powerful and attractive method for the formation of saturated and unsaturated ring systems from readily available starting materials. A new microwave-assisted intramolecular dehydrogenative DA reaction of styrenyl derivatives described herein generates a variety of functionalized cyclopenta[b]naphthalenes that could not be prepared using existing synthetic methods. When compared to conventional heating, microwave irradiation accelerates reaction rates, enhances yields, and limits the formation of undesired byproducts. The utility of this protocol is further demonstrated by the conversion of a DA cycloadduct into a novel solvatochromic fluorescent dye via a Buchwald-Hartwig palladium-catalyzed cross-coupling reaction. Fluorescence spectroscopy, as an informative and sensitive analytical technique, plays a key role in research fields including environmental science, medicine, pharmacology, and cellular biology. Access to a variety of new organic fluorophores provided by the microwave-assisted dehydrogenative DA reaction allows for further advancement in these fields. PMID:23609566

  17. Influence of surface oxides on the adsorption of naphthalene onto multiwalled carbon nanotubes.

    PubMed

    Cho, Hyun-Hee; Smith, Billy A; Wnuk, Joshua D; Fairbrother, D Howard; Ball, William P

    2008-04-15

    As greater quantities of carbon nanotubes (CNTs) enter the environment, they will have an increasingly important effect on the availability and transport of aqueous contaminants. As a consequence of purification, deliberate surface functionalization, and/or exposure to oxidizing agents after release to the environment, CNTs often contain surface oxides (i.e., oxygen containing functional groups). To probe the influence that surface oxides exert on CNT sorption properties, multiwalled CNTs (MWCNTs) with varying oxygen concentrations were studied with respect to their sorption properties toward naphthalene. For pristine (as-received) MWCNTs, the sorption capacity was intermediate between that of a natural char and a granular activated carbon. Sorption data also reveal that a linear relationship exists between the oxygen content of MWCNTs and their maximum adsorption capacity for naphthalene, with 10% surface oxygen concentration resulting in a roughly 70% decrease in maximum adsorption capacity. The relative distribution of sorption energies, as characterized by Freundlich isotherm exponents was, however, unaffected by oxidation. Thus, the data are consistent with the idea that incorporated surface oxides create polar regions that reduce the surface area available for naphthalene sorption. These results highlight the important role of surface chemistry in controlling the environmental properties of CNTs.

  18. Gas-phase naphthalene concentration data recovery in ambient air and its relevance as a tracer of sources of volatile organic compounds

    NASA Astrophysics Data System (ADS)

    Uria-Tellaetxe, Iratxe; Navazo, Marino; de Blas, Maite; Durana, Nieves; Alonso, Lucio; Iza, Jon

    2016-04-01

    Despite the toxicity of naphthalene and the fact that it is a precursor of atmospheric photooxidants and secondary aerosol, studies on ambient gas-phase naphthalene are generally scarce. Moreover, as far as we are concerned, this is the first published one using long-term hourly ambient gas-phase naphthalene concentrations. In this work, it has been also demonstrated the usefulness of ambient gas-phase naphthalene to identify major sources of volatile organic compounds (VOC) in complex scenarios. Initially, in order to identify main benzene emission sources, hourly ambient measurements of 60 VOC were taken during a complete year together with meteorological data in an urban/industrial area. Later, due to the observed co-linearity of some of the emissions, a procedure was developed to recover naphthalene concentration data from recorded chromatograms to use it as a tracer of the combustion and distillation of petroleum products. The characteristic retention time of this compound was determined comparing previous GC-MS and GC-FID simultaneous analysis by means of relative retention times, and its concentration was calculated by using relative response factors. The obtained naphthalene concentrations correlated fairly well with ethene (r = 0.86) and benzene (r = 0.92). Besides, the analysis of daily time series showed that these compounds followed a similar pattern, very different from that of other VOC, with minimum concentrations at day-time. This, together with the results from the assessment of the meteorological dependence pointed out a coke oven as the major naphthalene and benzene emitting sources in the study area.

  19. Synthesis, characterization, antimicrobial activity and DFT studies of 2-(pyrimidin-2-ylamino)naphthalene-1,4-dione and its Mn(II), Co(II), Ni(II) and Zn(II) complexes

    NASA Astrophysics Data System (ADS)

    Chioma, Festus; Ekennia, Anthony C.; Ibeji, Collins U.; Okafor, Sunday N.; Onwudiwe, Damian C.; Osowole, Aderoju A.; Ujam, Oguejiofo T.

    2018-07-01

    A pyrimidine-based ligand, 2-(pyrimidin-2-ylamino)naphthalene-1,4-dione (L), has been synthesized by the reaction of 2-aminopyrimidine with 2-hydroxy-1,4-napthoquinone. Reaction of the ligand with Ni(II), Co(II), Mn(II) and Zn(II) acetate gave the corresponding metal complexes which were characterized by spectroscopic techniques, (infrared, electronic), elemental analysis, room-temperature magnetometry, conductance measurements and thermogravimetry-differential scanning calorimetry (TG-DSC) analyses. The room-temperature magnetic data and electronic spectral measurements of the complexes gave evidence of 4-coordinate square planar/tetrahedral geometry. The thermal analyses values obtained indicated the monohydrate complexes. The antimicrobial screening of the compounds showed mild to very good results. The Mn(II) complex showed the best result within in the range of 11.5-29 mm. The electronic, structural and spectroscopic properties of the complexes were further discussed using density functional theory. Molecular docking studies showed significant binding affinity with the drug targets and the metal complexes have potentials to be used as drugs.

  20. Influence of laser wavelength on two-dimensional carbon nanosheet formation from laser-induced exfoliation of naphthalene

    NASA Astrophysics Data System (ADS)

    Qian, Min; Niu, Yue Ping; Gong, Shang Qing

    2018-01-01

    Pulsed Nd:YAG (532 nm) and Excimer (248 nm) lasers were employed to produce freestanding, two-dimensional (2D), carbon nanosheets (CNSs) from naphthalene, through laser-induced exfoliation. The polymer-to-carbon transition was investigated in terms of laser wavelengths, fluences, as well as target preparations. Continuous and porous CNSs of several nanometers in thickness and micrometers in size were obtained from 532 and 248 nm pulsed laser exfoliation of spin-coated naphthalene films, respectively. The porous morphology is ascribed to the photon-induced dissociation of chemical bonds dominated in 248 nm laser interaction with ablated naphthalene. With the increase of laser fluences from 1 to 5 J cm-2, amorphous carbon and ultrathin CNS structures were obtained in sequence. This work revealed a general mechanism of producing 2D structured carbon materials from pulsed laser exfoliation.

  1. Transcriptional responses in the rat nasal epithelium following subchronic inhalation of naphthalene vapor

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

    Clewell, H.J., E-mail: hclewell@thehamner.org; Efremenko, A.; Campbell, J.L.

    Male and female Fischer 344 rats were exposed to naphthalene vapors at 0 (controls), 0.1, 1, 10, and 30 ppm for 6 h/d, 5 d/wk, over a 90-day period. Following exposure, the respiratory epithelium and olfactory epithelium from the nasal cavity were dissected separately, RNA was isolated, and gene expression microarray analysis was conducted. Only a few significant gene expression changes were observed in the olfactory or respiratory epithelium of either gender at the lowest concentration (0.1 ppm). At the 1.0 ppm concentration there was limited evidence of an oxidative stress response in the respiratory epithelium, but not in themore » olfactory epithelium. In contrast, a large number of significantly enriched cellular pathway responses were observed in both tissues at the two highest concentrations (10 and 30 ppm, which correspond to tumorigenic concentrations in the NTP bioassay). The nature of these responses supports a mode of action involving oxidative stress, inflammation and proliferation. These results are consistent with a dose-dependent transition in the mode of action for naphthalene toxicity/carcinogenicity between 1.0 and 10 ppm in the rat. In the female olfactory epithelium (the gender/site with the highest incidences of neuroblastomas in the NTP bioassay), the lowest concentration at which any signaling pathway was significantly affected, as characterized by the median pathway benchmark dose (BMD) or its 95% lower bound (BMDL) was 6.0 or 3.7 ppm, respectively, while the lowest female olfactory BMD values for pathways related to glutathione homeostasis, inflammation, and proliferation were 16.1, 11.1, and 8.4 ppm, respectively. In the male respiratory epithelium (the gender/site with the highest incidences of adenomas in the NTP bioassay), the lowest pathway BMD and BMDL were 0.4 and 0.3 ppm, respectively, and the lowest male respiratory BMD values for pathways related to glutathione homeostasis, inflammation, and proliferation were 0.5, 0.7, and 0

  2. CORRELATION OF POLYCHLORINATED NAPHTHALENES WITH POLYCHLORINATED DIBENZOFURANS FORMED FROM WASTE INCINERATION

    EPA Science Inventory

    Isomer composition of polychlorinated naphthalenes (PCNs) was measured for municipal waste incinerator fly ash samples,and for emission samples produced from soot and copper deposit experiments conducted at EPA. Two types of PCN isomer patterns were identified. One pattern cxonta...

  3. Electron Acceptors Based on α-Substituted Perylene Diimide (PDI) for Organic Solar Cells

    DOE PAGES

    Zhao, Donglin; Wu, Qinghe; Cai, Zhengxu; ...

    2016-02-20

    The ortho-position functionalized perylene diimide derivatives (αPPID, αPBDT) were synthesized and used as the electron acceptors in nonfullerene organic photovoltaics. Due to the good planarity of ortho-position functionalized PDI, the αPPID and αPBDT show strong tendency to form aggregate because of their enhanced intermolecular pie-pie interaction. Moreover, they maintain the pure domains and the same packing order as in the pure film if they are blended with PBT7-TH and the SCLC measurement also shows the high electron mobility. The inverted OPVs employing αPDI-based compounds as acceptor and PBT7-TH as the donor give the highest PCE of 4.92 % for αPBDTmore » based device and 3.61 % for αPPID based device, which is 39 % and 4 % higher than that for their counterpart βPBDT and βPPID. The charge separation study shows the more efficient exciton dissociation at interfaces between PDI based compounds and PBT7-TH. In conclusion, the results suggest that compared to beta-substituted ones, alpha-substituted PDI derivatives are more promising electron acceptors for OPV.« less

  4. IRIS Toxicological Review of Naphthalene (2014, Scoping and Problem Formulation Materials)

    EPA Science Inventory

    In July 2014, EPA released scoping and problem formulation materials for new IRIS assessments of ethylbenzene and naphthalene for public comment and discussion. The scoping information was based on input from EPA's program and regional offices and was provided for informational p...

  5. Electronic Interactions of n-Doped Perylene Diimide Groups Appended to Polynorbornene Chains: Implications for Electron Transport in Organic Electronics.

    PubMed

    Nguyen, Minh T; Biberdorf, Joshua D; Holliday, Bradley J; Jones, Richard A

    2017-11-01

    A polymer consisting of a polynorbornene backbone with perylene diimide (PDI) pendant groups on each monomeric unit is synthesized via ring opening metathesis polymerization. The PDI pendant groups along the polymer backbone, studied by UV-vis absorption, fluorescence emission, and electron paramagnetic resonance spectroscopy in addition to electrochemical methods, show evidence of molecular aggregation and corresponding electronic coupling with neighboring groups, which forms pathways for efficient electron transport from one group to another in a specific reduced form. When n-doped, the title polymer shows redox conductivity of 5.4 × 10 -3 S cm -1 , comparable with crystalline PDI materials, and is therefore a promising material for use in organic electronics. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. NAPHTHALENE TOXICITY IN CD-1 MICE: GENERAL TOXICOLOGY AND IMMUNOTOXICOLOGY

    EPA Science Inventory

    The purpose of this study was to evaluate the acute and subchronic toxicity, and effects on immune function, of naphthalene (NAP) in random-bred CD-1 mice. The acute oral LD50 of this compound was 533 and 710 mg/kg in male and female mice, respectively. Fourteen- and ninety-day d...

  7. Molecular dynamics simulations of the auxin-binding protein 1 in complex with indole-3-acetic acid and naphthalen-1-acetic acid.

    PubMed

    Grandits, Melanie; Oostenbrink, Chris

    2014-10-01

    Auxin-binding protein 1 (ABP1) is suggested to be an auxin receptor which plays an important role in several processes in green plants. Maize ABP1 was simulated with the natural auxin indole-3-acetic acid (IAA) and the synthetic analog naphthalen-1-acetic acid (NAA), to elucidate the role of the KDEL sequence and the helix at the C-terminus. The KDEL sequence weakens the intermolecular interactions between the monomers but stabilizes the C-terminal helix. Conformational changes at the C-terminus occur within the KDEL sequence and are influenced by the binding of the simulated ligands. This observation helps to explain experimental findings on ABP1 interactions with antibodies that are modulated by the presence of auxin, and supports the hypothesis that ABP1 acts as an auxin receptor. Stable hydrogen bonds between the monomers are formed between Glu40 and Glu62, Arg10 and Thr97, Lys39, and Glu62 in all simulations. The amino acids Ile22, Leu25, Trp44, Pro55, Ile130, and Phe149 are located in the binding pocket and are involved in hydrophobic interactions with the ring system of the ligand. Trp151 is stably involved in a face to end interaction with the ligand. The calculated free energy of binding using the linear interaction energy approach showed a higher binding affinity for NAA as compared to IAA. Our simulations confirm the asymmetric behavior of the two monomers, the stronger interaction of NAA than IAA and offers insight into the possible mechanism of ABP1 as an auxin receptor. © 2014 Wiley Periodicals, Inc.

  8. Stable-Isotope Probing of Bacteria Capable of Degrading Salicylate, Naphthalene, or Phenanthrene in a Bioreactor Treating Contaminated Soil

    PubMed Central

    Singleton, David R.; Powell, Sabrina N.; Sangaiah, Ramiah; Gold, Avram; Ball, Louise M.; Aitken, Michael D.

    2005-01-01

    [13C6]salicylate, [U-13C]naphthalene, and [U-13C]phenanthrene were synthesized and separately added to slurry from a bench-scale, aerobic bioreactor used to treat soil contaminated with polycyclic aromatic hydrocarbons. Incubations were performed for either 2 days (salicylate, naphthalene) or 7 days (naphthalene, phenanthrene). Total DNA was extracted from the incubations, the “heavy” and “light” DNA were separated, and the bacterial populations associated with the heavy fractions were examined by denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone libraries. Unlabeled DNA from Escherichia coli K-12 was added to each sample as an internal indicator of separation efficiency. While E. coli was not detected in most analyses of heavy DNA, a low number of E. coli sequences was recovered in the clone libraries associated with the heavy DNA fraction of [13C]phenanthrene incubations. The number of E. coli clones recovered proved useful in determining the relative amount of light DNA contamination of the heavy fraction in that sample. Salicylate- and naphthalene-degrading communities displayed similar DGGE profiles and their clone libraries were composed primarily of sequences belonging to the Pseudomonas and Ralstonia genera. In contrast, heavy DNA from the phenanthrene incubations displayed a markedly different DGGE profile and was composed primarily of sequences related to the Acidovorax genus. There was little difference in the DGGE profiles and types of sequences recovered from 2- and 7-day incubations with naphthalene, so secondary utilization of the 13C during the incubation did not appear to be an issue in this experiment. PMID:15746319

  9. Kinetics of chromate reduction during naphthalene degradation in a mixed culture

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

    Shen, H.; Sewell, G.W.; Pritchard, P.H.

    A mixed culture of Bacillus sp. K1 and Sphingomonas paucimobilis EPA 505 was exposed to chromate and naphthalene. Batch experiments showed that chromate was reduced and naphthalene was degraded by the mixed culture. Chromate reduction occurred initially at a high rate followed by a decrease in rate until chromate reduction ceased. Chromate reduction decreased in the mixed culture when a lower ratio of S. paucimobilis EPA 505 to Bacillus sp. K1 was utilized. A kinetic model incorporating a term for the cell density ratio is proposed to describe chromate reduction in the mixed culture under both chromate limited and electronmore » donor limited conditions. The validity of the model, and its parameter values, was verified by experimental data generated under a variety of initial population compositions and a broad range of chromate concentrations. The consistent result of experimental data with model predictions implies that the model is useful for evaluating the interactions and the use of mixed culture for chromate removal.« less

  10. Synthesis, crystal growth, structural, thermal and optical properties of naphthalene picrate an organic NLO material.

    PubMed

    Chandramohan, A; Bharathikannan, R; Kandavelu, V; Chandrasekaran, J; Kandhaswamy, M A

    2008-12-01

    Crystalline substance of naphthalene picrate (NP) was synthesized and single crystals were grown using slow evaporation solution growth technique. The solubility of the naphthalene picrate complex was estimated using different solvents such as chloroform and benzene. The material was characterized by elemental analysis, powder X-ray diffraction (XRD), nuclear magnetic resonance (NMR) and fourier transform-infrared (FT-IR) techniques. The electronic absorption was studied through UV-vis spectrophotometer. Thermal behavior and stability of the crystal were studied using thermogravimetric (TG) and differential thermal analysis (DTA) techniques. The second harmonic generation (SHG) of the material was confirmed using Nd:YAG laser.

  11. Summary Review of Health Effects Associated with Naphthalene: Health Issue Assessment (1987)

    EPA Science Inventory

    Naphthalene is released into ambient air via industrial gaseous and particulate emissions, tobacco use, and through consumer use. The data base concerning exposure of humans via inhalation and associated health effects is virtually nonexistent. Overexposure often results in acute...

  12. Humidity effects on surface dielectric barrier discharge for gaseous naphthalene decomposition

    NASA Astrophysics Data System (ADS)

    Abdelaziz, Ayman A.; Ishijima, Tatsuo; Seto, Takafumi

    2018-04-01

    Experiments are performed using dry and humid air to clarify the effects of water vapour on the characteristics of surface dielectric barrier discharge (SDBD) and investigate its impact on the performance of the SDBD for decomposition of gaseous naphthalene in air stream. The current characteristics, including the discharge and the capacitive currents, are deeply analyzed and the discharge mechanism is explored. The results confirmed that the humidity affected the microdischarge distribution without affecting the discharge mode. Interestingly, it is found that the water vapour had a significant influence on the capacitance of the reactor due to its deposition on the discharge electrode and the dielectric, which, in turn, affects the power loss in the dielectric and the total power consumed in the reactor. Thus, the factor of the humidity effect on the power loss in the dielectric should be considered in addition to its effect on the attachment coefficient. Additionally, there was an optimum level of the humidity for the decomposition of naphthalene in the SDBD, and its value depended on the gas composition, where the maximum naphthalene decomposition efficiency in O2/H2O is achieved at the humidity level ˜10%, which was lower than that obtained in air/H2O (˜28%). The results also revealed that the role of the humidity in the decomposition efficiency was not significant in the humidified O2 at high power level. This was attributed to the significant increase in oxygen-derived species (such as O atoms and O3) at high power, which was enough to overcome the negative effects of the humidity.

  13. Stability and molecular properties of the boron-nitrogen alternating analogs of azulene and naphthalene: a computational study.

    PubMed

    Catão, Anderson José Lopes; López-Castillo, Alejandro

    2017-04-01

    In this work, the spectroscopic information, stability and aromaticity of the boron-nitrogen azulene and naphthalene molecules are provided by the use of CC2 (geometry optimization, dipole moment, UV-vis spectrum calculations) and DFT (vibrational spectrum and NMR calculations) methodologies. One isomer of the investigated boron-nitrogen naphthalene (boroazanaphthalene) and two isomers of boron-nitrogen azulene, 1,3,4,6,8-pentaaza-2,3a,5,7,8a-pentaboraazulene (BN-azulene) and 2,3a,5,7,8a-pentaaza-1,3,4,6,8- pentaboraazulene (NB-azulene), are stable systems. However, these molecules have different properties, i.e., different stability, dipole moment, and aromaticity based on the NICS approach. BN-naphthalene has a high dipole moment magnitude showing high polar character, while naphthalene is apolar. BN- and NB-azulene are weakly polar, while ordinary azulene is highly polar in character. Also, substitution of C atoms by B and N atoms decreases the aromaticity. In the case of NB-azulene, the seven-membered ring has anti-aromaticity behavior while both rings of BN-azulene exhibit aromaticity. We expect that the new theoretical data provided in this work will be useful in identifying and characterizing experimentally the compounds investigated, and in helping our understanding of the chemistry of boron-nitrogen molecules. Graphical abstract Boron-nitrogen alternating analogs of azulene. Spectral distinction between isomers.

  14. Photoinduced DNA Interstrand Cross-Link Formation by Naphthalene Boronates via a Carbocation.

    PubMed

    Wang, Yibin; Lin, Zechao; Fan, Heli; Peng, Xiaohua

    2016-07-18

    Most photoinduced DNA cross-link formation by a bifunctional aryl derivative is through a bisquinone methide. DNA cross-linking via a bisarylcarbocation remains a less explored area. We designed and synthesized a series of naphthalene boronates that produce DNA interstrand cross-links via a carbocation upon UV irradiation. A free radical was generated from the naphthalene boronates with 350 nm irradiation and further converted to a carbocation by electron transfer. The activation mechanism was determined using the orthogonal traps, 2,2,6,6-tetramethylpiperidin-1-oxyl (TEMPO) and methoxyamine that react with either the free radical or the carbocation but not both. This represents a novel example of photoinduced DNA cross-link formation via carbocations generated from a bisaryl derivative. This work provides information useful for the design of novel photoactivated DNA cross-linking agents. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Cadmium and naphthalene-induced hyperglycemia in the fiddler crab, Uca pugilator: Differential modes of action on the neutroendocrine system

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

    Reddy, P.S.; Katyayani, R.V.; Fingerman, M.

    1996-03-01

    Hyperglycemia is a typical response of aquatic organisms to heavy metals. In crustaceans, the medulla terminalis X-organ-sinus gland neuroendocrine complex in the eyestalk is the source of the crustacean hyperglycemic hormone (CHH). The role of CHH in pollutant-induced b1ood glucose changes has only recently begun to be studied. Reddy provided evidence that CHH mediates cadmium-induced hyperglycemia in the red swamp crayfish, Procambarus clarkii. In a study of another hormonally-regulated function, color changes, cadmium exposure resulted in pigment in the melanophores of the fiddler crab, Uca pugilator, becoming less dispersed than in unexposed crabs. Earlier studies showed that, like cadmium, bothmore » a PCB, Aroclor 1242, and naphthalene induced black pigment aggregation in Uca poor. In general, when crabs are exposed to a pollutant, hydrocarbon or cadmium, they aggregate the pigment in their melanophores, but apparently by different mechanisms. Hydrocarbons appear to inhibit release of black pigment-dispersing hormone (BDPH), whereas cadmium appears to inhibit its synthesis. These apparent different modes of action of cadmium and naphthalene on the color change mechanism led us to compare the impact of these pollutants on the hormonal regulation of blood glucose in Uca pugilator. The present study was performed to determine (1) whether cadmium and naphthalene induce hyperglycemia in Uca pugilator, (2) whether CH has a role, if naphthalene and cadmium do induce hyperglycemia, and (3) the effects, if any, of cadmium and naphthalene on CHH activity in the eyestalk neuroendocrine complex.« less

  16. Visualization of Stereoselective Supramolecular Polymers by Chirality-Controlled Energy Transfer.

    PubMed

    Sarkar, Aritra; Dhiman, Shikha; Chalishazar, Aditya; George, Subi J

    2017-10-23

    Chirality-driven self-sorting is envisaged to efficiently control functional properties in supramolecular materials. However, the challenge arises because of a lack of analytical methods to directly monitor the enantioselectivity of the resulting supramolecular assemblies. Presented herein are two fluorescent core-substituted naphthalene-diimide-based donor and acceptor molecules with minimal structural mismatch and they comprise strong self-recognizing chiral motifs to determine the self-sorting process. As a consequence, stereoselective supramolecular polymerization with an unprecedented chirality control over energy transfer has been achieved. This chirality-controlled energy transfer has been further exploited as an efficient probe to visualize microscopically the chirality driven self-sorting. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Simulated structure and imaging of NTCDI on Si(1 1 1)-7 × 7 : a combined STM, NC-AFM and DFT study

    NASA Astrophysics Data System (ADS)

    Jarvis, S. P.; Sweetman, A. M.; Lekkas, I.; Champness, N. R.; Kantorovich, L.; Moriarty, P.

    2015-02-01

    The adsorption of naphthalene tetracarboxylic diimide (NTCDI) on Si(1 1 1)-7 × 7 is investigated through a combination of scanning tunnelling microscopy (STM), noncontact atomic force microscopy (NC-AFM) and density functional theory (DFT) calculations. We show that NTCDI adopts multiple planar adsorption geometries on the Si(1 1 1)-7 × 7 surface which can be imaged with intramolecular bond resolution using NC-AFM. DFT calculations reveal adsorption is dominated by covalent bond formation between the molecular oxygen atoms and the surface silicon adatoms. The chemisorption of the molecule is found to induce subtle distortions to the molecular structure, which are observed in NC-AFM images.

  18. Fine-Tuning the Quasi-3D Geometry: Enabling Efficient Nonfullerene Organic Solar Cells Based on Perylene Diimides.

    PubMed

    Liu, Zhitian; Zhang, Linhua; Shao, Ming; Wu, Yao; Zeng, Di; Cai, Xiang; Duan, Jiashun; Zhang, Xiaolu; Gao, Xiang

    2018-01-10

    The geometries of acceptors based on perylene diimides (PDIs) are important for improving the phase separation and charge transport in organic solar cells. To fine-tune the geometry, biphenyl, spiro-bifluorene, and benzene were used as the core moiety to construct quasi-three-dimensional nonfullerene acceptors based on PDI building blocks. The molecular geometries, energy levels, optical properties, photovoltaic properties, and exciton kinetics were systematically studied. The structure-performance relationship was discussed as well. Owing to the finest phase separation, the highest charge mobility and smallest nongeminate recombination, the power conversion efficiency of nonfullerene solar cells using PDI derivatives with biphenyl core (BP-PDI 4 ) as acceptor reached 7.3% when high-performance wide band gap donor material poly[(2,6-(4,8-bis(5-(2-ethylhexyl)thiophen-2-yl)-benzo[1,2-b:4,5-b']dithiophene))-alt-(5,5-(1',3'-di-2-thienyl-5',7'-bis(2-ethylhexyl)benzo[1',2'-c:4',5'-c']dithiophene-4,8-dione))] was blended.

  19. Ice growth from supercooled aqueous solutions of benzene, naphthalene, and phenanthrene.

    PubMed

    Liyana-Arachchi, Thilanga P; Valsaraj, Kalliat T; Hung, Francisco R

    2012-08-23

    Classical molecular dynamics (MD) were performed to investigate the growth of ice from supercooled aqueous solutions of benzene, naphthalene, or phenanthrene. The main objective of this study is to explore the fate of those aromatic molecules after freezing of the supercooled aqueous solutions, i.e., if these molecules become trapped inside the ice lattice or if they are displaced to the QLL or to the interface with air. Ice growth from supercooled aqueous solutions of benzene, naphthalene, or phenanthrene result in the formation of quasi-liquid layers (QLLs) at the air/ice interface that are thicker than those observed when pure supercooled water freezes. Naphthalene and phenanthrene molecules in the supercooled aqueous solutions are displaced to the air/ice interface during the freezing process at both 270 and 260 K; no incorporation of these aromatics into the ice lattice is observed throughout the freezing process. Similar trends were observed during freezing of supercooled aqueous solutions of benzene at 270 K. In contrast, a fraction of the benzene molecules become trapped inside the ice lattice during the freezing process at 260 K, with the rest of the benzene molecules being displaced to the air/ice interface. These results suggest that the size of the aromatic molecule in the supercooled aqueous solution is an important parameter in determining whether these molecules become trapped inside the ice crystals. Finally, we also report potential of mean force (PMF) calculations aimed at studying the adsorption of gas-phase benzene and phenanthrene on atmospheric air/ice interfaces. Our PMF calculations indicate the presence of deep free energy minima for both benzene and phenanthrene at the air/ice interface, with these molecules adopting a flat orientation at the air/ice interface.

  20. Identification and preliminary evaluation of polychlorinated naphthalene emissions from hot dip galvanizing plants.

    PubMed

    Liu, Guorui; Lv, Pu; Jiang, Xiaoxu; Nie, Zhiqiang; Liu, Wenbin; Zheng, Minghui

    2015-01-01

    Hot dip galvanizing (HDG) processes are sources of polychlorinated-p-dioxins and dibenzofurans (PCDD/Fs). Close correlations have been found between the concentration of PCDD/Fs and polychlorinated naphthalenes (PCNs) that are produced and released during industrial thermal processes. We speculated, therefore, that HDG plants are potential PCN sources. In this preliminary study, PCNs were analyzed in solid residues, ash and precipitate from three HDG plants of different sizes. The total PCN concentrations (∑2-8PCNs) in the residue samples ranged from 60.3 to 226pgg(-1). The PCN emission factors for the combined ash and precipitate residues from the HDG plants ranged from 75 to 178ngt(-1) for the dichlorinated and octachlorinated naphthalenes. The preliminary results suggested that the HDG industry might not currently be a significant source of PCN emissions. The trichloronaphthalenes were the dominant homologs followed by the dichloronaphthalenes and the tetrachloronaphthalenes. The PCN congeners CN37/33/34, CN52/60, CN66/67, and CN73 dominated the tetrachlorinated, pentachlorinated, hexachlorinated, and heptachlorinated naphthalene homologs, respectively. The PCNs emitted from the HDG plants had similar homolog distributions and congener profiles to the PCNs emitted from combustion plants and other metallurgical processes. The identification and preliminary evaluation of PCN emissions from HDG plants presented here will help in the prioritization of measures for controlling PCN emissions from industrial sources. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Enhanced oxidation of naphthalene using plasma activation of TiO2/diatomite catalyst.

    PubMed

    Wu, Zuliang; Zhu, Zhoubin; Hao, Xiaodong; Zhou, Weili; Han, Jingyi; Tang, Xiujuan; Yao, Shuiliang; Zhang, Xuming

    2018-04-05

    Non-thermal plasma technology has great potential in reducing polycyclic aromatic hydrocarbons (PAHs) emission. But in plasma-alone process, various undesired by-products are produced, which causes secondary pollutions. Here, a dielectric barrier discharge (DBD) reactor has been developed for the oxidation of naphthalene over a TiO 2 /diatomite catalyst at low temperature. In comparison to plasma-alone process, the combination of plasma and TiO 2 /diatomite catalyst significantly enhanced naphthalene conversion (up to 40%) and CO x selectivity (up to 92%), and substantially reduced the formation of aerosol (up to 90%) and secondary volatile organic compounds (up to near 100%). The mechanistic study suggested that the presence of the TiO 2 /diatomite catalyst intensified the electron energy in the DBD. Meantime, the energized electrons generated in the discharge activated TiO 2 , while the presence of ozone enhanced the activity of the TiO 2 /diatomite catalyst. This plasma-catalyst interaction led to the synergetic effect resulting from the combination of plasma and TiO 2 /diatomite catalyst, consequently enhanced the oxidation of naphthalene. Importantly, we have demonstrated the effectiveness of plasma to activate the photocatalyst for the deep oxidation of PAH without external heating, which is potentially valuable in the development of cost-effective gas cleaning process for the removal of PAHs in vehicle applications during cold start conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Synthesis, molecular modelling, and preliminary anticonvulsant activity evaluation of novel naphthalen-2-yl acetate and 1,6-dithia-4,9-diazaspiro [4.4] nonane-3,8-dione derivatives.

    PubMed

    Ghareb, Nagat; Abdel Daim, Mohamed M; El-Sayed, Norhan M; Elgawish, Mohamed Saleh

    2017-04-01

    The synthesis, pharmacological evaluation and molecular modelling study of novel naphthalen-2-yl acetate and 1,6-dithia-4,9-diazaspiro [4.4]nonane-3,8-dione derivatives as potential anticonvulsant agents are described. The newly synthesized compounds were characterized by both analytical and spectral data. Alkylation of 1H-imidazole or substituted piperazine with 1-(2-naphthyl)-2-bromoethanone (2) gave naphthalen-2-yl 2-(1H-imidazol-1-yl) acetate (3) and naphthalen-2-yl 2-(substituted piperazin-1-yl) acetate (4-8). Moreover, condensation of naphthalen-2-yl 2-bromoacetate or 2-bromo-1-(naphthalen-2-yl) ethanone with hydrazine hydrate and acetylacetone resulted in the formation of the cyclic pyrazole products 9 and 13. Sonication of naphthalen-2-yl acetate (1) with 2-chloropyridine, 2-chloropyrimidine and 2-(chloromethyl) oxirane gave naphthalen-2-yl 2-(pyridin-2-yl) acetate (10), naphthalen-2-yl 2-(pyrimidin-2-yl) acetate (11) and naphthalen-2-yl-3-(oxiran-2-yl) propanoate (12) respectively. Cyclocondensation reaction of 2-iminothiazolidin-4-one (14) with thioglycolic acid, thiolactic acid and thiomalic acid gave 1,6-dithia-4,9-diazaspiro [4.4]nonane-3,8-dione derivatives (15-17). The compounds were testedin vivofor the anticonvulsant activity by delaying strychnine-induced seizures. The diazaspirononane (17) and 1-(2-naphthyl)-2-bromoethanone (2) showed a high significant delay in the onset of convulsion and prolongation of survival time compared to phenobarbital. The molecular modelling study of anticonvulsant activity of synthesized compounds showed a CNS depressant activity via modulation of benzodiazepine allosteric site in GABA-A receptors. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. 40 CFR 61.134 - Standard: Naphthalene processing, final coolers, and final-cooler cooling towers.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... POLLUTANTS National Emission Standard for Benzene Emissions from Coke By-Product Recovery Plants § 61.134... are allowed from naphthalene processing, final coolers and final-cooler cooling towers at coke by...

  4. 40 CFR 61.134 - Standard: Naphthalene processing, final coolers, and final-cooler cooling towers.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... POLLUTANTS National Emission Standard for Benzene Emissions from Coke By-Product Recovery Plants § 61.134... are allowed from naphthalene processing, final coolers and final-cooler cooling towers at coke by...

  5. 40 CFR 61.134 - Standard: Naphthalene processing, final coolers, and final-cooler cooling towers.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... POLLUTANTS National Emission Standard for Benzene Emissions from Coke By-Product Recovery Plants § 61.134... are allowed from naphthalene processing, final coolers and final-cooler cooling towers at coke by...

  6. 40 CFR 61.134 - Standard: Naphthalene processing, final coolers, and final-cooler cooling towers.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... POLLUTANTS National Emission Standard for Benzene Emissions from Coke By-Product Recovery Plants § 61.134... are allowed from naphthalene processing, final coolers and final-cooler cooling towers at coke by...

  7. Elucidating the role of surface passivating ligand structural parameters in hole wave function delocalization in semiconductor cluster molecules.

    PubMed

    Teunis, Meghan B; Nagaraju, Mulpuri; Dutta, Poulami; Pu, Jingzhi; Muhoberac, Barry B; Sardar, Rajesh; Agarwal, Mangilal

    2017-09-28

    This article describes the mechanisms underlying electronic interactions between surface passivating ligands and (CdSe) 34 semiconductor cluster molecules (SCMs) that facilitate band-gap engineering through the delocalization of hole wave functions without altering their inorganic core. We show here both experimentally and through density functional theory calculations that the expansion of the hole wave function beyond the SCM boundary into the ligand monolayer depends not only on the pre-binding energetic alignment of interfacial orbitals between the SCM and surface passivating ligands but is also strongly influenced by definable ligand structural parameters such as the extent of their π-conjugation [π-delocalization energy; pyrene (Py), anthracene (Anth), naphthalene (Naph), and phenyl (Ph)], binding mode [dithiocarbamate (DTC, -NH-CS 2 - ), carboxylate (-COO - ), and amine (-NH 2 )], and binding head group [-SH, -SeH, and -TeH]. We observe an unprecedentedly large ∼650 meV red-shift in the lowest energy optical absorption band of (CdSe) 34 SCMs upon passivating their surface with Py-DTC ligands and the trend is found to be Ph- < Naph- < Anth- < Py-DTC. This shift is reversible upon removal of Py-DTC by triethylphosphine gold(i) chloride treatment at room temperature. Furthermore, we performed temperature-dependent (80-300 K) photoluminescence lifetime measurements, which show longer lifetime at lower temperature, suggesting a strong influence of hole wave function delocalization rather than carrier trapping and/or phonon-mediated relaxation. Taken together, knowledge of how ligands electronically interact with the SCM surface is crucial to semiconductor nanomaterial research in general because it allows the tuning of electronic properties of nanomaterials for better charge separation and enhanced charge transfer, which in turn will increase optoelectronic device and photocatalytic efficiencies.

  8. Horizontal Transfer of phnAc Dioxygenase Genes within One of Two Phenotypically and Genotypically Distinctive Naphthalene-Degrading Guilds from Adjacent Soil Environments

    PubMed Central

    Wilson, Mark S.; Herrick, James B.; Jeon, Che Ok; Hinman, David E.; Madsen, Eugene L.

    2003-01-01

    Several distinct naphthalene dioxygenases have been characterized to date, which provides the opportunity to investigate the ecological significance, relative distribution, and transmission modes of the different analogs. In this study, we showed that a group of naphthalene-degrading isolates from a polycyclic aromatic hydrocarbon (PAH)-contaminated hillside soil were phenotypically and genotypically distinct from naphthalene-degrading organisms isolated from adjacent, more highly contaminated seep sediments. Mineralization of 14C-labeled naphthalene by soil slurries suggested that the in situ seep community was more acclimated to PAHs than was the in situ hillside community. phnAc-like genes were present in diverse naphthalene-degrading isolates cultured from the hillside soil, while nahAc-like genes were found only among isolates cultured from the seep sediments. The presence of a highly conserved nahAc allele among gram-negative isolates from the coal tar-contaminated seep area provided evidence for in situ horizontal gene transfer and was reported previously (J. B. Herrick, K. G. Stuart-Keil, W. C. Ghiorse, and E. L. Madsen, Appl. Environ. Microbiol. 63:2330-2337, 1997). Natural horizontal transfer of the phnAc sequence was also suggested by a comparison of the phnAc and 16S ribosomal DNA sequences of the hillside isolates. Analysis of metabolites produced by cell suspensions and patterns of amplicons produced by PCR analysis suggested both genetic and metabolic diversity among the naphthalene-degrading isolates of the contaminated hillside. These results provide new insights into the distribution, diversity, and transfer of phnAc alleles and increase our understanding of the acclimation of microbial communities to pollutants. PMID:12676698

  9. A Critical Review of Naphthalene Sources and Exposures Relevant to Indoor and Outdoor Air

    PubMed Central

    Jia, Chunrong; Batterman, Stuart

    2010-01-01

    Both the recent classification of naphthalene as a possible human carcinogen and its ubiquitous presence motivate this critical review of naphthalene’s sources and exposures. We evaluate the environmental literature on naphthalene published since 1990, drawing on nearly 150 studies that report emissions and concentrations in indoor, outdoor and personal air. While naphthalene is both a volatile organic compound and a polycyclic aromatic hydrocarbon, concentrations and exposures are poorly characterized relative to many other pollutants. Most airborne emissions result from combustion, and key sources include industry, open burning, tailpipe emissions, and cigarettes. The second largest source is off-gassing, specifically from naphthalene’s use as a deodorizer, repellent and fumigant. In the U.S., naphthalene’s use as a moth repellant has been reduced in favor of para-dichlorobenzene, but extensive use continues in mothballs, which appears responsible for some of the highest indoor exposures, along with off-label uses. Among the studies judged to be representative, average concentrations ranged from 0.18 to 1.7 μg m−3 in non-smoker’s homes, and from 0.02 to 0.31 μg m−3 outdoors in urban areas. Personal exposures have been reported in only three European studies. Indoor sources are the major contributor to (non-occupational) exposure. While its central tendencies fall well below guideline levels relevant to acute health impacts, several studies have reported maximum concentrations exceeding 100 μg m−3, far above guideline levels. Using current but draft estimates of cancer risks, naphthalene is a major environmental risk driver, with typical individual risk levels in the 10−4 range, which is high and notable given that millions of individuals are exposed. Several factors influence indoor and outdoor concentrations, but the literature is inconsistent on their effects. Further investigation is needed to better characterize naphthalene’s sources and

  10. Responses of Tabanidae (Diptera) to canopy traps baited with 4-methylphenol, 3-isopropylphenol, and naphthalene.

    PubMed

    Krcmar, Stjepan

    2007-12-01

    The attraction of female tabanids to unbaited and single-baited canopy traps using 4-methylphenol, 3-isopropylphenol, and naphthalene was studied in three forest localities in eastern Croatia. Tabanids were collected in a significantly higher number in traps baited with these chemicals compared to unbaited control traps. The number of females of Tabanus bromius, Tabanus sudeticus, Tabanus tergestinus, Hybomitra ciureai, Haematopota pluvialis, and Tabanus maculicornis collected from 4-methylphenol baited canopy traps and traps baited with other attractants differed significantly. A total of 89.0% of tabanids collected belonged to these six species. The response of the other species to used chemicals was not analyzed because of small sample sizes. Moreover, the results with 3-isopropylphenol and naphthalene are very similar and not significant for some tabanids. Tabanus bromius was the most abundant species with 48.4% in the sample collected by canopy traps. Finally, the 4-methylphenol baited canopy traps collected 16 times more tabanids than unbaited traps, while 3-isopropylphenol and naphthalene baited traps collected 3.5 and 2 times as many tabanids, respectively, than unbaited traps. Also, 4-methylphenol appeared to be a very effective attractant for Lucilia caesar (Calliphoridae), Sarcophaga carnaria (Sarcophagidae), and Musca domestica (Muscidae).

  11. Adsorptive removal of naphthalene induced by structurally different Gemini surfactants in a soil-water system.

    PubMed

    Wei, Jia; Li, Jun; Huang, Guohe; Wang, Xiujie; Chen, Guanghui; Zhao, Baihang

    2016-09-01

    A new generation of surfactant, Gemini surfactants, have been synthesized and have attracted the attention of various industrial and academic research groups. This study focused on the use of symmetric and dissymmetric quaternary ammonium Gemini surfactants to immobilize naphthalene onto soil particles, and is used as an example of an innovative application to remove HOC in situ using the surfactant-enhanced sorption zone. The sorption capacity of modified soils by Gemini surfactant and natural soils was compared and the naphthalene sorption efficiency, in the absence and presence of Gemini surfactants with different alkyl chain lengths, was investigated in the soil-water system. The results have shown that the increased added Gemini surfactant formed admicelles at the interface of soil/water having superior capability to retard contaminant. Symmetric and dissymmetric Gemini surfactants have opposite effect on the aspect of removing of PAH attributing to their solubilization and sorption behavior in soil-water system. Compared with the natural soil, sorption of naphthalene by Gemini-modified soil is noticeably enhanced following the order of C12-2-16 < C12-2-12 < C12-2-8. However, the symmetric Gemini surfactant C12-2-12 is the optimized one for in situ barrier remediation, which is not only has relative high retention ability but also low dosage.

  12. 40 CFR 61.134 - Standard: Naphthalene processing, final coolers, and final-cooler cooling towers.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... POLLUTANTS National Emission Standard for Benzene Emissions from Coke By-Product Recovery Plants § 61.134... are allowed from naphthalene processing, final coolers and final-cooler cooling towers at coke by-product recovery plants. ...

  13. Ultraviolet Irradiation of Naphthalene in H2O Ice: Implications for Meteorites and Biogenesis

    NASA Technical Reports Server (NTRS)

    Bernstein, Max P.; Dworkin, Jason; Sandford, Scott A.; Allamandola, Louis J.; DeVincenzi, Donald L. (Technical Monitor)

    2000-01-01

    The polycyclic aromatic hydrocarbon (PAH) naphthalene was exposed to ultraviolet radiation in H2O ice under astrophysical conditions, and the products were analyzed using infrared spectroscopy and high performance liquid chromatography. As we found in our earlier studies on the photoprocessing of coronene in H2O ice, aromatic alcohols and ketones (quinones) were formed. The regiochemistry of the reactions is described and leads to specific predictions of the relative abundances of various oxidized naphthalenes that should exist in meteorites if interstellar ice photochemistry influenced their aromatic inventory. Since oxidized PAHs are present in carbon-rich meteorites and interplanetary dust particles (IDPs), and ubiquitous in and fundamental to biochemistry, the delivery of such extraterrestrial molecules to the early Earth may have played a role in the origin and evolution of life.

  14. Arene-mercury complexes stabilized by gallium chloride: relative rates of H/D and arene exchange.

    PubMed

    Branch, Catherine S; Barron, Andrew R

    2002-11-27

    We have previously proposed that the Hg(arene)(2)(GaCl(4))(2) catalyzed H/D exchange reaction of C(6)D(6) with arenes occurs via an electrophilic aromatic substitution reaction in which the coordinated arene protonates the C(6)D(6). To investigate this mechanism, the kinetics of the Hg(C(6)H(5)Me)(2)(GaCl(4))(2) catalyzed H/D exchange reaction of C(6)D(6) with naphthalene has been studied. Separate second-order rate constants were determined for the 1- and 2-positions on naphthalene; that is, the initial rate of H/D exchange = k(1i)[Hg][C-H(1)] + k(2i)[Hg][C-H(2)]. The ratio of k(1i)/k(2i) ranges from 11 to 2.5 over the temperature range studied, commensurate with the proposed electrophilic aromatic substitution reaction. Observation of the reactions over an extended time period shows that the rates change with time, until they again reach a new and constant second-order kinetics regime. The overall form of the rate equation is unchanged: final rate = k(1f)[Hg][C-H(1)] + k(2f)[Hg][C-H(2)]. This change in the H/D exchange is accompanied by ligand exchange between Hg(C(6)D(6))(2)(GaCl(4))(2) and naphthalene to give Hg(C(10)H(8))(2)(GaCl(4))(2,) that has been characterized by (13)C CPMAS NMR and UV-visible spectroscopy. The activation parameters for the ligand exchange may be determined and are indicative of a dissociative reaction and are consistent with our previously calculated bond dissociation for Hg(C(6)H(6))(2)(AlCl(4))(2). The initial Hg(arene)(2)(GaCl(4))(2) catalyzed reaction of naphthalene with C(6)D(6) involves the deuteration of naphthalene by coordinated C(6)D(6); however, as ligand exchange progresses, the pathway for H/D exchange changes to where the protonation of C(6)D(6) by coordinated naphthalene dominates. The site selectivity for the H/D exchange is initially due to the electrophilic aromatic substitution of naphthalene. As ligand exchange occurs, this selectivity is controlled by the activation of the naphthalene C-H bonds by mercury.

  15. Effect of the Molecular Configuration of Perylene Diimide Acceptors on Charge Transfer and Device Performance

    DOE PAGES

    Qu, Jianfei; Mu, Zhao; Lai, Hanjian; ...

    2018-01-25

    Three perylene diimides (PDI)-based small molecules, T2-SePDI2, T3B-SePDI3, and T4B-SePDI4, with different molecular configurations are synthesized. Due to a large steric hindrance, the molecular configuration of T3B-SePDI3 is the most distorted, followed by T4BSePDI4, while T2-SePDI2 shows the smallest steric hindrance. Inverted bulk heterojunction solar cells based on T3B-SePDI3 and PBDB-T show the highest power conversion efficiency (PCE) of 5.82% with an open-circuit voltage of 0.98 V, a high short-circuit current density of 10.52 mA/cm2, and a fill factor of 56.31%. The PCEs of the T2-SePDI2- and T4B-SePDI4- based devices are 4.10% and 5.10%, respectively. Furthermore, the results demonstrate thatmore » the molecular configuration of the PDI-based small molecule acceptor is critical and that increasing the steric hindrance is helpful in suppressing aggregation and improving device performance.« less

  16. Effect of the Molecular Configuration of Perylene Diimide Acceptors on Charge Transfer and Device Performance

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

    Qu, Jianfei; Mu, Zhao; Lai, Hanjian

    Three perylene diimides (PDI)-based small molecules, T2-SePDI2, T3B-SePDI3, and T4B-SePDI4, with different molecular configurations are synthesized. Due to a large steric hindrance, the molecular configuration of T3B-SePDI3 is the most distorted, followed by T4BSePDI4, while T2-SePDI2 shows the smallest steric hindrance. Inverted bulk heterojunction solar cells based on T3B-SePDI3 and PBDB-T show the highest power conversion efficiency (PCE) of 5.82% with an open-circuit voltage of 0.98 V, a high short-circuit current density of 10.52 mA/cm2, and a fill factor of 56.31%. The PCEs of the T2-SePDI2- and T4B-SePDI4- based devices are 4.10% and 5.10%, respectively. Furthermore, the results demonstrate thatmore » the molecular configuration of the PDI-based small molecule acceptor is critical and that increasing the steric hindrance is helpful in suppressing aggregation and improving device performance.« less

  17. Nearly Perfect Triplet-Triplet Energy Transfer from Wannier Excitons to Naphthalene in Organic-Inorganic Hybrid Quantum-Well Materials

    NASA Astrophysics Data System (ADS)

    Ema, K.; Inomata, M.; Kato, Y.; Kunugita, H.; Era, M.

    2008-06-01

    We report the observation of extremely efficient energy transfer (greater than 99%) in an organic-inorganic hybrid quantum-well structure consisting of perovskite-type lead bromide well layers and naphthalene-linked ammonium barrier layers. Time-resolved photoluminescence measurements confirm that the transfer is triplet-triplet Dexter-type energy transfer from Wannier excitons in the inorganic well to the triplet state of naphthalene molecules in the organic barrier. Using measurements in the 10 300 K temperature range, we also investigated the temperature dependence of the energy transfer.

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

    PubMed

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

    2016-03-01

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

  19. EFFECT OF PH AND CONCENTRATION ON THE TRANSPORT OF NAPHTHALENE IN SATURATED AQUIFER MEDIA

    EPA Science Inventory

    Sorption is one of the primary mechanisms for retarding the movement of organic contaminants in groundwater. Sorption of hydrophobic compounds such as toluene, naphthalene, and DDT is generally assumed to be linearly proportional to solution phase concentration. In the present re...

  20. PBTK Modeling Demonstrates Contribution of Dermal and Inhalation Exposure Components to End-Exhaled Breath Concentrations of Naphthalene

    PubMed Central

    Kim, David; Andersen, Melvin E.; Chao, Yi-Chun E.; Egeghy, Peter P.; Rappaport, Stephen M.; Nylander-French, Leena A.

    2007-01-01

    Background Dermal and inhalation exposure to jet propulsion fuel 8 (JP-8) have been measured in a few occupational exposure studies. However, a quantitative understanding of the relationship between external exposures and end-exhaled air concentrations has not been described for occupational and environmental exposure scenarios. Objective Our goal was to construct a physiologically based toxicokinetic (PBTK) model that quantitatively describes the relative contribution of dermal and inhalation exposures to the end-exhaled air concentrations of naphthalene among U.S. Air Force personnel. Methods The PBTK model comprised five compartments representing the stratum corneum, viable epidermis, blood, fat, and other tissues. The parameters were optimized using exclusively human exposure and biological monitoring data. Results The optimized values of parameters for naphthalene were a) permeability coefficient for the stratum corneum 6.8 × 10−5 cm/hr, b) permeability coefficient for the viable epidermis 3.0 × 10−3 cm/hr, c) fat:blood partition coefficient 25.6, and d) other tissue:blood partition coefficient 5.2. The skin permeability coefficient was comparable to the values estimated from in vitro studies. Based on simulations of workers’ exposures to JP-8 during aircraft fuel-cell maintenance operations, the median relative contribution of dermal exposure to the end-exhaled breath concentration of naphthalene was 4% (10th percentile 1% and 90th percentile 11%). Conclusions PBTK modeling allowed contributions of the end-exhaled air concentration of naphthalene to be partitioned between dermal and inhalation routes of exposure. Further study of inter- and intraindividual variations in exposure assessment is required to better characterize the toxicokinetic behavior of JP-8 components after occupational and/or environmental exposures. PMID:17589597

  1. PBTK modeling demonstrates contribution of dermal and inhalation exposure components to end-exhaled breath concentrations of naphthalene.

    PubMed

    Kim, David; Andersen, Melvin E; Chao, Yi-Chun E; Egeghy, Peter P; Rappaport, Stephen M; Nylander-French, Leena A

    2007-06-01

    Dermal and inhalation exposure to jet propulsion fuel 8 (JP-8) have been measured in a few occupational exposure studies. However, a quantitative understanding of the relationship between external exposures and end-exhaled air concentrations has not been described for occupational and environmental exposure scenarios. Our goal was to construct a physiologically based toxicokinetic (PBTK) model that quantitatively describes the relative contribution of dermal and inhalation exposures to the end-exhaled air concentrations of naphthalene among U.S. Air Force personnel. The PBTK model comprised five compartments representing the stratum corneum, viable epidermis, blood, fat, and other tissues. The parameters were optimized using exclusively human exposure and biological monitoring data. The optimized values of parameters for naphthalene were a) permeability coefficient for the stratum corneum 6.8 x 10(-5) cm/hr, b) permeability coefficient for the viable epidermis 3.0 x 10(-3) cm/hr, c) fat:blood partition coefficient 25.6, and d) other tissue:blood partition coefficient 5.2. The skin permeability coefficient was comparable to the values estimated from in vitro studies. Based on simulations of workers' exposures to JP-8 during aircraft fuel-cell maintenance operations, the median relative contribution of dermal exposure to the end-exhaled breath concentration of naphthalene was 4% (10th percentile 1% and 90th percentile 11%). PBTK modeling allowed contributions of the end-exhaled air concentration of naphthalene to be partitioned between dermal and inhalation routes of exposure. Further study of inter- and intraindividual variations in exposure assessment is required to better characterize the toxicokinetic behavior of JP-8 components after occupational and/or environmental exposures.

  2. [Properties of maize stalk biochar produced under different pyrolysis temperatures and its sorption capability to naphthalene].

    PubMed

    Huang, Hua; Wang, Ya-Xiong; Tang, Jing-Chun; Tang, Jing-Chun; Zhu, Wen-Ying

    2014-05-01

    Biochar was made from maize stalk under three different temperatures of 300, 500 and 700 degreeC. The elemental composition of biochar was measured by elemental analyzer. Scanning electron microscope (SEM) was used to measure the surface morphology. Sorption of naphthalene to biochar was researched by batch sorption experiments. Results showed that, with the increase of temperature, C content increased from 66. 79% to 76. 30% , H and O contents decreased from 4.92% and 19. 25% to 3. 18% and 9.53%, respectively; H/C, O/C, (O + N)/C, aromaticity and hydrophobicity increased, and polarity decreased. SEM results showed that maize stalk biochar was platy particles, and its roughness of surface increased with increasing temperature. The sorption of naphthalene on biochar followed the Lagergren pseudo-second order dynamic sorption model. Initial sorption rate and equilibrium sorption capacity increased as preparation temperatures increased at the same initial concentration of naphthalene. The isotherm sorption behavior can be described by the Freundlich model, which indicated that, as pyrolysis temperature increased, the sorption capacity of biochar increased, and nonlinearity increased first and then decreased. Biochar derived from maize stalk had distinct features when compared with other feedstocks, and its elemental composition, surface features and sorption behaviors were significantly influenced by pyrolysis temperature.

  3. Enhanced biodegradation of mixed PAHs by mutated naphthalene 1,2-dioxygenase encoded by Pseudomonas putida strain KD6 isolated from petroleum refinery waste.

    PubMed

    Dutta, Kunal; Shityakov, Sergey; Das, Prangya P; Ghosh, Chandradipa

    2017-12-01

    Polycyclic aromatic hydrocarbons (PAHs) are a group of environmental pollutant that are given top priority to maintain water and soil quality to the most amenable standard. Biodegradation of PAHs by bacteria is the convenient option for decontamination on site or off site. The aim of the present study was to isolate and identify naturally occurring bacteria having mixed PAHs biodegradation ability. The newly isolated Pseudomonas putida strain KD6 was found to efficiently degrade 97.729% of 1500 mg L -1 mixed PAHs within 12 days in carbon-deficient minimal medium (CSM). The half-life ( t 1/2 ) and degradation rate constant ( k ) were estimated to be 3.2 and 0.2165 days, respectively. The first-order kinetic parameters in soil by strain KD6 had shown efficient biodegradation potency with the higher concentration of total PAHs (1500 mg kg -1 soil), t 1/2  = 10.44 days -1 . However, the biodegradation by un-inoculated control soil was found slower ( t 1/2  = 140 days -1 ) than the soil inoculated with P. putida strain KD6. The enzyme kinetic constants are also in agreement with chemical data obtained from the HPLC analysis. In addition, the sequence analysis and molecular docking studies showed that the strain KD6 encodes a mutant version of naphthalene 1,2-dioxygenase which have better Benzpyrene binding energy (-9.90 kcal mol -1 ) than wild type (-8.18 kcal mol -1 ) enzyme (chain A, 1NDO), respectively, with 0.00 and 0.08 RMSD values. The mutated naphthalene 1,2-dioxygenase nah Ac has six altered amino acid residues near to the ligand binding site. The strain KD6 could be a good bioresource for in situ or ex situ biodegradation of polycyclic aromatic hydrocarbon.

  4. Development of Methods for Sampling and Analysis of Polychlorinated Naphthalenes in Ambient Air

    ERIC Educational Resources Information Center

    Erickson, Mitchell D.; And Others

    1978-01-01

    The procedure and sampler described permits detection of less than 50pg of one polychlorinated naphthalene (PCN) isomer. The method uses gas chromatography-mass spectrometry. The PCNs are collected on a glass fiber filter and two polyurethane foam plugs and extracted with toluene at 25 degrees Celsius. (BB)

  5. Pressure-dependent rate constants for PAH growth: formation of indene and its conversion to naphthalene

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

    Mebel, Alexander M.; Georgievskii, Yuri; Jasper, Ahren W.

    2016-01-01

    Unraveling the mechanisms for growth of polycyclic aromatic hydrocarbons (PAHs) requires accurate temperature- and pressure-dependent rate coefficients for a great variety of feasible pathways. Even the pathways for the formation of the simplest PAHs, indene and naphthalene, are fairly complex. These pathways provide important prototypes for modeling larger PAH growth. In this work we employ the ab initio RRKM theory-based master equation approach to predict the rate constants involved in the formation of indene and its conversion to naphthalene. The reactions eventually leading to indene involve C9Hx (x = 8–11) potential energy surfaces (PESs) and include C6H5 + C3H4 (allenemore » and propyne), C6H6 + C3H3, benzyl + C2H2, C6H5 + C3H6, C6H6 + C3H5 and C6H5 + C3H5. These predictions allow us to make a number of valuable observations on the role of various mechanisms. For instance, we demonstrate that reactions which can significantly contribute to the formation of indene include phenyl + allene and H-assisted isomerization to indene of its major product, 3-phenylpropyne, benzyl + acetylene, and the reactions of the phenyl radical with propene and the allyl radical, both proceeding via the 3-phenylpropene intermediate. 3-Phenylpropene can be activated to a 1-phenylallyl radical, which in turn rapidly decomposes to indene. Next, indene can be converted to benzofulvene or naphthalene under typical combustion conditions, via its activation by H atom abstraction and methyl substitution on the five-membered ring followed by isomerization and decomposition of the resulting 1-methylindenyl radical, C10H9 → C10H8 + H. Alternatively, the same region of the C10H9 PES can be accessed through the reaction of benzyl with propargyl, C7H7 + C3H3 → C10H10 → C10H9 + H, which therefore can also contribute to the formation of benzofulvene or naphthalene. Benzofulvene easily transforms to naphthalene by H-assisted isomerization. An analysis of the effect of pressure on the

  6. Quantitative photoabsorption and fluorescence spectroscopy of benzene, naphthalene, and some derivatives at 106-295 nm

    NASA Technical Reports Server (NTRS)

    Suto, Masako; Wang, Xiuyan; Shan, Jun; Lee, L. C.

    1992-01-01

    Photoabsorption and fluorescence cross sections of benzene, (o-, m-, p-) xylenes, naphthalene, 1-methylnaphthalene, and 2-ethylnaphthalene in the gas phase are measured at 106-295 nm using synchrotron radiation as a light source. Fluorescences are observed from the photoexcitation of benzene and xylenes at 230-280 nm and from naphthalene and its derivatives at 190-295 nm. The absolute fluorescence cross section is determined by calibration with respect to the emission intensity of the NO(A-X) system, for which the fluorescence quantum yield is equal to 1. To cross-check the current calibration method, the quantum yield of the SO2(C-X) system at 220-230 nm was measured since it is about equal to 1. The current quantum-yield data are compared with previously published values measured by different methods.

  7. The effect of chlorpyrifos-oxon and other xenobiotics on the human cytochrome P450-dependent metabolism of naphthalene and deet.

    PubMed

    Cho, Taehyeon M; Rose, Randy L; Hodgson, Ernest

    2007-01-01

    Chlorpyrifos-oxon (CPO), a metabolite of chlorpyrifos, is a potent inhibitor of acetylcholinesterase and, although the neurotoxicological impact of this organophosphorus compound has been broadly studied both in vitro and in vivo, there are few studies of metabolic interactions of CPO with other xenobiotics. CPO significantly activated the production of 1-naphthol (5-fold), 2-naphthol (10-fold), trans-1,2-dihydro-1,2-naphthalenediol (1.5-fold), and 1,4-naphthoquinone from naphthalene by human liver microsomes (HLM). It was further demonstrated that the production of naphthalene metabolites by CYP2C8, 2C9*(1), 2C19, 2D6*(1), 3A4, 3A5, and 3A7 was activated by CPO, while the production of naphthalene metabolites by CYP1A1, 1A2, 1B1, and 2B6 was inhibited by CPO. CPO inhibited CYP1A2 production of naphthalene metabolites, while activating their production by CYP3A4. Similarly, CPO inhibited the production of N,N-diethyl-m-hydroxymethylbenzamide (BALC) from DEET by human liver microsomes, but activated the production of N-ethyl-m-toluamide (ET) from this substrate. CYP2B6, the most efficient isoform for BALC production, was inhibited by CPO, while CYP3A4, the most efficient isoform for ET production, was activated by CPO. CPO inhibited CYP2B6 production of both BALC and ET from DEET, but activated CYP3A4 production of ET, while inhibiting CYP3A4 BALC production. CPO appears to facilitate the binding of naphthalene to CYP3A4. This metabolic activation is independent of cytochrome b5, suggesting that activation of CYP3A4 by CPO is associated with a conformational change of the isoform rather than facilitating electron transfer.

  8. Synthesis, photophysical, and electrochemical properties of wide band gap tetraphenylsilane-carbazole derivatives: Effect of the substitution position and naphthalene side chain

    NASA Astrophysics Data System (ADS)

    Ho, Kar Wei; Ariffin, A.

    2016-12-01

    Four tetraphenylsilane-carbazole derivatives with wide bandgaps (3.38-3.55 eV) were synthesized. The effects of the substitution position and of the presence of naphthalene groups on the photophysical, electrochemical and thermal properties were investigated. The derivatives exhibited maximum absorption peaks ranging from 293 to 304 nm and maximum emission peaks ranging from 347 to 386 nm. Changing the carbazole substitution position on the tetraphenylsilane did not significantly change the photophysical and electrochemical properties. However, p-substituted compounds exhibited higher glass transition temperatures than m-substituted compounds. Naphthalene groups with bulky structures had extended the conjugation lengths that red-shifted both the absorption and emission spectra. The LUMO level was decreased, which reduced the optical bandgap and triplet energy level. However, the naphthalene groups significantly improved the thermal stability by increasing the glass transition temperature of the compounds.

  9. pn-Heterojunction effects of perylene tetracarboxylic diimide derivatives on pentacene field-effect transistor.

    PubMed

    Yu, Seong Hun; Kang, Boseok; An, Gukil; Kim, BongSoo; Lee, Moo Hyung; Kang, Moon Sung; Kim, Hyunjung; Lee, Jung Heon; Lee, Shichoon; Cho, Kilwon; Lee, Jun Young; Cho, Jeong Ho

    2015-01-28

    We investigated the heterojunction effects of perylene tetracarboxylic diimide (PTCDI) derivatives on the pentacene-based field-effect transistors (FETs). Three PTCDI derivatives with different substituents were deposited onto pentacene layers and served as charge transfer dopants. The deposited PTCDI layer, which had a nominal thickness of a few layers, formed discontinuous patches on the pentacene layers and dramatically enhanced the hole mobility in the pentacene FET. Among the three PTCDI molecules tested, the octyl-substituted PTCDI, PTCDI-C8, provided the most efficient hole-doping characteristics (p-type) relative to the fluorophenyl-substituted PTCDIs, 4-FPEPTC and 2,4-FPEPTC. The organic heterojunction and doping characteristics were systematically investigated using atomic force microscopy, 2D grazing incidence X-ray diffraction studies, and ultraviolet photoelectron spectroscopy. PTCDI-C8, bearing octyl substituents, grew laterally on the pentacene layer (2D growth), whereas 2,4-FPEPTC, with fluorophenyl substituents, underwent 3D growth. The different growth modes resulted in different contact areas and relative orientations between the pentacene and PTCDI molecules, which significantly affected the doping efficiency of the deposited adlayer. The differences between the growth modes and the thin-film microstructures in the different PTCDI patches were attributed to a mismatch between the surface energies of the patches and the underlying pentacene layer. The film-morphology-dependent doping effects observed here offer practical guidelines for achieving more effective charge transfer doping in thin-film transistors.

  10. Chiral Redox-Active Isosceles Triangles

    DOE PAGES

    Nalluri, Siva Krishna Mohan; Liu, Zhichang; Wu, Yilei; ...

    2016-04-12

    Designing small-molecule organic redox-active materials, with potential applications in energy storage, has received considerable interest of late. Herein, we report on the synthesis, characterization, and application of two rigid chiral triangles, each of which consist of non-identical pyromellitic diimide (PMDI) and naphthalene diimide (NDI)-based redox-active units. 1H and 13C NMR spectroscopic investigations in solution confirm the lower symmetry (C2 point group) associated with these two isosceles triangles. Single-crystal X-ray diffraction analyses reveal their rigid triangular prism-like geometries. Unlike previously investigated equilateral triangle containing three identical NDI subunits, both isosceles triangles do not choose to form one-dimensional supramolecular nanotubes by dintmore » of [C–H···O] interaction-driven columnar stacking. The rigid isosceles triangle, composed of one NDI and two PMDI subunits, forms—in the presence of N,N-dimethylformamide—two different types of intermolecular NDI–NDI and NDI–PMDI π–π stacked dimers with opposite helicities in the solid state. Cyclic voltammetry reveals that both isosceles triangles can accept reversibly up to six electrons. Continuous-wave electron paramagnetic resonance and electron–nuclear double-resonance spectroscopic investigations, supported by density functional theory calculations, on the single-electron reduced radical anions of the isosceles triangles confirm the selective sharing of unpaired electrons among adjacent redox-active NDI subunit(s) within both molecules. The isosceles triangles have been employed as electrode-active materials in organic rechargeable lithium-ion batteries. The evaluation of the structure–performance relationships of this series of diimide-based triangles reveals that the increase in the number of NDI subunits, replacing PMDI ones, within the molecules improves the electrochemical cell performance of the batteries.« less

  11. The naphthalene state of the science symposium: objectives, organization, structure, and charge.

    PubMed

    Belzer, Richard B; Bus, James S; Cavalieri, Ercole L; Lewis, Steven C; North, D Warner; Pleus, Richard C

    2008-07-01

    This report provides a summary of the objectives, organization, structure and charge for the naphthalene state of the science symposium (NS(3)), Monterey, CA, October 9-12, 2006. A 1-day preliminary conference was held followed by a 3-day state of the science symposium covering four topics judged by the Planning Committee to be crucial for developing valid and reliable scientific estimates of low-dose human cancer risk from naphthalene. The Planning Committee reviewed the relevant scientific literature to identify singularly knowledgeable researchers and a pool of scientists qualified to serve as expert panelists. In two cases, independent scientists were commissioned to develop comprehensive reviews of the relevant science in a specific area for which no leading researcher could be identified. Researchers and expert panelists alike were screened for conflicts of interest. All policy issues related to risk assessment practices and risk management were scrupulously excluded. NS(3) was novel in several ways and provides an innovative model for the effective use of peer review to identify scientific uncertainties and propose research strategies for reducing or eliminating them prior to the conduct of risk assessment.

  12. Naphthalene Planar Laser-Induced Fluorescence Imaging of Orion Multi-Purpose Crew Vehicle Heat Shield Ablation Products

    NASA Astrophysics Data System (ADS)

    Combs, Christopher S.; Clemens, Noel T.; Danehy, Paul M.

    2013-11-01

    The Orion Multi-Purpose Crew Vehicle (MPCV) calls for an ablative heat shield. In order to better design this heat shield and others that will undergo planetary entry, an improved understanding of the ablation process is required. Given that ablation is a multi-physics process involving heat and mass transfer, codes aiming to predict heat shield ablation are in need of experimental data pertaining to the turbulent transport of ablation products for validation. At The University of Texas at Austin, a technique is being developed that uses planar laser-induced fluorescence (PLIF) of a low-temperature sublimating ablator (naphthalene) to visualize the transport of ablation products in a supersonic flow. Since ablation at reentry temperatures can be difficult to recreate in a laboratory setting it is desirable to create a limited physics problem and simulate the ablation process at relatively low temperature conditions using naphthalene. A scaled Orion MPCV model with a solid naphthalene heat shield has been tested in a Mach 5 wind tunnel at various angles of attack in the current work. PLIF images have shown high concentrations of scalar in the capsule wake region, intermittent turbulent structures on the heat shield surface, and interesting details of the capsule shear layer structure. This work was supported by a NASA Office of the Chief Technologist's Space Technology Research Fellowship (NNX11AN55H).

  13. LigandRNA: computational predictor of RNA–ligand interactions

    PubMed Central

    Philips, Anna; Milanowska, Kaja; Łach, Grzegorz; Bujnicki, Janusz M.

    2013-01-01

    RNA molecules have recently become attractive as potential drug targets due to the increased awareness of their importance in key biological processes. The increase of the number of experimentally determined RNA 3D structures enabled structure-based searches for small molecules that can specifically bind to defined sites in RNA molecules, thereby blocking or otherwise modulating their function. However, as of yet, computational methods for structure-based docking of small molecule ligands to RNA molecules are not as well established as analogous methods for protein-ligand docking. This motivated us to create LigandRNA, a scoring function for the prediction of RNA–small molecule interactions. Our method employs a grid-based algorithm and a knowledge-based potential derived from ligand-binding sites in the experimentally solved RNA–ligand complexes. As an input, LigandRNA takes an RNA receptor file and a file with ligand poses. As an output, it returns a ranking of the poses according to their score. The predictive power of LigandRNA favorably compares to five other publicly available methods. We found that the combination of LigandRNA and Dock6 into a “meta-predictor” leads to further improvement in the identification of near-native ligand poses. The LigandRNA program is available free of charge as a web server at http://ligandrna.genesilico.pl. PMID:24145824

  14. 6-Substituted 3,4-dihydro-naphthalene-2-carboxylic acids: synthesis and structure-activity studies in a novel class of human 5alpha reductase inhibitors.

    PubMed

    Baston, Eckhard; Salem, Ola I A; Hartmann, Rolf W

    2002-10-01

    Novel 3,4-dihydro-naphthalene-2-carboxylic acids were synthesized and evaluated for 5alpha reductase inhibitory activity. This enzyme exists in two isoforms and is a pharmacological target for the treatment of benign prostatic hyperplasia, male pattern baldness and acne. In the present study non-steroidal compounds capable of mimicking the transition state of the steroidal substrates were prepared. The synthetic strategy for the preparation of compounds 1-6 consisted of triflation followed by subsequent Heck-type carboxylation or methoxy carbonylation for 6-phenyl-3,4-dihydronaphthalen-2(1H)-one 1c. A Negishi-type coupling reaction between 6-(trifluoro-methanesulfonyloxy)-3,4-dihydro-naphthalene-2-carboxylic acid methyl ester 7b and various aryl bromides led, after further transformations, to 6-substituted 3,4-dihydro-naphthalene-2-carboxylic acids 7-15. In a similar way the corresponding naphthalene-2-carboxylic acids 16 and 17 were obtained. The DU 145 cell line and prostate homogenates served as enzyme sources for the human type 1 and type 2 isozymes, whereas ventral prostate was employed to evaluate rat isozyme inhibitory potency. The most active inhibitors identified in this study were 6-[4-(N,N-dicyclohexylaminocarbonyl)phenyl]-3,4-dihydro-naphthalene-2-carboxylic acid (3) (IC50 = 0.09 microM, rat type 1), 6-[3-(N,N-dicyclohexylaminocarbonyl)phenyl]-3,4-dihydro-naphthalene-2-carboxylic acid (13) (IC50 = 0.75 microM, human type 2; IC50 = 0.81 microM, human type 1) and 6-[4-(N,N-diisopropylamino-carbonyl)phenyl]naphthalene-2-carboxylic acid (16) (IC50 = 0.2 microM, human type 2). The latter compound was shown to deactivate the enzyme in an uncompetitive manner (Ki = 90 nM; Km, Testosterone = 0.8-1.0 microM) similar to the steroidal inhibitor Epristeride. Select inhibitors (13 and 16) were tested in vivo using testosterone propionate-treated, juvenile, orchiectomized SD-rats. None of the compounds was active at a dose of 25 mg/kg. This result might in part be

  15. Conformationally constrained farnesoid X receptor (FXR) agonists: heteroaryl replacements of the naphthalene.

    PubMed

    Bass, Jonathan Y; Caravella, Justin A; Chen, Lihong; Creech, Katrina L; Deaton, David N; Madauss, Kevin P; Marr, Harry B; McFadyen, Robert B; Miller, Aaron B; Mills, Wendy Y; Navas, Frank; Parks, Derek J; Smalley, Terrence L; Spearing, Paul K; Todd, Dan; Williams, Shawn P; Wisely, G Bruce

    2011-02-15

    To improve on the drug properties of GSK8062 1b, a series of heteroaryl bicyclic naphthalene replacements were prepared. The quinoline 1c was an equipotent FXR agonist with improved drug developability parameters relative to 1b. In addition, analog 1c lowered body weight gain and serum glucose in a DIO mouse model of diabetes. Copyright © 2010 Elsevier Ltd. All rights reserved.

  16. Analysis of macromolecules, ligands and macromolecule-ligand complexes

    DOEpatents

    Von Dreele, Robert B [Los Alamos, NM

    2008-12-23

    A method for determining atomic level structures of macromolecule-ligand complexes through high-resolution powder diffraction analysis and a method for providing suitable microcrystalline powder for diffraction analysis are provided. In one embodiment, powder diffraction data is collected from samples of polycrystalline macromolecule and macromolecule-ligand complex and the refined structure of the macromolecule is used as an approximate model for a combined Rietveld and stereochemical restraint refinement of the macromolecule-ligand complex. A difference Fourier map is calculated and the ligand position and points of interaction between the atoms of the macromolecule and the atoms of the ligand can be deduced and visualized. A suitable polycrystalline sample of macromolecule-ligand complex can be produced by physically agitating a mixture of lyophilized macromolecule, ligand and a solvent.

  17. A Naphtho- p-quinodimethane Exhibiting Baird’s (Anti)Aromaticity, Broken Symmetry, and Attractive Photoluminescence

    DOE PAGES

    Shokri, Siamak; Li, Jingbai; Manna, Manoj K.; ...

    2017-08-24

    In this paper, we report a novel reductive desulfurization reaction involving π-acidic naphthalene diimides 1 (NDI) using thionating agents such as Lawesson’s reagent. Along with the expected thionated NDI derivatives 2-6, new heterocyclic naphtho-p-quinodimethane compounds 7 depicting broken/reduced symmetry were successfully isolated and fully characterized. Empirical studies and theoretical modeling suggest that was formed via a six-membered ring oxathiaphosphenine intermediate rather than the usual four-membered ring oxathiaphosphetane of 2-6. Aside from the reduced symmetry in 7 as confirmed by single-crystal XRD analysis, we established that the ground state UV-vis absorption of 7 is red-shifted in comparison to the parent NDImore » 1. This result was expected in the case of thionated polycyclic diimides. However, unusual low energy transitions originate from Baird 4nπ aromaticity of compounds 7 in lieu of the intrinsic Huckel (4n + 2)π aromaticity as encountered in NDI 1. Moreover, complementary theoretical modeling results also corroborate this change in aromaticity of 7. Consequently, photophysical investigations show that, compared to parent NDI 1, 7 can easily access and emit from its T 1 state with a phosphorescence 3(7a)* lifetime of τ P = 395 μs at 77 K indicative of the formation of the corresponding “aromatic triplet” species according to the Baird’s rule of aromaticity.« less

  18. Effects of petroleum on adrenocortical activity and on hepatic naphthalene-metabolizing activity in mallard ducks

    USGS Publications Warehouse

    Gorsline, J.; Holmes, W.N.

    1981-01-01

    Unstressed mallard ducks (Anas platyrhychos), given uncontaminated food and maintained on a short photoperiod, show two daily maxima in plasma corticosterone concentration ([B]); one occurring early in the light phase and a second just before the onset of darkness. After one week of exposure to food containing 3% (v/w) South Louisiana crude oil, plasma [B] were significantly lowered throughout the day. Similar abrupt declines in plasma [B] also occurred during the first 10 days of exposure to food containing 1% and 0.5% crude oil. Although the plasma [B] in birds consuming food contaminated with 0.5% crude oil increased between 10 and 50 days of exposure, the concentration after 50 days was still lower than normal. During the same interval, normal plasma [B] were restored in birds consuming food containing 1% and 3% crude oil. Significant increases occurred in the naphthalene-metabolizing properties of hepatic microsomes prepared from birds acutely exposed to all levels of petroleum-contaminated food and elevated levels were sustained throughout the first 50 days of exposure. Birds given food containing 3% crude oil for more than 50 days, however, showed steady declines in hepatic naphthalene-metabolizing activity. After 500 days, the activity was similar to that found in contemporaneous controls. During the same interval, the plasma [B] increased until the levels were higher than normal after 500 days of exposure; at this time, an inverse relationship, similar to that seen during the first week of exposure to contaminated food, was once more established between plasma [B] and the concomitant hepatic naphthalene-metabolizing activity.

  19. Development and characterization of a cell line from Pacific herring, Clupea harengus pallasi, sensitive to both naphthalene cytotoxicity and infection by viral hemorrhagic septicemia virus.

    PubMed

    Ganassin, R C; Sanders, S M; Kennedy, C J; Joyce, E M; Bols, N C

    1999-01-01

    A cell line, PHL, has been successfully established from newly hatched herring larvae. The cells are maintained in growth medium consisting of Leibovitz's L-15 supplemented with 15% fetal bovine serum (FBS), and have been cryopreserved and maintain viability after thawing. These cells retain a diploid karotype after 65 population doublings. PHL are susceptible to infection by the North American strain of viral hemorrhagic septicemia (VHS) virus, and are sensitive to the cytotoxic effects of naphthalene, a common environmental contaminant. Naphthalene is a component of crude and refined oil, and may be found in the marine environment following acute events such as oil spills. In addition, chronic sources of naphthalene contamination include offshore drilling and petroleum contamination from areas such as docks and marinas that have creosote-treated docks and pilings and also receive constant small inputs of petroleum products. This cell line should be useful for investigations of the toxicity of naphthalene and other petroleum components to juvenile herring. In addition, studies of the VHS virus will be facilitated by the availability of a susceptible cell line from an alternative species.

  20. Electron spin resonance of gamma-irradiated poly/ethylene 2,6-naphthalene dicarboxylate/.

    NASA Technical Reports Server (NTRS)

    Rogowski, R. S.; Pezdirtz, G. F.

    1971-01-01

    The two types of radicals trapped in gamma-irradiated PEN 2,6 are identified by ESR as - O - CH - CH2 - O - (radical I) and a radical located on the naphthalene ring (radical II). The concentrations of the radicals in the gross polyer are 10 to 20% of I and 80 to 90% of II. Similar trapped radicals are established in beta-irradiated PET, a structurally related polymer.

  1. Time-resolved measurement of intramolecular photoinduced electron transfer processes in perylene diimides (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Döring, Robin Carl; Baal, Eduard; Sundermeyer, Jörg; Chatterjee, Sangam

    2017-02-01

    Perylene-3,4,9,10-tetracarboxylic acid (PTCDA) and respective derivatives (e.g. perylene diimide - PDI) are widely used as dyes but also for device applications such as organic field effect transistors or in organic photovoltaics. Due to their intrinsically high quantum efficiencies they are also used as spectroscopic standards. One major drawback of these materials is their low solubility in organic solvents which can be addressed by long alkyl substitutions. When introducing a tertiary amine into the molecule a mechanism known as photoinduced electron transfer (PET) can occur. Here, following an optically excited HOMO-LUMO transition of the core, an electron from the electron lone pair of the amine is transferred to the HOMO of the perylene core. Hence, radiative recombination is disallowed and photoluminescence effectively quenched. Here, we perform a systematic study of the distance dependence of the PET by introducing alkyle groups as spacer units between PDI core and the tertiary amine. Dynamics of the PET are extracted from ultrafast time-resolved photoluminescence measurement data. A rate equation model, simulating a three level system, reveals rate constant of the back electron transfer, otherwise not accessible with our experimental methods. Assuming a Marcus model of electron transfer, electronic coupling strength between the electronic states involved in the respective transitions can be calculated. In addition to the distance dependence, the effects of protonation and methylation of the the tertiary amine units are studied.

  2. PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures.

    PubMed

    Shin, Jae-Min; Cho, Doo-Ho

    2005-01-01

    PDB-Ligand (http://www.idrtech.com/PDB-Ligand/) is a three-dimensional structure database of small molecular ligands that are bound to larger biomolecules deposited in the Protein Data Bank (PDB). It is also a database tool that allows one to browse, classify, superimpose and visualize these structures. As of May 2004, there are about 4870 types of small molecular ligands, experimentally determined as a complex with protein or DNA in the PDB. The proteins that a given ligand binds are often homologous and present the same binding structure to the ligand. However, there are also many instances wherein a given ligand binds to two or more unrelated proteins, or to the same or homologous protein in different binding environments. PDB-Ligand serves as an interactive structural analysis and clustering tool for all the ligand-binding structures in the PDB. PDB-Ligand also provides an easier way to obtain a number of different structure alignments of many related ligand-binding structures based on a simple and flexible ligand clustering method. PDB-Ligand will be a good resource for both a better interpretation of ligand-binding structures and the development of better scoring functions to be used in many drug discovery applications.

  3. Interactive effects of naphthalene treatment and the onset of vitellogenesis on energy metabolism in liver and gonad, and plasma steroid hormones of rainbow trout Oncorhynchus mykiss.

    PubMed

    Tintos, Adrián; Gesto, Manuel; Alvarez, Rosa; Míguez, Jesús M; Soengas, José L

    2006-10-01

    The purpose of the study was to assess in female fish the possible interaction between treatment with a polycyclic aromatic hydrocarbon (PAH) like naphthalene and the onset of vitellogenesis. In a first experiment, female rainbow trout (Oncorhynchus mykiss) at stages 2-3 (previtellogenesis) or 4 (early vitellogenesis) were intraperitoneally injected (2 microl g(-1)) with vegetable oil alone (control) or containing naphthalene (50 mg kg(-1)) to be sampled 3 h later. A second experiment was similarly designed but using fish intraperitoneally implanted (10 microl g(-1)) with slow-release coconut oil implants alone (control) or containing 50 mg naphthalene kg(-1) body mass that were sampled 3 days after injection. On each sampling time, plasma levels of cortisol and 17beta-estradiol, and several metabolic parameters in plasma, liver and gonad were assessed. In controls, early vitellogenic fish compared with previtellogenic fish displayed changes that in some cases are confirmatory of previous studies whereas in other cases provide new information in plasma (increased amino acid levels), liver (decreased capacity for exporting glucose and reduced amino acid levels) and gonad (decreased amino acid levels). Naphthalene treatment produced in previtellogenic fish decreased 17beta-estradiol levels in plasma, increased plasma glucose or decreased liver gluconeogenic capacity whereas no major effects were noticed on parameters involved in lipid, amino acid and lactate metabolism. Differential effects of naphthalene treatment were noticed in early vitellogenic fish such as decreased 17beta-estradiol and glucose levels in plasma, increased hexokinase and glucokinase and lack of changes in fructose 1,6-bisphosphatase activities in liver, and a lower decrease of amino acid levels in gonad. Those alterations produced by naphthalene treatment resulted in a decreased capacity for covering the energy demand of vitellogenesis in liver and gonad that could contribute to a delay and

  4. Complete Genome Sequence of the Naphthalene-Degrading Bacterium Pseudomonas stutzeri AN10 (CCUG 29243)

    PubMed Central

    Brunet-Galmés, Isabel; Busquets, Antonio; Peña, Arantxa; Gomila, Margarita; Nogales, Balbina; García-Valdés, Elena; Lalucat, Jorge; Bennasar, Antonio

    2012-01-01

    Pseudomonas stutzeri AN10 (CCUG 29243) can be considered a model strain for aerobic naphthalene degradation. We report the complete genome sequence of this bacterium. Its 4.71-Mb chromosome provides insights into other biodegradative capabilities of strain AN10 (i.e., benzoate catabolism) and suggests a high number of horizontal gene transfer events. PMID:23144395

  5. Low and High Molecular Mass Dithienopyrrole-Naphthalene Bisimide Donor-Acceptor Compounds: Synthesis, Electrochemical and Spectroelectrochemical Behaviour.

    PubMed

    Rybakiewicz, Renata; Glowacki, Eric D; Skorka, Lukasz; Pluczyk, Sandra; Zassowski, Pawel; Apaydin, Dogukan Hazar; Lapkowski, Mieczyslaw; Zagorska, Malgorzata; Pron, Adam

    2017-02-24

    Two low molecular weight electroactive donor-acceptor-donor (DAD)-type molecules are reported, namely naphthalene bisimide (NBI) symmetrically core-functionalized with dithienopyrrole (NBI-(DTP) 2 ) and an asymmetric core-functionalized naphthalene bisimide with dithienopyrrole (DTP) substituent on one side and 2-ethylhexylamine on the other side (NBI-DTP-NHEtHex). Both compounds are characterized by low optical bandgaps (1.52 and 1.65 eV, respectively). NBI-(DTP) 2 undergoes oxidative electropolymerization giving the electroactive polymer of ambipolar character. Its two-step reversible reduction and oxidation is corroborated by complementary EPR and UV/Vis-NIR spectroelectrochemical investigations. The polymer turned out to be electrochemically active not only in aprotic solvents but also in aqueous electrolytes, showing a distinct photocathodic current attributed to proton reduction. Additionally, poly(NBI-(DTP) 2 ) was successfully tested as a photodiode material. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Emission of Polychlorinated Naphthalenes during Thermal Related Processes

    NASA Astrophysics Data System (ADS)

    Liu, Guorui; Zheng, Minghui; Du, Bing; Liu, Wenbin; Zhang, Bing; Xiao, Ke

    2010-05-01

    Due to the structural similarity of polychlorinated naphthalenes (PCNs) to those of dioxins, PCNs exhibit toxicological properties similar to dioxins (Olivero-Verbel et al., 2004). Based on their high toxicity, persistence, bioaccumulation, and long-distance transmission, PCNs were also selected as a candidate POP for the UN-ECE (United Nations Economic Commission for Europe) POP protocol (Lerche et al., 2002). In addition, some studies suggested that PCNs contributed a greater proportion of the dioxin-like activity than polychlorinated biphenyls (PCBs) and polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) contributed in some locations (Kannan et al., 1998). However, the identification and quantitation for PCN sources are very scarce compared with PCDD/Fs. Understanding the emission levels and developing the emission inventory of PCNs is important for regulatory and source reduction purposes. In this study, several potential sources were preliminarily investigated for PCN release. Coking process (CP), iron ore sintering (IOS), and electric arc furnace steel making units (AF) were selected due to their huge activity level of industrial production in China. Municipal solid waste incineration (MSWI) and medical waste incineration (MWI) were also investigated because of the possible high concentration of PCNs in stack gas. Two plants were investigated for each thermal related process, except for MWI with one incinerator was investigated. The stack gas samples were collected by automatic isokinetic sampling system (Isostack Basic, TCR TECORA, Milan Italy). Isotope dilution high resolution gas chromatography coupled with high resolution mass spectrometry (HRGC/HRMS) technique was used for the identification and quantitation of PCN congeners. The concentrations of PCNs from the selected thermal processes were determined in this study. The average concentrations of total PCNs were 26 ng Nm-3 for CP, 65 ng Nm-3 for IOS, 720 ng Nm-3 for AF, 443 ng Nm-3 for MSWI, and

  7. Two new coordination polymers constructed by naphthalene-1,4-dicarboxylic acid and 2,4-diamino-6-methyl-triazine

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

    Li, Yamin, E-mail: liyamin@henu.edu.cn; Xiao, Changyu; Zhang, Xudong

    2013-08-15

    Two new transition metal coordination complexes, ([MnO(nda)](H{sub 2}dmt)(H{sub 2}O)){sub n} (1), [Ag{sub 5}(nda){sub 2.5}(dmt)]{sub n} (2), (H{sub 2}nda=naphthalene-1,4-dicarboxylic acid, dmt=2,4-diamine-6-methyl-1,3,5-triazine) have been hydrothermally synthesized by the reactions of H{sub 2}nda and dmt with the homologous MnCl{sub 2}·4H{sub 2}O and AgNO{sub 3}, respectively, and characterized by single-crystal X-ray diffraction, IR spectra, elemental analysis, thermogravimetric analysis (TGA). The compound 1 exhibits a 3D network comprising 1D metal chain (MnO(CO{sub 2}){sub 2}){sub n} connected by the ligand nda{sup 2−}, featuring a four-connected uninodal diamond -like topology. In compound 2, it is firstly observed that decanuclear silver units as secondary building units to constructmore » 3D network by the ligands dmt and nda{sup 2−}, with a rare 2-nodal (3,8)-connected tfz-d topology ((4{sup 3}){sub 2}(4{sup 6}.6{sup 18}.8{sup 4})). The interactions within each Mn(II)—Mn(II) pair of compound 1 are antiferromagnetic (g=2.07, J=−1.42(1) cm{sup −1}, zj′=−0.73(2) cm{sup −1}). In addition, compound 2 exhibits photoluminescent property at about 472 nm (λ{sub ex}=394 nm). - Graphical abstract: Two new transition metal coordination complexes 1–2 have been hydrothermally synthesized and characterized by single-crystal X-ray diffraction, IR spectra, elemental analysis thermogravimetric analysis (TGA). Highlights: • The compound 1 exhibits a 3D network with four-connected uninodal diamond-like topology. • The first 3D network of 2 with a rare tfz-d topology consists of decanuclear silver clusters as secondary building units. • The magnetic measurement indicates the compound 1 shows antiferromagnetic interactions. • The photoluminescent property of 2 has been measured.« less

  8. Synthesis, crystal structures, quantum chemical studies and corrosion inhibition potentials of 4-(((4-ethylphenyl)imino)methyl)phenol and (E)-4-((naphthalen-2-ylimino) methyl) phenol Schiff bases

    NASA Astrophysics Data System (ADS)

    Elemike, Elias E.; Nwankwo, Henry U.; Onwudiwe, Damian C.; Hosten, Eric C.

    2017-11-01

    Two Schiff base ligands, 4-(((4-ethylphenyl)imino)methyl)phenol (4EMP) and (E)-4-((naphthalen-2-ylimino) methyl) phenol (4NMP) were synthesized by the reaction of 4-hydroxybenzaldehyde with 4-ethylaniline, 4EMP, or naphthalene-2-amine, 4NMP. The compounds were characterized using NMR (1H and 13C), Fourier transform infra-red (FTIR) and mass spectroscopic techniques. The proton NMR identified the OH peaks at 9.73 and 9.77 ppm for 4EMP and 4NMP respectively, while the 13C NMR showed the imine carbons at 172.57 ppm for 4EMP and at 160.89 ppm for 4NMP. The FTIR spectra showed characteristic peaks at 1605 cm-1 (4EMP) and 1600 cm-1 (4NMP) typical of the azomethine group, and the mass spectra results gave molecular ion peaks of 226.12 and 248.10 respectively. The structures of the compounds were further established by single crystal X-ray analysis. The corrosion inhibition potential of the compounds were studied on mild steel surface in a 1 M hydrochloric acid (HCl) solution, and was analysed using potentiodynamic polarization (PDP) and electrochemical impedance spectroscopy (EIS). The results of the electrochemical methods showed that the studied molecules imparted high resistance in allowing flow of electrons across the metal-electrolyte platform and behaved as mixed type inhibitors with 4EMP showing better inhibition properties than 4NMP. Scanning electron microscopy (SEM) showed the formation of film on the mild steel surface. Quantum chemical calculations achieved by density functional theory (DFT) was further applied to explain the adsorption as well as inhibition abilities of the molecules on the mild steel surface. Thermodynamics studies showed that the two compounds obeyed the Langmuir isotherm with 4EMP conforming to chemisorption mechanism while 4NMP involved competitive physisorption and chemisorption mechanism.

  9. What Is the Structure of the Naphthalene-Benzene Heterodimer Radical Cation? Binding Energy, Charge Delocalization, and Unexpected Charge-Transfer Interaction in Stacked Dimer and Trimer Radical Cations.

    PubMed

    Attah, Isaac K; Platt, Sean P; Meot-Ner Mautner, Michael; El-Shall, M Samy; Peverati, Roberto; Head-Gordon, Martin

    2015-04-02

    The binding energy of the naphthalene(+•)(benzene) heterodimer cation has been determined to be 7.9 ± 1 kcal/mol for C10H8(+•)(C6H6) and 8.1 ± 1 kcal/mol for C10H8(+•)(C6D6) by equilibrium thermochemical measurements using the mass-selected drift cell technique. A second benzene molecule binds to the C10H8(+•)(C6D6) dimer with essentially the same energy (8.4 ± 1 kcal/mol), suggesting that the two benzene molecules are stacked on opposite sides of the naphthalene cation in the (C6D6)C10H8(+•)(C6D6) heterotrimer. The lowest-energy isomers of the C10H8(+•)(C6D6) and (C6D6)C10H8(+•)(C6D6) dimer and trimer calculated using the M11/cc-pVTZ method have parallel stacked structures with enthalpies of binding (-ΔH°) of 8.4 and 9.0 kcal/mol, respectively, in excellent agreement with the experimental values. The stacked face-to-face class of isomers is calculated to have substantial charge-transfer stabilization of about 45% of the total interaction energy despite the large difference between the ionization energies of benzene and naphthalene. Similarly, significant delocalization of the positive charge is found among all three fragments of the (C6D6)C10H8(+•)(C6D6) heterotrimer, thus leaving only 46% of the total charge on the central naphthalene moiety. This unexpectedly high charge-transfer component results in activating two benzene molecules in the naphthalene(+•)(benzene)2 heterotrimer cation to associate with a third benzene molecule at 219 K to form a benzene trimer cation and a neutral naphthalene molecule. The global minimum of the C10H8(+•)(C6H6)2 heterotrimer is found to be the one where the naphthalene cation is sandwiched between two benzene molecules. It is remarkable, and rather unusual, that the binding energy of the second benzene molecule is essentially the same as that of the first. This is attributed to the enhanced charge-transfer interaction in the stacked trimer radical cation.

  10. Ligand placement based on prior structures: the guided ligand-replacement method

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

    Klei, Herbert E.; Bristol-Myers Squibb, Princeton, NJ 08543-4000; Moriarty, Nigel W., E-mail: nwmoriarty@lbl.gov

    2014-01-01

    A new module, Guided Ligand Replacement (GLR), has been developed in Phenix to increase the ease and success rate of ligand placement when prior protein-ligand complexes are available. The process of iterative structure-based drug design involves the X-ray crystal structure determination of upwards of 100 ligands with the same general scaffold (i.e. chemotype) complexed with very similar, if not identical, protein targets. In conjunction with insights from computational models and assays, this collection of crystal structures is analyzed to improve potency, to achieve better selectivity and to reduce liabilities such as absorption, distribution, metabolism, excretion and toxicology. Current methods formore » modeling ligands into electron-density maps typically do not utilize information on how similar ligands bound in related structures. Even if the electron density is of sufficient quality and resolution to allow de novo placement, the process can take considerable time as the size, complexity and torsional degrees of freedom of the ligands increase. A new module, Guided Ligand Replacement (GLR), was developed in Phenix to increase the ease and success rate of ligand placement when prior protein–ligand complexes are available. At the heart of GLR is an algorithm based on graph theory that associates atoms in the target ligand with analogous atoms in the reference ligand. Based on this correspondence, a set of coordinates is generated for the target ligand. GLR is especially useful in two situations: (i) modeling a series of large, flexible, complicated or macrocyclic ligands in successive structures and (ii) modeling ligands as part of a refinement pipeline that can automatically select a reference structure. Even in those cases for which no reference structure is available, if there are multiple copies of the bound ligand per asymmetric unit GLR offers an efficient way to complete the model after the first ligand has been placed. In all of these applications

  11. Accumulation of 14C-naphthalene in the tissues of redhead ducks fed oil-contaminated crayfish

    USGS Publications Warehouse

    Tarshis, I.B.; Rattner, B.A.

    1982-01-01

    Crayfish, artificially contaminated with14C-naphthalene-5% water-soluble fraction of No. 2 fuel oil, were force-fed to one-year-old redhead ducks to determine the accumulation of petroleum hydrocarbons. The relative distribution of carbon-14 activity in the gall bladder containing bile, and fat were similar, and significantly greater (P < 0.05) than the activity in the blood, brain, liver, and kidney. There was a significant increase (P < 0.05) in the disintegrations per minute per gram (dpm/g) in the blood, brain, kidney, and liver between days 1 and 3 of feeding, indicating a progressive accumulation of carbon-14 activity (naphthalene and presumably its metabolites). There was no significant effect of sex or the interaction of the duration of feeding and sex on carbon-14 activity in any of the tissues. The low daily dose of petroleum hydrocarbons (a total of approximately 1.25 mg/day) received by the ducks from the crayfish and the relatively short feeding regimen did not cause any overt signs of toxicity in the ducks.

  12. Human health risk constrained naphthalene-contaminated groundwater remediation management through an improved credibility method.

    PubMed

    Li, Jing; Lu, Hongwei; Fan, Xing; Chen, Yizhong

    2017-07-01

    In this study, a human health risk constrained groundwater remediation management program based on the improved credibility is developed for naphthalene contamination. The program integrates simulation, multivariate regression analysis, health risk assessment, uncertainty analysis, and nonlinear optimization into a general framework. The improved credibility-based optimization model for groundwater remediation management with consideration of human health risk (ICOM-HHR) is capable of not only effectively addressing parameter uncertainties and risk-exceeding possibility in human health risk but also providing a credibility level that indicates the satisfaction of the optimal groundwater remediation strategies with multiple contributions of possibility and necessity. The capabilities and effectiveness of ICOM-HHR are illustrated through a real-world case study in Anhui Province, China. Results indicate that the ICOM-HHR would generate double remediation cost yet reduce approximately 10 times of the naphthalene concentrations at monitoring wells, i.e., mostly less than 1 μg/L, which implies that the ICOM-HHR usually results in better environmental and health risk benefits. And it is acceptable to obtain a better environmental quality and a lower health risk level with sacrificing a certain economic benefit.

  13. Copper and manganese complexes based on 1,4-naphthalene dicarboxylic acid ligand and its derivative: Syntheses, crystal structures, and magnetic properties

    NASA Astrophysics Data System (ADS)

    Xing, Yubo; Liu, Yuqi; Xue, Xiaofei; Wang, Xinying; Li, Wei

    2018-02-01

    Three new metal-organic coordination polymers, {[Mn2(1,4-NDC)2 (C2H5OH) (DMF) (H2O)]·CH3OH}n(1), {[Mn(III)(1,4-NDC)(C2H5O)][Mn(II)(1,4-NDC)(DMF)(H2O)]}n(2) and {[Cu2(C13H9O4)4(H2O)2]}n(3) based on1,4-H2NDC and its derivative were hydrothermally synthesized (1,4-H2NDC = 1,4-naphthalene-dicarboxylic acid, C13H10O4 = 4-methyl formate-1-naphthalenecarboxylic acid), and characterized by techniques of single crystal X-ray diffraction, infrared spectra (IR), elemental analysis, powder X-ray diffraction(PXRD) and variable-temperature magnetic susceptibility measurements. X-ray crystal structure analyses reveal that complexes 1 and 2 show a same 3,5-connected fsc 3D topology network with the Schlȁfli symbol of {4·6·8}{4·66·83}. But, the valence of some Mn atom in complex 2 take place transition from the +II oxidation state to the +III oxidation state, which may be the effect of the different solvent ratio. In complex 3, the Cu⋯Cu distance of 2.620(13) Å is significantly shorter than the sum of the van der Waals radii of Cu (1.40 Å), resulting in a strong ferromagnetic interaction between the Cu(II) centers. Furthermore, the temperature-dependent magnetic susceptibility measurements exhibit overall antiferromagnetic interactions between manganese ions for complexes 1 and 2, and a strong ferromagnetic interaction between the Cu(II) centers for complex 3.

  14. Final Report from the External Peer Review of the IRIS Reassessment of the Inhalation Carcinogenicity of Naphthalene

    EPA Science Inventory

    This document is the final report for the 2004 external peer review for the EPA IRIS Reassessment of the Inhalation Carcinogenicity of Naphthalene, prepared by the Office of Research and Development's National Center for Environmental Assessment (NCEA), for the Integrated ...

  15. Mechanical and kinetic study on gas-phase formation of dinitro-naphthalene from 1- and 2-nitronaphthalene.

    PubMed

    Huang, Zixiao; Zhang, Qingzhu; Wang, Wenxing

    2016-08-01

    Nitrated polycyclic aromatic hydrocarbons have received an increasing number of considerations because of their higher mutagens than parent PAHs. In this paper, the formation of dinitro-naphthalene was investigated mechanistically using 1- and 2-nitronaphthalene as precursors with the aid of high-accuracy quantum chemistry calculation. The geometrical parameters, as well as vibrational frequencies, were calculated at the BB1K/6-31+G(d,p) level. Water molecule plays an important role in the formation of dinitro-naphthalene. The rate constants were deduced by canonical variational transition-state theory with small curvature tunneling contribution over the temperature range of 273-333 K. Meanwhile, the Arrhenius formulas were fitted for the OH addition of both 1- and 2-nitronaphthalene. The calculated overall rate constants for 1-nitronaphthalene and 2-nitronaphthalene at 298 K and 1 atm are 7.43 × 10(-13) and 7.48 × 10(-13) cm(3) molecule(-1) s(-1), respectively. The rate constants of NO3 addition to 1-nitronaphthalene and 2-nitronaphthalene by RRKM method at 298 K and 1 atm are 3.55 × 10(-15) and 3.47 × 10(-15) cm(3) molecule(-1) s(-1), respectively. This study provides a comprehensive investigation of the formation process of dinitro-naphthalenes, initiated by OH and NO3 radicals and should facilitate to illuminate its atmospheric source. Oxygen may probably be competitive with the second NO2 addition step when the concentration of NO2 is at low level. Copyright © 2016. Published by Elsevier Ltd.

  16. Spectral Dissimilarities Between AZULENE(C10H_8) and NAPHTHALENE(C10H_8)

    NASA Astrophysics Data System (ADS)

    Baba, Masaaki

    2010-06-01

    Polycyclic aromatic hydrocarbons (PAHs) are of great interest in the molecular structure and excited-state dynamics, and there have been extensive spectroscopic and theoretical studies. Azulene and naphthalene are bicyclic aromatic hydrocarbons composed of odd- and even-membered rings, respectively. First, they were discriminated by a theory of mutual polarizability. Naphthalene is an alternant hydrocarbon, but azulene is not. In contrast, spectral resemblances were found by John Platt et al., and were explained by their simple model of molecular orbital. However, the absorption and emission feature of the S_1 and S_2 states is completely different each other. We have investigated each rotational and vibrational structures, and radiative and nonradiative processes by means of high-resolution spectroscopy and ab initio calculation. The equilibrium structures in the S_0, S_1, and S_2 states are similar. This small structural change upon electronic excitation is common to PAH molecules composed of six-membered rings. The fluorescence quantum yield is high because radiationless transitions such as intersystem crossing (ISC) to the triplet state and internal conversion (IC) to the S_0 state are very slow in the S_1 state. In contrast, the S_1 state of azulene is nonfluorescent and the S_1 ← S_0 excitation energy is abnormally small. We consider that the potential energy curve of a b_2 vibration is shallower in the S_1 state, and therefore the vibronic coupling with the S_0 state is strong to enhance the IC process remarkably. This situation is, of course, due to its peculiar characteristics of odd-membered rings and molecular symmetry, which are completely different from the naphthalene molecule. C. A. Coulson and H. C. Longuet-Higgins, Proc. Roy. Soc. A, 191, 39 (1947) D. E. Mann, J. R. Platt, and H. B. Klevens, J. Chem. Phys., 17, 481 (1949) Y. Semba, M. Baba, et al., J. Chem. Phys., 131, 024303 (2009) K. Yoshida, M. Baba, et al., J. Chem. Phys., 130, 194304 (2009)

  17. Chemical and cellular oxidant production induced by naphthalene secondary organic aerosol (SOA): effect of redox-active metals and photochemical aging.

    PubMed

    Tuet, Wing Y; Chen, Yunle; Fok, Shierly; Gao, Dong; Weber, Rodney J; Champion, Julie A; Ng, Nga L

    2017-11-09

    Exposure to air pollution is a leading global health risk. Secondary organic aerosol (SOA) constitute a large portion of ambient particulate matter (PM). In this study, the water-soluble oxidative potential (OP) determined by dithiothreitol (DTT) consumption and intracellular reactive oxygen and nitrogen species (ROS/RNS) production was measured for SOA generated from the photooxidation of naphthalene in the presence of iron sulfate and ammonium sulfate seed particles. The measured intrinsic OP varied for aerosol formed using different initial naphthalene concentrations, however, no trends were observed between OP and bulk aerosol composition or seed type. For all experiments, aerosol generated in the presence of iron-containing seed induced higher ROS/RNS production compared to that formed in the presence of inorganic seed. This effect was primarily attributed to differences in aerosol carbon oxidation state [Formula: see text]. In the presence of iron, radical concentrations are elevated via iron redox cycling, resulting in more oxidized species. An exponential trend was also observed between ROS/RNS and [Formula: see text] for all naphthalene SOA, regardless of seed type or aerosol formation condition. This may have important implications as aerosol have an atmospheric lifetime of a week, over which [Formula: see text] increases due to continued photochemical aging, potentially resulting in more toxic aerosol.

  18. Solvothermal syntheses, structures, and magnetic properties of three cobalt coordination polymers constructed from naphthalene-1,4-dicarboxylic acid and bis(imidazole) linkers

    NASA Astrophysics Data System (ADS)

    Dong, Jun-Liang; He, Kun-Huan; Wang, Duo-Zhi; Zhang, Ying-Hui; Wang, Dan-Hong

    2018-07-01

    Three new Co(II) coordination polymers with formulas of {[Co2(L1)(1,4-NDC)2]·3H2O}n (1), [Co3(L2)2(HCOO)2(1,4-NDC)2]n (2) and [Co2(L2)(μ3-OH)(1,4-NDC)1.5]n (3) (1,4-H2NDC = Naphthalene-1,4-dicarboxylic acid, L1 = di(1H-imidazol-1-yl)methane, L2 = 1,4-di(1H-imidazol-1-yl)benzene) were solvothermal synthesized from 1,4-H2NDC with the aid of three different length-controllable auxiliary ligands and fully characterized. Their structures are determined by single-crystal X-ray diffraction, IR spectra, elemental analysis, powder X-ray diffraction and thermogravimetric analysis. Complexes 1 and 3 display 3D framework structures, corresponding to a 6-connected (412·63) net, a 8-connected (424·5·63) net, respectively. However, it is noteworthy that the complex 1 displays a 2-fold interpenetrating framework structure, complex 3 possesses a self-interpenetrating framework structure. Complex 2 displays 2D 4-connected undulating plane net structure. Moreover, magnetic studies indicate antiferromagnetic interactions between the Co(II) ions in the four complexes.

  19. Urinary naphthalene and phenanthrene as biomarkers of occupational exposure to polycyclic aromatic hydrocarbons

    PubMed Central

    Sobus, Jon R.; Waidyanatha, Suramya; McClean, Michael D.; Herrick, Robert F.; Smith, Thomas J.; Garshick, Eric; Laden, Francine; Hart, Jaime E.; Zheng, Yuxin; Rappaport, Stephen M.

    2009-01-01

    Objectives We investigated the utility of unmetabolized naphthalene (Nap) and phenanthrene (Phe) in urine as surrogates for exposures to mixtures of polycyclic aromatic hydrocarbons (PAHs). Methods Our study included workers exposed to diesel exhausts (low PAH exposure level, n = 39) as well as those exposed to emissions from asphalt (medium PAH exposure level, n = 26) and coke ovens (high PAH exposure level, n = 28). Levels of Nap and Phe were measured in urine from each subject using head space-solid phase microextraction and gas chromatography-mass spectrometry. Published levels of airborne Nap, Phe, and other PAHs in the coke-producing and aluminum industries were also investigated. Results In post-shift urine, the highest estimated geometric mean concentrations of Nap and Phe were observed in coke-oven workers (Nap: 2,490 ng/l; Phe: 975 ng/l), followed by asphalt workers (Nap: 71.5 ng/l; Phe: 54.3 ng/l), and by diesel-exposed workers (Nap: 17.7 ng/l; Phe: 3.60 ng/l). After subtracting logged background levels of Nap and Phe from the logged post-shift levels of these PAHs in urine, the resulting values [referred to as ln(adjNap) and ln(adjPhe), respectively] were significantly correlated in each group of workers (0.71 ≤ Pearson r ≤ 0.89), suggesting a common exposure source in each case. Surprisingly, multiple linear regression analysis of ln(adjNap) on ln(adjPhe) showed no significant effect of the source of exposure (coke ovens, asphalt, and diesel exhaust) and further suggested that the ratio of urinary Nap/Phe (in natural scale) decreased with increasing exposure levels. These results were corroborated with published data for airborne Nap and Phe in the coke-producing and aluminum industries. The published air measurements also indicated that Nap and Phe levels were proportional to the levels of all combined PAHs in those industries. Conclusion Levels of Nap and Phe in urine reflect airborne exposures to these compounds and are promising surrogates for

  20. Doping effect of nano-Ho{sub 2}O{sub 3} and naphthalene in MgB{sub 2} superconductor prepared by powder-in-sealed-tube method

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

    Hansdah, J. S.; Sarun, P. M., E-mail: sarun.res@gmail.com

    2015-03-21

    The effect on crystal structure, critical temperature (T{sub C}), and critical current density (J{sub C}) of bulk MgB{sub 2} doped with nano-Ho{sub 2}O{sub 3} and naphthalene was studied. Among all the samples studied, the sample doped with 2.5 wt. % nano-Ho{sub 2}O{sub 3} have shown the best field dependent critical current density [J{sub C}(H)], i.e., 0.77 × 10{sup 5 }A/cm{sup 2} at 2 T and 10 K. While naphthalene doped MgB{sub 2} sample has shown the least J{sub C}(H) characteristics. The improved J{sub C}(H) characteristics in the nano-Ho{sub 2}O{sub 3} doped MgB{sub 2} samples are attributed to improved flux pinning properties due to the formation ofmore » HoB{sub 4} and in naphthalene doped MgB{sub 2} samples. The slight lower T{sub C} value (37.01 K) in naphthalene doped samples is attributed to the occurrence of lattice defect by the substitution of carbon at boron site of MgB{sub 2} superconductor. Lower ΔT{sub C} value implies the lesser anisotropy in all the synthesized samples. The flux pinning force density (F{sub P}/F{sub Pmax}) curves are theoretically analyzed using Dew-Hughes model. The result revealed that point pinning is the dominant pinning mechanism for nano-Ho{sub 2}O{sub 3} doped MgB{sub 2} samples, while, surface and grain boundary pinning become dominant with increasing naphthalene addition in nano-Ho{sub 2}O{sub 3} doped MgB{sub 2} samples.« less

  1. Investigating the 3.3 micron infrared fluorescence from naphthalene following ultraviolet excitation

    NASA Technical Reports Server (NTRS)

    Williams, Richard M.; Leone, Stephen R.

    1994-01-01

    Polycyclic aromatic hydrocarbon (PAH) type molecules are proposed as the carriers of the unidentified infrared (UIR) bands. Detailed studies of the 3.3 micrometer infrared emission features from naphthalene, the simplest PAH, following ultraviolet laser excitation are used in the interpretation of the 3.29 micrometer (3040 cm(sup -1)) UIR band. A time-resolved Fourier transform spectrometer is used to record the infrared emission spectrum of gas-phase naphthalene subsequent to ultraviolet excitation facilitated by an excimer laser operated at either 193 nm or 248 nm. The emission spectra differ significantly from the absorption spectrum in the same spectral region. Following 193 nm excitation the maximum in the emission profile is red-shifted 45 cm(sup -1) relative to the absorption maximum; a 25 cm(sup -1) red-shift is observed after 248 nm excitation. The red-shifting of the emission spectrum is reduced as collisional and radiative relaxation removes energy from the highly vibrationally excited molecules. Coupling between the various vibrational modes is thought to account for the differences between absorption and emission spectra. Strong visible emission is also observed following ultraviolet excitation. Visible emission may play an important role in the rate of radiative relaxation, which according to the interstellar PAH hypothesis occurs only by the slow emission of infrared photons. Studying the visible emission properties of PAH type molecules may be useful in the interpretation of the DIB's observed in absorption.

  2. Two novel mixed-ligand complexes containing organosulfonate ligands.

    PubMed

    Li, Mingtian; Huang, Jun; Zhou, Xuan; Fang, Hua; Ding, Liyun

    2008-07-01

    The structures reported herein, viz. bis(4-aminonaphthalene-1-sulfonato-kappaO)bis(4,5-diazafluoren-9-one-kappa(2)N,N')copper(II), [Cu(C(10)H(8)NO(3)S)(2)(C(11)H(6)N(2)O)(2)], (I), and poly[[[diaquacadmium(II)]-bis(mu-4-aminonaphthalene-1-sulfonato)-kappa(2)O:N;kappa(2)N:O] dihydrate], {[Cd(C(10)H(8)NO(3)S)(2)(H(2)O)(2)].2H(2)O}(n), (II), are rare examples of sulfonate-containing complexes where the anion does not fulfill a passive charge-balancing role, but takes an active part in coordination as a monodentate and/or bridging ligand. Monomeric complex (I) possesses a crystallographic inversion center at the Cu(II) atom, and the asymmetric unit contains one-half of a Cu atom, one complete 4-aminonaphthalene-1-sulfonate (ans) ligand and one 4,5-diazafluoren-9-one (DAFO) ligand. The Cu(II) atom has an elongated distorted octahedral coordination geometry formed by two O atoms from two monodentate ans ligands and by four N atoms from two DAFO molecules. Complex (II) is polymeric and its crystal structure is built up by one-dimensional chains and solvent water molecules. Here also the cation (a Cd(II) atom) lies on a crystallographic inversion center and adopts a slightly distorted octahedral geometry. Each ans anion serves as a bridging ligand linking two Cd(II) atoms into one-dimensional infinite chains along the [010] direction, with each Cd(II) center coordinated by four ans ligands via O and N atoms and by two aqua ligands. In both structures, there are significant pi-pi stacking interactions between adjacent ligands and hydrogen bonds contribute to the formation of two- and three-dimensional networks.

  3. Impairment of Fas-ligand-caveolin-1 interaction inhibits Fas-ligand translocation to rafts and Fas-ligand-induced cell death.

    PubMed

    Glukhova, Xenia A; Trizna, Julia A; Proussakova, Olga V; Gogvadze, Vladimir; Beletsky, Igor P

    2018-01-22

    Fas-ligand/CD178 belongs to the TNF family proteins and can induce apoptosis through death receptor Fas/CD95. The important requirement for Fas-ligand-dependent cell death induction is its localization to rafts, cholesterol- and sphingolipid-enriched micro-domains of membrane, involved in regulation of different signaling complexes. Here, we demonstrate that Fas-ligand physically associates with caveolin-1, the main protein component of rafts. Experiments with cells overexpressing Fas-ligand revealed a FasL N-terminal pre-prolin-rich region, which is essential for the association with caveolin-1. We found that the N-terminal domain of Fas-ligand bears two caveolin-binding sites. The first caveolin-binding site binds the N-terminal domain of caveolin-1, whereas the second one appears to interact with the C-terminal domain of caveolin-1. The deletion of both caveolin-binding sites in Fas-ligand impairs its distribution between cellular membranes, and attenuates a Fas-ligand-induced cytotoxicity. These results demonstrate that the interaction of Fas-ligand and caveolin-1 represents a molecular basis for Fas-ligand translocation to rafts, and the subsequent induction of Fas-ligand-dependent cell death. A possibility of a similar association between other TNF family members and caveolin-1 is discussed.

  4. Mechanism of 1,4,5,8-naphthalene tetracarboxylic acid dianhydride hydrolysis and formation in aqueous solution.

    PubMed

    Barros, T C; Cuccovia, I M; Farah, J P S; Masini, J C; Chaimovich, H; Politi, M J

    2006-01-07

    The study of highly conjugated, carbonyl-containing molecules such as 1,4,5,8-naphthalene tetracarboxylic dianhydride, III, is of interest since reactivity differences and transmission of electronic effects through the conjugated framework can be evidenced. The kinetics of hydrolysis of III in aqueous solution were determined from 5 M acid to pH 10. In basic solution hydrolysis of III yields, sequentially, 1,4,5,8-naphthalene diacid monoanhydride, II, and 1,4,5,8-naphthalene tetracarboxylic acid, I. The second order rate constant for alkaline hydrolysis is 200 fold higher for the first ring opening. The water-catalyzed hydrolysis of III yields a pH-dependent mixture of ionic forms of I and II. The rate constant for water-catalyzed hydrolysis of III is 25 fold higher than that for II. In concentrated acid the rates for reaching equilibrium (I, II and III) increase and III is the major product. The pK(a)s of I (3.24, 5.13 and 6.25) and II (3.05, 5.90) were determined by potentiometric, fluorescence and UV spectroscopy titrations and by quantitative fit of the kinetic and equilibrium data. The apparent, pH-dependent, equilibrium constants, K(EqII), for anhydride formation between I and II were obtained from the UV spectra. The quantitative fit of kinetic and equilibrium data are consistent with the assumption that anhydride formation only proceeds with the fully protonated species for both I and II and permitted the estimation of the equilibrium constants for anhydride formation, K(EqII). The value of K(EqII) (I <==> II) between pH 1 and 6 was ca. 5. Geometry optimization calculations in the gas phase of the reactions of III in alkaline, neutral and acid conditions, at the DFT level of theory, gave electronic distributions that were qualitatively consistent with the experimental results.

  5. AutoSite: an automated approach for pseudo-ligands prediction—from ligand-binding sites identification to predicting key ligand atoms

    PubMed Central

    Ravindranath, Pradeep Anand; Sanner, Michel F.

    2016-01-01

    Motivation: The identification of ligand-binding sites from a protein structure facilitates computational drug design and optimization, and protein function assignment. We introduce AutoSite: an efficient software tool for identifying ligand-binding sites and predicting pseudo ligand corresponding to each binding site identified. Binding sites are reported as clusters of 3D points called fills in which every point is labelled as hydrophobic or as hydrogen bond donor or acceptor. From these fills AutoSite derives feature points: a set of putative positions of hydrophobic-, and hydrogen-bond forming ligand atoms. Results: We show that AutoSite identifies ligand-binding sites with higher accuracy than other leading methods, and produces fills that better matches the ligand shape and properties, than the fills obtained with a software program with similar capabilities, AutoLigand. In addition, we demonstrate that for the Astex Diverse Set, the feature points identify 79% of hydrophobic ligand atoms, and 81% and 62% of the hydrogen acceptor and donor hydrogen ligand atoms interacting with the receptor, and predict 81.2% of water molecules mediating interactions between ligand and receptor. Finally, we illustrate potential uses of the predicted feature points in the context of lead optimization in drug discovery projects. Availability and Implementation: http://adfr.scripps.edu/AutoDockFR/autosite.html Contact: sanner@scripps.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27354702

  6. Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand

    PubMed Central

    DeLuca, Samuel; Khar, Karen; Meiler, Jens

    2015-01-01

    RosettaLigand has been successfully used to predict binding poses in protein-small molecule complexes. However, the RosettaLigand docking protocol is comparatively slow in identifying an initial starting pose for the small molecule (ligand) making it unfeasible for use in virtual High Throughput Screening (vHTS). To overcome this limitation, we developed a new sampling approach for placing the ligand in the protein binding site during the initial ‘low-resolution’ docking step. It combines the translational and rotational adjustments to the ligand pose in a single transformation step. The new algorithm is both more accurate and more time-efficient. The docking success rate is improved by 10–15% in a benchmark set of 43 protein/ligand complexes, reducing the number of models that typically need to be generated from 1000 to 150. The average time to generate a model is reduced from 50 seconds to 10 seconds. As a result we observe an effective 30-fold speed increase, making RosettaLigand appropriate for docking medium sized ligand libraries. We demonstrate that this improved initial placement of the ligand is critical for successful prediction of an accurate binding position in the ‘high-resolution’ full atom refinement step. PMID:26207742

  7. Ligand Depot: a data warehouse for ligands bound to macromolecules.

    PubMed

    Feng, Zukang; Chen, Li; Maddula, Himabindu; Akcan, Ozgur; Oughtred, Rose; Berman, Helen M; Westbrook, John

    2004-09-01

    Ligand Depot is an integrated data resource for finding information about small molecules bound to proteins and nucleic acids. The initial release (version 1.0, November, 2003) focuses on providing chemical and structural information for small molecules found as part of the structures deposited in the Protein Data Bank. Ligand Depot accepts keyword-based queries and also provides a graphical interface for performing chemical substructure searches. A wide variety of web resources that contain information on small molecules may also be accessed through Ligand Depot. Ligand Depot is available at http://ligand-depot.rutgers.edu/. Version 1.0 supports multiple operating systems including Windows, Unix, Linux and the Macintosh operating system. The current drawing tool works in Internet Explorer, Netscape and Mozilla on Windows, Unix and Linux.

  8. Spectroscopic investigation of oxygen- and water-induced electron trapping and charge transport instabilities in n-type polymer semiconductors.

    PubMed

    Di Pietro, Riccardo; Fazzi, Daniele; Kehoe, Tom B; Sirringhaus, Henning

    2012-09-12

    We present an optical spectroscopy study on the role of oxygen and water in electron trapping and storage/bias-stress degradation of n-type polymer field-effect transistors based on one of the most widely studied electron transporting conjugated polymers, poly{[N,N9-bis(2-octyldodecyl)-naphthalene-1,4,5,8-bis(dicarboximide)-2,6-diyl]-alt-5,59-(2,29-bisthiophene)} (P(NDI2OD-T2)). We combine results obtained from charge accumulation spectroscopy, which allow optical quantification of the concentration of mobile and trapped charges in the polymer film, with electrical characterization of P(NDI2OD-T2) organic field-effect transistors to study the mechanism for storage and bias-stress degradation upon exposure to dry air/oxygen and humid nitrogen/water environments, thus separating the effect of the two molecules and determining the nature of their interaction with the polymer. We find that the stability upon oxygen exposure is limited by an interaction between the neutral polymer and molecular oxygen leading to a reduction in electron mobility in the bulk of the semiconductor. We use density functional theory quantum chemical calculations to ascribe the drop in mobility to the formation of a shallow, localized, oxygen-induced trap level, 0.34 eV below the delocalized lowest unoccupied molecular orbital of P(NDI2OD-T2). In contrast, the stability of the polymer anion against water is limited by two competing reactions, one involving the electrochemical oxidation of the polymer anion by water without degradation of the polymer and the other involving a radical anion-catalyzed chemical reaction of the polymer with water, in which the electron can be recycled and lead to further degradation reactions, such that a significant portion of the film is degraded after prolonged bias stressing. Using Raman spectroscopy, we have been able to ascribe this to a chemical interaction of water with the naphthalene diimide unit of the polymer. The degradation mechanisms identified here

  9. Near-IR core-substituted naphthalenediimide fluorescent chemosensors for zinc ions: ligand effects on PET and ICT channels.

    PubMed

    Lu, Xinyu; Zhu, Weihong; Xie, Yongshu; Li, Xin; Gao, Yuan; Li, Fuyou; Tian, He

    2010-07-26

    Near-IR (NIR) emission can offer distinct advantages for both in vitro and in vivo biological applications. Two NIR fluorescent turn-on sensors N,N'-di-n-butyl-2-(N-{2-[bis(pyridin-2-ylmethyl)amino]ethyl})-6-(N-piperidinyl)naphthalene-1,4,5,8-tetracarboxylic acid bisimide and N,N'-di- n-butyl-2-[N,N,N'-tri(pyridin-2-ylmethyl)amino]ethyl-6-(N-piperidinyl)naphthalene-1,4,5,8-tetracarboxylic acid bisimide (PND and PNT) for Zn(2+) based on naphthalenediimide fluorophore are reported. Our strategy was to choose core-substituted naphthalenediimide (NDI) as a novel NIR fluorophore and N,N-di(pyridin-2-ylmethyl)ethane-1,2-diamine (DPEA) or N,N,N'-tri(pyridin-2-ylmethyl)ethane-1,2-diamine (TPEA) as the receptor, respectively, so as to improve the selectivity to Zn(2+). In the case of PND, the negligible shift in absorption and emission spectra is strongly suggestive that the secondary nitrogen atom (directly connected to the NDI moiety, N(1)) is little disturbed with Zn(2+). The fluorescence enhancement of PND with Zn(2+) titration is dominated with a typical photoinduced electron-transfer (PET) process. In contrast, the N(1) atom for PNT can participate in the coordination of Zn(2+) ion, diminishing the electron delocalization of the NDI moiety and resulting in intramolecular charge-transfer (ICT) disturbance. For PNT, the distinct blueshift in both absorbance and fluorescence is indicative of a combination of PET and ICT processes, which unexpectedly decreases the sensitivity to Zn(2+). Due to the differential binding mode caused by the ligand effect, PND shows excellent selectivity to Zn(2+) over other metal ions, with a larger fluorescent enhancement centered at 650 nm. Also both PND and PNT were successfully used to image intracellular Zn(2+) ions in the living KB cells.

  10. 2,4-Dinitrotoluene dioxygenase from Burkholderia sp. strain DNT: similarity to naphthalene dioxygenase.

    PubMed Central

    Suen, W C; Haigler, B E; Spain, J C

    1996-01-01

    2,4-Dinitrotoluene (DNT) dioxygenase from Burkholderia sp. strain DNT catalyzes the initial oxidation of DNT to form 4-methyl-5-nitrocatechol (MNC) and nitrite. The displacement of the aromatic nitro group by dioxygenases has only recently been described, and nothing is known about the evolutionary origin of the enzyme systems that catalyze these reactions. We have shown previously that the gene encoding DNT dioxygenase is localized on a degradative plasmid within a 6.8-kb NsiI DNA fragment (W.-C. Suen and J. C. Spain, J. Bacteriol. 175:1831-1837, 1993). We describe here the sequence analysis and the substrate range of the enzyme system encoded by this fragment. Five open reading frames were identified, four of which have a high degree of similarity (59 to 78% identity) to the components of naphthalene dioxygenase (NDO) from Pseudomonas strains. The conserved amino acid residues within NDO that are involved in cofactor binding were also identified in the gene encoding DNT dioxygenase. An Escherichia coli clone that expressed DNT dioxygenase converted DNT to MNC and also converted naphthalene to (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. In contrast, the E. coli clone that expressed NDO did not oxidize DNT. Furthermore, the enzyme systems exhibit similar broad substrate specificities and can oxidize such compounds as indole, indan, indene, phenetole, and acenaphthene. These results suggest that DNT dioxygenase and the NDO enzyme system share a common ancestor. PMID:8759857

  11. Synthesis, photophysical properties, and computational studies of four-coordinate copper(I) complexes based on benzimidazolylidene N-heterocyclic carbene (NHC) ligands bearing aryl substituents

    NASA Astrophysics Data System (ADS)

    Xu, Shengxian; Wang, Jinglan; Liu, Shaobo; Zhao, Feng; Xia, Hongying; Wang, Yibo

    2018-02-01

    Three four-coordinate N-heterocyclic carbene (NHC) copper(I) complexes, [Cu(Ph-BenIm-Py)(POP)]PF6 (1), [Cu(Naph-BenIm-Py)(POP)]PF6 (2), and [Cu(Anthr-BenIm-Py)(POP)]PF6 (3) (Ph-BenIm-Py = 3-benzyl-1-(pyridin-2-yl)-1H-benzimidazolylidene, Naph-BenIm-Py = 3-(naphthalen-2-yl-1-(pyridin-2-yl)-1H- benzimidazolylidene, Anthr-BenIm-Py = 3-(anthracen-9-yl)-1-(pyridin-2-yl)-1H-benzimidazolylidene, and POP = bis[2-diphenylphosphino]-phenyl)ether) have been synthesized and characterized. The different aryl substituents (phenyl, naphthyl, and anthracyl groups) were introduced into NHC ligands and the corresponding photophysical properties of the complexes were systematically investigated. The absorption spectra of all NHCsbnd Cu(I) complexes show a characteristic feature of metal-to-ligand charge transfer (MLCT) in the lower-energy region. Complex 1 exhibited good photoluminescence (PL) properties companying with the high quantum yields and long excited-state lifetimes, whereas 2 and 3 with naphthyl and anthracyl groups show the low PL efficiency caused by the strong π-π stacking interactions. Density functional theory (DFT) and time dependent density functional theory (TDDFT) calculations were employed to rationalize the photophysical properties of the NHCsbnd Cu(I) complexes.

  12. Impact of protein and ligand impurities on ITC-derived protein-ligand thermodynamics.

    PubMed

    Grüner, Stefan; Neeb, Manuel; Barandun, Luzi Jakob; Sielaff, Frank; Hohn, Christoph; Kojima, Shun; Steinmetzer, Torsten; Diederich, François; Klebe, Gerhard

    2014-09-01

    The thermodynamic characterization of protein-ligand interactions by isothermal titration calorimetry (ITC) is a powerful tool in drug design, giving valuable insight into the interaction driving forces. ITC is thought to require protein and ligand solutions of high quality, meaning both the absence of contaminants as well as accurately determined concentrations. Ligands synthesized to deviating purity and protein of different pureness were titrated by ITC. Data curation was attempted also considering information from analytical techniques to correct stoichiometry. We used trypsin and tRNA-guanine transglycosylase (TGT), together with high affinity ligands to investigate the effect of errors in protein concentration as well as the impact of ligand impurities on the apparent thermodynamics. We found that errors in protein concentration did not change the thermodynamic properties obtained significantly. However, most ligand impurities led to pronounced changes in binding enthalpy. If protein binding of the respective impurity is not expected, the actual ligand concentration was corrected for and the thus revised data compared to thermodynamic properties obtained with the respective pure ligand. Even in these cases, we observed differences in binding enthalpy of about 4kJ⋅mol(-1), which is considered significant. Our results indicate that ligand purity is the critical parameter to monitor if accurate thermodynamic data of a protein-ligand complex are to be recorded. Furthermore, artificially changing fitting parameters to obtain a sound interaction stoichiometry in the presence of uncharacterized ligand impurities may lead to thermodynamic parameters significantly deviating from the accurate thermodynamic signature. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Pathway diversity leads to 2D-nanostructure in photo-triggered supramolecular assembly.

    PubMed

    Ghosh, Suhrit; Pal, Deep Sankar

    2018-03-31

    This communication reports photo-triggered supramolecular assembly of a naphthalene-diimide (NDI) derivative, appended with a photo-labile ortho-nitrobenzyl (ONB)-ester protected carboxylic acid. Photo-irradiation produces the free COOH group which facilitates H-bonding driven face-to-face stacking of the NDI chromophores producing an ultra-thin (height < 2.0 nm) two-dimensional (2D) nano-sheet. In contrast, spontaneous supramolecular assembly of the same active monomer exhibits entirely different features such as uncontrolled growth, J-aggregation and fibrillar morphology. A completely different pathway for photo-triggered assembly is attributed to the dual function of the photo-caged pro-monomer in (i) producing the carboxylic acid in controlled manner and (ii) simultaneously inhibiting the spontaneous J-aggregation of the photo-generated monomers by ester-carboxylic acid H-bonding and in turn directing a distinct growth mechanism. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Water-Gated n-Type Organic Field-Effect Transistors for Complementary Integrated Circuits Operating in an Aqueous Environment.

    PubMed

    Porrazzo, Rossella; Luzio, Alessandro; Bellani, Sebastiano; Bonacchini, Giorgio Ernesto; Noh, Yong-Young; Kim, Yun-Hi; Lanzani, Guglielmo; Antognazza, Maria Rosa; Caironi, Mario

    2017-01-31

    The first demonstration of an n-type water-gated organic field-effect transistor (WGOFET) is here reported, along with simple water-gated complementary integrated circuits, in the form of inverting logic gates. For the n-type WGOFET active layer, high-electron-affinity organic semiconductors, including naphthalene diimide co-polymers and a soluble fullerene derivative, have been compared, with the latter enabling a high electric double layer capacitance in the range of 1 μF cm -2 in full accumulation and a mobility-capacitance product of 7 × 10 -3 μF/V s. Short-term stability measurements indicate promising cycling robustness, despite operating the device in an environment typically considered harsh, especially for electron-transporting organic molecules. This work paves the way toward advanced circuitry design for signal conditioning and actuation in an aqueous environment and opens new perspectives in the implementation of active bio-organic interfaces for biosensing and neuromodulation.

  15. Tunable Crystallinity and Charge Transfer in Two-Dimensional G-Quadruplex Organic Frameworks.

    PubMed

    Wu, Yi-Lin; Bobbitt, N Scott; Logsdon, Jenna L; Powers-Riggs, Natalia E; Nelson, Jordan N; Liu, Xiaolong; Wang, Timothy C; Snurr, Randall Q; Hupp, Joseph T; Farha, Omar K; Hersam, Mark C; Wasielewski, Michael R

    2018-04-03

    DNA G-quadruplex structures were recently discovered to provide reliable scaffolding for two-dimensional organic frameworks due to the strong hydrogen-bonding ability of guanine. Herein, 2,7-diaryl pyrene building blocks with high HOMO energies and large optical gaps are incorporated into G-quadruplex organic frameworks. The adjustable substitution on the aryl groups provides an opportunity to elucidate the framework formation mechanism; molecular non-planarity is found to be beneficial for restricting interlayer slippage, and the framework crystallinity is highest when intermolecular interaction and non-planarity strike a fine balance. When guanine-functionalized pyrenes are co-crystallized with naphthalene diimide, charge-transfer (CT) complexes are obtained. The photophysical properties of the pyrene-only and CT frameworks are characterized by UV/Vis and steady-state and time-resolved photoluminescence spectroscopies, and by EPR spectroscopy for the CT complex frameworks. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Building 1D lanthanide chains and non-symmetrical [Ln2] "triple-decker" clusters using salen-type ligands: magnetic cooling and relaxation phenomena.

    PubMed

    Canaj, Angelos B; Siczek, Milosz; Otręba, Marta; Lis, Tadeusz; Lorusso, Giulia; Evangelisti, Marco; Milios, Constantinos J

    2016-11-22

    A solvothermal reaction between Ln(NO 3 ) 3 ·6H 2 O (Ln: Gd, Tb and Dy), 2-hydroxy-1-naphthaldehyde, 2-OH-naphth, and ethylenediamine, en, in MeOH in the presence of a base, NEt 3 , led to the formation of the 1D coordination polymers [Ln(L)(MeO)(MeOH) 0.5 ] n ·MeOH (Ln = Gd (1·MeOH), Tb(2), Dy (3·MeOH); H 2 L = 1,1'-((1E,1'E)-(ethane-1,2-diylbis(azanylylidene))bis(methanylylidene))bis(naphthalen-2-ol), the Schiff-base ligand derived from the condensation of 2-OH-naphth and en), while a similar reaction in an excess of NaN 3 yielded 1D coordination polymers [Ln(L)(N 3 ) 0.75 (MeO) 0.25 (MeOH)] n (Ln = Gd (4), Tb (5), Dy (6)). Finally, upon replacing ethylenediamine with o-phenylenediamine, o-phen, we managed to isolate the discrete dimers [Dy 2 (L') 3 (MeOH)]·2MeOH (7·2MeOH) and [Gd 2 (L') 3 (MeOH)]·2MeOH (8·2MeOH) (H 2 L' = 1,1'-((1E,1'E)-(1,2-phenylenebis(azanylylidene))bis(methanylylidene))bis (naphthalen-2-ol), the Schiff-base ligand from the condensation of 2-OH-naphth and o-phen). Polymers 1-3 describe one-dimensional chains, containing alternating seven- and eight-coordinate Ln III metal centers, polymers 4-6 contain eight-coordinate lanthanide ions, while in both 7 and 8 the two Ln III centers are eight- and seven-coordinate, adopting square antiprismatic and "piano-stool" geometry, respectively. The magnetocaloric properties of the three Gd III analogues were determined from magnetic measurements, yielding the magnetic entropy change -ΔS m = 21.8, 23.0 and 16.0 J kg -1 K -1 at T = 3.0 K on demagnetization of 7 T to 0, for 1, 4 and 8, respectively. The study of the magnetic properties also revealed that all three Dy III analogues (3, 6 and 7) display out-of-phase signals, therefore suggesting slow magnetic relaxation, while such behaviour was not established in the Tb III analogues.

  17. Group Additivity in Ligand Binding Affinity: An Alternative Approach to Ligand Efficiency.

    PubMed

    Reynolds, Charles H; Reynolds, Ryan C

    2017-12-26

    Group additivity is a concept that has been successfully applied to a variety of thermochemical and kinetic properties. This includes drug discovery, where functional group additivity is often assumed in ligand binding. Ligand efficiency can be recast as a special case of group additivity where ΔG/HA is the group equivalent (HA is the number of non-hydrogen atoms in a ligand). Analysis of a large data set of protein-ligand binding affinities (K i ) for diverse targets shows that in general ligand binding is distinctly nonlinear. It is possible to create a group equivalent scheme for ligand binding, but only in the context of closely related proteins, at least with regard to size. This finding has broad implications for drug design from both experimental and computational points of view. It also offers a path forward for a more general scheme to assess the efficiency of ligand binding.

  18. Thalassospira permensis sp. nov., a new terrestrial halotolerant bacterium isolated from a naphthalene-utilizing microbial consortium.

    PubMed

    Plotnikova, E G; Anan'ina, L N; Krausova, V I; Ariskina, E V; Prisyazhnaya, N V; Lebedev, A T; Demakov, V A; Evtushenko, L I

    2011-01-01

    A halotolerant bacterium, strain SMB34T, was isolated from a naphthalene-utilizing bacterial consortium obtained from primitive technogeneous soil (Vrkhnekamsk salt deposit, Perm region, Russia) by enrichment procedure. The strain itself was unable to degrade naphthalene and grew at NaCl concentrations up to 11% (w/v). The 16S rRNA-based phylogenetic analysis showed that the strain belongs to the genus Thalassospira. The DNA-DNA hybridization values between SMB34T and the type strains of phylogenetically closest species (T. xiamenensis, T. profundimaris and T. tepidiphila) did not exceed 50%. The novel strain could be distinguished from the above species by the cell motility, MALDI/TOF mass spectra of whole cells and a range of physiological and biochemical characteristics. SMB34T also considerably differs from the recently described species T. xianhensis, with the most striking differences in the DNA G + C content (53.7 +/- 1.0 vs. 61.2 +/- 1.0 mol.%) and predominant ubiquinones (Q-10 vs. Q-9). The data obtained suggest strain SMB34T (=VKM B-2527T = NBRC 106175T), designated as the type strain, represents a novel species, named Thalassospira permensis sp. nov.

  19. Noncatalytic hydrogenation of naphthalene in nanosized membrane reactors with accumulated hydrogen and controlled adjustment of their reaction zone volumes

    NASA Astrophysics Data System (ADS)

    Soldatov, A. P.

    2017-05-01

    As part of ongoing studies aimed at designing the next generation of nanosized membrane reactors (NMRs) with accumulated hydrogen, the noncatalytic hydrogenation of naphthalene in pores of ceramic membranes (TRUMEM ultrafiltration membranes with D av = 50 and 90 nm) is performed for the first time, using hydrogen preadsorbed in a hybrid carbon nanostructure: mono- and multilayered oriented carbon nanotubes with graphene walls (OCNTGs) that form on inner pore surfaces. In this technique, the reaction proceeds in the temperature range of 330-390°C at contact times of 10-16 h. The feedstock is an 8% naphthalene solution in decane. The products are analyzed via chromatography on a quartz capillary column coated with polydimethylsiloxane (SE-30). It is established for the first time that in NMRs, the noncatalytic hydrogenation of naphthalene occurs at 370-390°C, forming 1,2,3,4-tetrahydronaphthalene in amounts of up to 0.61%. The rate constants and activation energy (123.5 kJ/mol) of the noncatalytic hydrogenation reaction are determined for the first time. The possibility of designing an NMR with an adjustable reaction zone volume is explored. Changes in the pore structure of the membranes after their modification with pyrocarbon nanosized crystallites (PNCs) are therefore studied as well. It is shown that lengthening the process time reduces pore size: within 23 h after the deposition of PNCs, the average pore radius ( r av) falls from 25 to 3.1 nm. The proposed approach would allow us to design nanoreactors of molecular size and conduct hydrogenation reactions within certain guidelines to synthesize new chemical compounds.

  20. The development of a MIP-optosensor for the detection of monoamine naphthalenes in drinking water.

    PubMed

    Valero-Navarro, Angel; Salinas-Castillo, Alfonso; Fernández-Sánchez, Jorge F; Segura-Carretero, Antonio; Mallavia, Ricardo; Fernández-Gutiérrez, Alberto

    2009-03-15

    To enhance the advantages of fluorescent flow-through sensing for drinking water we have designed a novel sensing matrix based on molecularly imprinted polymers (MIPs). The synergic combination of a tailor-made MIP recognition with a selective room temperature fluorescence detection is a novel concept for optosensing devices and is assessed here for the simple and selective determination of pollutants in water. We describe a simple approach to preparing synthetic receptors for monoamine naphthalene compounds (MA-NCs) using non-covalent molecular imprinting techniques and naphthalene as template. We examine in detail the binding characteristics of the imprinted polymer and describe the flow-through sensor of MA-NCs by solid-surface fluorescence. Its detection limits for recognizing 1-naphthylamine (1-NA) and 2-naphthylamine (2-NA) separately are 26 ngmL(-1) and 50 ngmL(-1), respectively, and it also determines 1-NA and 2-NA simultaneously with a detection limit of 45 ngmL(-1). All the instrumental, chemical and flow variables were carefully optimized and an interference study was carried out to demonstrate its applicability and selectivity. Finally, we applied it to the analysis of 1-NA and 2-NA in tap and mineral waters, obtaining a 98% average recovery rate.

  1. Abundance of Dioxygenase Genes Similar to Ralstonia sp. Strain U2 nagAc Is Correlated with Naphthalene Concentrations in Coal Tar-Contaminated Freshwater Sediments

    PubMed Central

    Dionisi, Hebe M.; Chewning, Christopher S.; Morgan, Katherine H.; Menn, Fu-Min; Easter, James P.; Sayler, Gary S.

    2004-01-01

    We designed a real-time PCR assay able to recognize dioxygenase large-subunit gene sequences with more than 90% similarity to the Ralstonia sp. strain U2 nagAc gene (nagAc-like gene sequences) in order to study the importance of organisms carrying these genes in the biodegradation of naphthalene. Sequencing of PCR products indicated that this real-time PCR assay was specific and able to detect a variety of nagAc-like gene sequences. One to 100 ng of contaminated-sediment total DNA in 25-μl reaction mixtures produced an amplification efficiency of 0.97 without evident PCR inhibition. The assay was applied to surficial freshwater sediment samples obtained in or in close proximity to a coal tar-contaminated Superfund site. Naphthalene concentrations in the analyzed samples varied between 0.18 and 106 mg/kg of dry weight sediment. The assay for nagAc-like sequences indicated the presence of (4.1 ± 0.7) × 103 to (2.9 ± 0.3) × 105 copies of nagAc-like dioxygenase genes per μg of DNA extracted from sediment samples. These values corresponded to (1.2 ± 0.6) × 105 to (5.4 ± 0.4) × 107 copies of this target per g of dry weight sediment when losses of DNA during extraction were taken into account. There was a positive correlation between naphthalene concentrations and nagAc-like gene copies per microgram of DNA (r = 0.89) and per gram of dry weight sediment (r = 0.77). These results provide evidence of the ecological significance of organisms carrying nagAc-like genes in the biodegradation of naphthalene. PMID:15240274

  2. Long-Lived Charge Separation at Heterojunctions between Semiconducting Single-Walled Carbon Nanotubes and Perylene Diimide Electron Acceptors

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

    Kang, Hyun Suk; Sisto, Thomas J.; Peurifoy, Samuel

    Nonfullerene electron acceptors have facilitated a recent surge in the efficiencies of organic solar cells, although fundamental studies of the nature of exciton dissociation at interfaces with nonfullerene electron acceptors are still relatively sparse. Semiconducting single-walled carbon nanotubes (s-SWCNTs), unique one-dimensional electron donors with molecule-like absorption and highly mobile charges, provide a model system for studying interfacial exciton dissociation. Here, we investigate excited-state photodynamics at the heterojunction between (6,5) s-SWCNTs and two perylene diimide (PDI)-based electron acceptors. Each of the PDI-based acceptors, hPDI2-pyr-hPDI2 and Trip-hPDI2, is deposited onto (6,5) s-SWCNT films to form a heterojunction bilayer. Transient absorption measurements demonstratemore » that photoinduced hole/electron transfer occurs at the photoexcited bilayer interfaces, producing long-lived separated charges with lifetimes exceeding 1.0 us. Both exciton dissociation and charge recombination occur more slowly for the hPDI2-pyr-hPDI2 bilayer than for the Trip-hPDI2 bilayer. To explain such differences, we discuss the potential roles of the thermodynamic charge transfer driving force available at each interface and the different molecular structure and intermolecular interactions of PDI-based acceptors. As a result, detailed photophysical analysis of these model systems can develop the fundamental understanding of exciton dissociation between organic electron donors and nonfullerene acceptors, which has not been systematically studied.« less

  3. Long-Lived Charge Separation at Heterojunctions between Semiconducting Single-Walled Carbon Nanotubes and Perylene Diimide Electron Acceptors

    DOE PAGES

    Kang, Hyun Suk; Sisto, Thomas J.; Peurifoy, Samuel; ...

    2018-04-13

    Nonfullerene electron acceptors have facilitated a recent surge in the efficiencies of organic solar cells, although fundamental studies of the nature of exciton dissociation at interfaces with nonfullerene electron acceptors are still relatively sparse. Semiconducting single-walled carbon nanotubes (s-SWCNTs), unique one-dimensional electron donors with molecule-like absorption and highly mobile charges, provide a model system for studying interfacial exciton dissociation. Here, we investigate excited-state photodynamics at the heterojunction between (6,5) s-SWCNTs and two perylene diimide (PDI)-based electron acceptors. Each of the PDI-based acceptors, hPDI2-pyr-hPDI2 and Trip-hPDI2, is deposited onto (6,5) s-SWCNT films to form a heterojunction bilayer. Transient absorption measurements demonstratemore » that photoinduced hole/electron transfer occurs at the photoexcited bilayer interfaces, producing long-lived separated charges with lifetimes exceeding 1.0 us. Both exciton dissociation and charge recombination occur more slowly for the hPDI2-pyr-hPDI2 bilayer than for the Trip-hPDI2 bilayer. To explain such differences, we discuss the potential roles of the thermodynamic charge transfer driving force available at each interface and the different molecular structure and intermolecular interactions of PDI-based acceptors. As a result, detailed photophysical analysis of these model systems can develop the fundamental understanding of exciton dissociation between organic electron donors and nonfullerene acceptors, which has not been systematically studied.« less

  4. Naphthalenetetracarboxylic diimide layer-based transistors with nanometer oxide and side chain dielectrics operating below one volt.

    PubMed

    Jung, Byung Jun; Martinez Hardigree, Josue F; Dhar, Bal Mukund; Dawidczyk, Thomas J; Sun, Jia; See, Kevin Cua; Katz, Howard E

    2011-04-26

    We designed a new naphthalenetetracarboxylic diimide (NTCDI) semiconductor molecule with long fluoroalkylbenzyl side chains. The side chains, 1.2 nm long, not only aid in self-assembly and kinetically stabilize injected electrons but also act as part of the gate dielectric in field-effect transistors. On Si substrates coated only with the 2 nm thick native oxide, NTCDI semiconductor films were deposited with thicknesses from 17 to 120 nm. Top contact Au electrodes were deposited as sources and drains. The devices showed good transistor characteristics in air with 0.1-1 μA of drain current at 0.5 V of V(G) and V(DS) and W/L of 10-20, even though channel width (250 μm) is over 1000 times the distance (20 nm) between gate and drain electrodes. The extracted capacitance-times-mobility product, an expression of the sheet transconductance, can exceed 100 nS V(-1), 2 orders of magnitude higher than typical organic transistors. The vertical low-frequency capacitance with gate voltage applied in the accumulation regime reached as high as 650 nF/cm(2), matching the harmonic sum of capacitances of the native oxide and one side chain and indicating that some gate-induced carriers in such devices are distributed among all of the NTCDI core layers, although the preponderance of the carriers are still near the gate electrode. Besides demonstrating and analyzing thickness-dependent NTCDI-based transistor behavior, we also showed <1 V detection of dinitrotoluene vapor by such transistors.

  5. Insights into an original pocket-ligand pair classification: a promising tool for ligand profile prediction.

    PubMed

    Pérot, Stéphanie; Regad, Leslie; Reynès, Christelle; Spérandio, Olivier; Miteva, Maria A; Villoutreix, Bruno O; Camproux, Anne-Claude

    2013-01-01

    Pockets are today at the cornerstones of modern drug discovery projects and at the crossroad of several research fields, from structural biology to mathematical modeling. Being able to predict if a small molecule could bind to one or more protein targets or if a protein could bind to some given ligands is very useful for drug discovery endeavors, anticipation of binding to off- and anti-targets. To date, several studies explore such questions from chemogenomic approach to reverse docking methods. Most of these studies have been performed either from the viewpoint of ligands or targets. However it seems valuable to use information from both ligands and target binding pockets. Hence, we present a multivariate approach relating ligand properties with protein pocket properties from the analysis of known ligand-protein interactions. We explored and optimized the pocket-ligand pair space by combining pocket and ligand descriptors using Principal Component Analysis and developed a classification engine on this paired space, revealing five main clusters of pocket-ligand pairs sharing specific and similar structural or physico-chemical properties. These pocket-ligand pair clusters highlight correspondences between pocket and ligand topological and physico-chemical properties and capture relevant information with respect to protein-ligand interactions. Based on these pocket-ligand correspondences, a protocol of prediction of clusters sharing similarity in terms of recognition characteristics is developed for a given pocket-ligand complex and gives high performances. It is then extended to cluster prediction for a given pocket in order to acquire knowledge about its expected ligand profile or to cluster prediction for a given ligand in order to acquire knowledge about its expected pocket profile. This prediction approach shows promising results and could contribute to predict some ligand properties critical for binding to a given pocket, and conversely, some key pocket

  6. Insights into an Original Pocket-Ligand Pair Classification: A Promising Tool for Ligand Profile Prediction

    PubMed Central

    Reynès, Christelle; Spérandio, Olivier; Miteva, Maria A.; Villoutreix, Bruno O.; Camproux, Anne-Claude

    2013-01-01

    Pockets are today at the cornerstones of modern drug discovery projects and at the crossroad of several research fields, from structural biology to mathematical modeling. Being able to predict if a small molecule could bind to one or more protein targets or if a protein could bind to some given ligands is very useful for drug discovery endeavors, anticipation of binding to off- and anti-targets. To date, several studies explore such questions from chemogenomic approach to reverse docking methods. Most of these studies have been performed either from the viewpoint of ligands or targets. However it seems valuable to use information from both ligands and target binding pockets. Hence, we present a multivariate approach relating ligand properties with protein pocket properties from the analysis of known ligand-protein interactions. We explored and optimized the pocket-ligand pair space by combining pocket and ligand descriptors using Principal Component Analysis and developed a classification engine on this paired space, revealing five main clusters of pocket-ligand pairs sharing specific and similar structural or physico-chemical properties. These pocket-ligand pair clusters highlight correspondences between pocket and ligand topological and physico-chemical properties and capture relevant information with respect to protein-ligand interactions. Based on these pocket-ligand correspondences, a protocol of prediction of clusters sharing similarity in terms of recognition characteristics is developed for a given pocket-ligand complex and gives high performances. It is then extended to cluster prediction for a given pocket in order to acquire knowledge about its expected ligand profile or to cluster prediction for a given ligand in order to acquire knowledge about its expected pocket profile. This prediction approach shows promising results and could contribute to predict some ligand properties critical for binding to a given pocket, and conversely, some key pocket

  7. Role of ligand-ligand vs. core-core interactions in gold nanoclusters.

    PubMed

    Milowska, Karolina Z; Stolarczyk, Jacek K

    2016-05-14

    The controlled assembly of ligand-coated gold nanoclusters (NCs) into larger structures paves the way for new applications ranging from electronics to nanomedicine. Here, we demonstrate through rigorous density functional theory (DFT) calculations employing novel functionals accounting for van der Waals forces that the ligand-ligand interactions determine whether stable assemblies can be formed. The study of NCs with different core sizes, symmetry forms, ligand lengths, mutual crystal orientations, and in the presence of a solvent suggests that core-to-core van der Waals interactions play a lesser role in the assembly. The dominant interactions originate from combination of steric effects, augmented by ligand bundling on NC facets, and related to them changes in electronic properties induced by neighbouring NCs. We also show that, in contrast to standard colloidal theory approach, DFT correctly reproduces the surprising experimental trends in the strength of the inter-particle interaction observed when varying the length of the ligands. The results underpin the importance of understanding NC interactions in designing gold NCs for a specific function.

  8. (18-Crown-6)potassium [(1,2,5,6-η)-cyclo-octa-1,5-diene][(1,2,3,4-η)-naph-tha-lene]-ferrate(-I).

    PubMed

    Brennessel, William W; Ellis, John E

    2012-10-01

    The title salt, [K(C(12)H(24)O(6))][Fe(C(8)H(12))(C(10)H(8))], is the only known naphthalene complex containing iron in a formally negative oxidation state. Each (naphthalene)(1,5-cod)ferrate(-I) anion is in contact with one (18-crown-6)potassium cation via K⋯C contacts to the outer four carbon atoms of the naphthalene ligand (cod = 1,5-cyclo-octa-diene, 18-crown-6 = 1,4,7,10,13,16-hexa-oxacyclo-octa-deca-ne). When using the midpoints of the coordinating olefin bonds, the overall geometry of the coordination sphere around iron can be best described as distorted tetra-hedral. The naphthalene fold angle between the plane of the iron-coordinating butadiene unit and the plane containing the exo-benzene moiety is 19.2 (1)°.

  9. The effect of polychlorinated naphthalenes and tributyltin on the occurrence of aberrant nuclei in erythroid cells of medaka

    USGS Publications Warehouse

    Talykina, Melaniya G.; Papoulias, Diana M.; Allert, J. Alan; Izyuov, Y.U.; Villalobos, Sergio A.; Giesy, John P.; Tillitt, Donald E.

    2003-01-01

    The micronucleus test using erythrocytes of the peripheral blood of fish is often conducted to evaluate the genotoxic effects of pollutants under experimental and natural conditions. This report presents information on the production of micronuclei and other nuclear anomalies in erythrocytes of medaka (Oryzias latipes) exposed to three polychlorinated naphthalene (PCN) formulations (Halowaxes 1014, 1031 and 1051) or tributyltin (TBT). Three types of deviation in the morphology of interphase nuclei were observed in medaka erythrocytes: micronuclei, nuclei fragmented into two equal or unequal parts, and nuclei at different stages of invagination. The number of erythrocytes with nuclear anomalies typically increased after chemical exposure. However, differential dose-response patterns were observed with exposures to PCNs or TBT. Polychlorinated naphthalenes caused genotoxicity, while TBT caused an amitotic effect. Gender did not influence the frequency of nuclear anomalies. This is the first report on the application of the piscine micronuclear test with medaka and is the first study that investigated the potential for detecting micronuclei in erythrocytes from adult medaka exposed in ovo to mutagens.

  10. Ligand solvation in molecular docking.

    PubMed

    Shoichet, B K; Leach, A R; Kuntz, I D

    1999-01-01

    Solvation plays an important role in ligand-protein association and has a strong impact on comparisons of binding energies for dissimilar molecules. When databases of such molecules are screened for complementarity to receptors of known structure, as often occurs in structure-based inhibitor discovery, failure to consider ligand solvation often leads to putative ligands that are too highly charged or too large. To correct for the different charge states and sizes of the ligands, we calculated electrostatic and non-polar solvation free energies for molecules in a widely used molecular database, the Available Chemicals Directory (ACD). A modified Born equation treatment was used to calculate the electrostatic component of ligand solvation. The non-polar component of ligand solvation was calculated based on the surface area of the ligand and parameters derived from the hydration energies of apolar ligands. These solvation energies were subtracted from the ligand-receptor interaction energies. We tested the usefulness of these corrections by screening the ACD for molecules that complemented three proteins of known structure, using a molecular docking program. Correcting for ligand solvation improved the rankings of known ligands and discriminated against molecules with inappropriate charge states and sizes.

  11. Effects of cadmium, naphthalene, and DDVP on gut carbohydrases activity in bream (Abramis brama L. ) and Mozambique tilapia (Oreochromis mossambicus Peters)

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

    Golovanova, I.L.; Chuiko, G.M.; Pavlov, D.F.

    1994-03-01

    Previous research has shown that sublethal concentrations of cadmium, naphthalene and dichlorvos (DDVP) decreased growth rates in bream and Mozambique tilapia. One of the factors known to affect fish growth is the activity of gut digestive enzymes such as of lipases, proteases, carbohydrases. We assumed that toxicant-induced inhibition of the digestive enzyme activity and, consequently, the impaired digestion of food may contribute to the reduction of growth in fish exposed to toxicants. However, the influence of toxicants on digestive enzyme activities is poorly studied. The contribution of toxicant-induced changes of digestive enzymes activity to growth rate retardation in exposed fishmore » remains unknown. The goal of this study was to examine the influence of an organophosphorus insecticide DDVP, a polyaromatic hydrocarbon naphthalene, and a metal cadmium on fish gut carbohydrase (CH) activity. 14 refs., 2 tabs.« less

  12. Ligand interaction scan: a general method for engineering ligand-sensitive protein alleles.

    PubMed

    Erster, Oran; Eisenstein, Miriam; Liscovitch, Mordechai

    2007-05-01

    The ligand interaction scan (LIScan) method is a general procedure for engineering small molecule ligand-regulated forms of a protein that is complementary to other 'reverse' genetic and chemical-genetic methods for drug-target validation. It involves insertional mutagenesis by a chemical-genetic 'switch', comprising a genetically encoded peptide module that binds with high affinity to a small-molecule ligand. We demonstrated the method with TEM-1 beta-lactamase, using a tetracysteine hexapeptide insert and a biarsenical fluorescein ligand (FlAsH).

  13. Time-resolved spectroscopy of solid poly/1-vinyl naphthalene/ following electron beam pulse radiolysis - Pulse radiolytic studies on polymers

    NASA Technical Reports Server (NTRS)

    Coulter, D. R.; Liang, R. H.; Di Stefano, S.; Moacanin, J.; Gupta, A.

    1982-01-01

    Transient emission studies following pulse radiolysis of solid poly(1-vinyl naphthalene) show existence of excited monomers and two excimers. Quenching experiments indicate that excimers are not formed directly by recombination of ions but probably by trapping of migrating monomeric excitation in preformed traps whose density is approximately one in 1000.

  14. Concentration-dependent antagonistic persuasion of SDS and naphthalene derivatives on the fibrillation of stem bromelain.

    PubMed

    Qadeer, Atiyatul; Ahmad, Ejaz; Zaman, Masihuz; Khan, Mohd Wasif; Khan, Javed Masood; Rabbani, Gulam; Tarique, Khaja Faisal; Sharma, Gaurav; Gourinath, Samudrala; Nadeem, Sajid; Badr, Gamal; Khan, Rizwan Hasan

    2013-12-01

    Sodium dodecyl sulfate, a biological membrane mimetic, can be used to study the conversion of globular proteins into amyloid fibrils in vitro. Using multiple approaches, the effect of SDS was examined on stem bromelain (SB), a widely recognized therapeutic protein. SB is known to exist as a partially folded intermediate at pH 2.0, situation also encountered in the gastrointestinal tract (its site of absorption). In the presence of sub-micellar SDS concentration (500-1000 μM), this intermediate was found to exhibit great propensity to form large-sized β-sheeted aggregates with fibrillar morphology, the hall marks of amyloid structure. We also observed inhibition of fibrillation by two naphthalene-based compounds, ANS and bis-ANS. While bis-ANS significantly inhibited fibril formation at 50 μM, ANS did so at relatively higher concentration (400 μM). Alcohols, but not salts, were found to weaken the inhibitory action of these compounds suggesting the possible involvement of hydrophobic interactions in their binding to protein. Besides, isothermal titration calorimetry and molecular docking studies suggested that inhibition of fibrillation by these naphthalene derivatives is mediated not just through hydrophobic forces, but also by disruption of π-π interactions between the aromatic residues together with the inter-polypeptide chain repulsion among negatively charged ANS/bis-ANS bound SB. Copyright © 2013 Elsevier Inc. All rights reserved.

  15. Structure-Activity Relationship Studies and Molecular Modeling of Naphthalene-Based Sphingosine Kinase 2 Inhibitors.

    PubMed

    Congdon, Molly D; Kharel, Yugesh; Brown, Anne M; Lewis, Stephanie N; Bevan, David R; Lynch, Kevin R; Santos, Webster L

    2016-03-10

    The two isoforms of sphingosine kinase (SphK1 and SphK2) are the only enzymes that phosphorylate sphingosine to sphingosine-1-phosphate (S1P), which is a pleiotropic lipid mediator involved in a broad range of cellular processes including migration, proliferation, and inflammation. SphKs are targets for various diseases such as cancer, fibrosis, and Alzheimer's and sickle cell disease. Herein, we disclose the structure-activity profile of naphthalene-containing SphK inhibitors and molecular modeling studies that reveal a key molecular switch that controls SphK selectivity.

  16. Considerations of the Effects of Naphthalene Moieties on the Design of Proton-Conductive Poly(arylene ether ketone) Membranes for Direct Methanol Fuel Cells.

    PubMed

    Wang, Baolong; Hong, Lihua; Li, Yunfeng; Zhao, Liang; Wei, Yuxue; Zhao, Chengji; Na, Hui

    2016-09-14

    Novel sulfonated poly(arylene ether ketones) (SDN-PAEK-x), consisting of dual naphthalene and flexible sulfoalkyl groups, were prepared via polycondensation, demethylation, and sulfobutylation grafting reaction. Among them, SDN-PAEK-1.94 membrane with the highest ion exchange capacity (IEC = 2.46 mequiv·g(-1)) exhibited the highest proton conductivity, which was 0.147 S· cm(-1) at 25 °C and 0.271 S·cm(-1) at 80 °C, respectively. The introduction of dual naphthalene moieties is expected to achieve much enhanced properties compared to those of sulfonated poly(arylene ether ketones) (SNPAEK-x), consisting of single naphthalene and flexible sulfoalkyl groups. Compared with SNPAEK-1.60 with a similar IEC, SDN-PAEK-1.74 membrane showed higher proton conductivity, higher IEC normalized conductivity, and higher effective proton mobility, although it had lower analytical acid concentration. The SDN-PAEK-x membranes with IECs higher than 1.96 mequiv·g(-1) also exhibited higher proton conductivity than that of recast Nafion membrane. Furthermore, SDN-PAEK-1.94 displayed a better single cell performance with a maximum power density of 60 mW·cm(-2) at 80 °C. Considering its high proton conductivity, excellent single cell performance, good mechanical stabilities, low membrane swelling, and methanol permeability, SDN-PAEK-x membranes are promising candidates as alternative polymer electrolyte membranes to Nafion for direct methanol fuel cell applications.

  17. Mapping the force field of a hydrogen-bonded assembly

    NASA Astrophysics Data System (ADS)

    Sweetman, A. M.; Jarvis, S. P.; Sang, Hongqian; Lekkas, I.; Rahe, P.; Wang, Yu; Wang, Jianbo; Champness, N. R.; Kantorovich, L.; Moriarty, P.

    2014-05-01

    Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism.

  18. Dye-Incorporated Polynaphthalenediimide Acceptor for Additive-Free High-Performance All-Polymer Solar Cells.

    PubMed

    Chen, Dong; Yao, Jia; Chen, Lie; Yin, Jingping; Lv, Ruizhi; Huang, Bin; Liu, Siqi; Zhang, Zhi-Guo; Yang, Chunhe; Chen, Yiwang; Li, Yongfang

    2018-04-16

    All-polymer solar cells (all-PSCs) can offer unique advantages for applications in flexible devices, and naphthalene diimide (NDI)-based polymer acceptors are the widely used polymer acceptors. However, their power conversion efficiency (PCE) still lags behind that of state-of-the-art polymer solar cells, due to low light absorption, suboptimal energy levels and the strong aggregation of the NDI-based polymer acceptor. Herein, a rhodanine-based dye molecule was introduced into the NDI-based polymer acceptor by simple random copolymerization and showed an improved light absorption coefficient, an up-shifted lowest unoccupied molecular orbital level and reduced crystallization. Consequently, additive-free all-PSCs demonstrated a high PCE of 8.13 %, which is one of the highest performance characteristics reported for all-PSCs to date. These results indicate that incorporating a dye into the n-type polymer gives insight into the precise design of high-performance polymer acceptors for all-PSCs. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Improved ambient-stable perovskite solar cells enabled by a hybrid polymeric electron-transporting layer

    DOE PAGES

    Zhu, Zonglong; Chueh, Chu -Chen; Zhang, Guangye; ...

    2016-08-26

    In this study, an efficient inverted perovskite solar cell with decent ambient stability is successfully demonstrated by employing an n-type polymer, poly{[ N,N’-bis(2-octyldodecyl)- 1,4,5,8-naphthalene diimide-2,6-diyl]- alt-5,5’-(2,2’-bithiophene)} (N2200), as the electron-transporting layer (ETL). The device performance can be further enhanced from a power conversion efficiency (PCE) of 15 to 16.8% by tailoring the electronic properties of N2200 with a polymeric additive, poly[9,9-bis(6’- ( N,N’-diethylamino)propyl)-fluorene- alt-9,9-bis(3-ethyl(oxetane- 3-ethyloxy)-hexyl) fluorene] (PFN-Ox). More importantly, the device derived from this hybrid ETL can maintain good ambient stability inherent from the pristine N2200 ETL, for which 60–70% of initial PCE can be retained after being stored inmore » air with 10–20% humidity for 45 days.« less

  20. Water-Gated n-Type Organic Field-Effect Transistors for Complementary Integrated Circuits Operating in an Aqueous Environment

    PubMed Central

    2017-01-01

    The first demonstration of an n-type water-gated organic field-effect transistor (WGOFET) is here reported, along with simple water-gated complementary integrated circuits, in the form of inverting logic gates. For the n-type WGOFET active layer, high-electron-affinity organic semiconductors, including naphthalene diimide co-polymers and a soluble fullerene derivative, have been compared, with the latter enabling a high electric double layer capacitance in the range of 1 μF cm–2 in full accumulation and a mobility–capacitance product of 7 × 10–3 μF/V s. Short-term stability measurements indicate promising cycling robustness, despite operating the device in an environment typically considered harsh, especially for electron-transporting organic molecules. This work paves the way toward advanced circuitry design for signal conditioning and actuation in an aqueous environment and opens new perspectives in the implementation of active bio-organic interfaces for biosensing and neuromodulation. PMID:28180187

  1. Effect of phytoremediation on concentrations of benzene, toluene, naphthalene, and dissolved oxygen in groundwater at a former manufactured gas plant site, Charleston, South Carolina, USA, 1998–2014

    USGS Publications Warehouse

    Landmeyer, James E.; Effinger, Thomas N.

    2016-01-01

    Concentrations of benzene, toluene, naphthalene, and dissolved oxygen in groundwater at a former manufactured gas plant site near Charleston, South Carolina, USA, have been monitored since the installation of a phytoremediation system of hybrid poplar trees in 1998. Between 2000 and 2014, the concentrations of benzene, toluene, and naphthalene (BT&N) in groundwater in the planted area have decreased. For example, in the monitoring well containing the highest concentrations of BT&N, benzene concentrations decreased from 10,200 µg/L to less than 4000 µg/L, toluene concentrations decreased from 2420 µg/L to less than 20 µg/L, and naphthalene concentrations decreased from 6840 µg/L to less than 3000 µg/L. Concentrations of BT&N in groundwater in all wells were observed to be lower during the summer months relative to the winter months of a particular year during the first few years after installing the phytoremediation system, most likely due to increased transpiration and contaminant uptake by the hybrid poplar trees during the warm summer months; this pathway of uptake by trees was confirmed by the detection of benzene, toluene, and naphthalene in trees during sampling events in 2002, and later in the study in 2012. These data suggest that the phytoremediation system affects the groundwater contaminants on a seasonal basis and, over multiple years, has resulted in a cumulative decrease in dissolved-phase contaminant concentrations in groundwater. The removal of dissolved organic contaminants from the aquifer has resulted in a lower demand on dissolved oxygen supplied by recharge and, as a result, the redox status of the groundwater has changed from anoxic to oxic conditions. This study provides much needed information for water managers and other scientists on the viability of the long-term effectiveness of phytoremediation in decreasing groundwater contaminants and increasing dissolved oxygen at sites contaminated by benzene, toluene, and naphthalene.

  2. (18-Crown-6)potassium [(1,2,5,6-η)-cyclo­octa-1,5-diene][(1,2,3,4-η)-naph­tha­lene]­ferrate(−I)

    PubMed Central

    Brennessel, William W.; Ellis, John E.

    2012-01-01

    The title salt, [K(C12H24O6)][Fe(C8H12)(C10H8)], is the only known naphthalene complex containing iron in a formally negative oxidation state. Each (naphthalene)(1,5-cod)ferrate(−I) anion is in contact with one (18-crown-6)potassium cation via K⋯C contacts to the outer four carbon atoms of the naphthalene ligand (cod = 1,5-cyclo­octa­diene, 18-crown-6 = 1,4,7,10,13,16-hexa­oxacyclo­octa­deca­ne). When using the midpoints of the coordinating olefin bonds, the overall geometry of the coordination sphere around iron can be best described as distorted tetra­hedral. The naphthalene fold angle between the plane of the iron-coordinating butadiene unit and the plane containing the exo-benzene moiety is 19.2 (1)°. PMID:23125569

  3. Quantification of biodegradation for o-xylene and naphthalene using first order decay models, Michaelis-Menten kinetics and stable carbon isotopes.

    PubMed

    Blum, Philipp; Hunkeler, Daniel; Weede, Matthias; Beyer, Christof; Grathwohl, Peter; Morasch, Barbara

    2009-04-01

    At a former wood preservation plant severely contaminated with coal tar oil, in situ bulk attenuation and biodegradation rate constants for several monoaromatic (BTEX) and polyaromatic hydrocarbons (PAH) were determined using (1) classical first order decay models, (2) Michaelis-Menten degradation kinetics (MM), and (3) stable carbon isotopes, for o-xylene and naphthalene. The first order bulk attenuation rate constant for o-xylene was calculated to be 0.0025 d(-1) and a novel stable isotope-based first order model, which also accounted for the respective redox conditions, resulted in a slightly smaller biodegradation rate constant of 0.0019 d(-1). Based on MM-kinetics, the o-xylene concentration decreased with a maximum rate of k(max)=0.1 microg/L/d. The bulk attenuation rate constant of naphthalene retrieved from the classical first order decay model was 0.0038 d(-1). The stable isotope-based biodegradation rate constant of 0.0027 d(-1) was smaller in the reduced zone, while residual naphthalene in the oxic part of the plume further downgradient was degraded at a higher rate of 0.0038 d(-1). With MM-kinetics a maximum degradation rate of k(max)=12 microg/L/d was determined. Although best fits were obtained by MM-kinetics, we consider the carbon stable isotope-based approach more appropriate as it is specific for biodegradation (not overall attenuation) and at the same time accounts for the dominant electron-accepting process. For o-xylene a field based isotope enrichment factor epsilon(field) of -1.4 could be determined using the Rayleigh model, which closely matched values from laboratory studies of o-xylene degradation under sulfate-reducing conditions.

  4. Strong Ligand-Protein Interactions Derived from Diffuse Ligand Interactions with Loose Binding Sites.

    PubMed

    Marsh, Lorraine

    2015-01-01

    Many systems in biology rely on binding of ligands to target proteins in a single high-affinity conformation with a favorable ΔG. Alternatively, interactions of ligands with protein regions that allow diffuse binding, distributed over multiple sites and conformations, can exhibit favorable ΔG because of their higher entropy. Diffuse binding may be biologically important for multidrug transporters and carrier proteins. A fine-grained computational method for numerical integration of total binding ΔG arising from diffuse regional interaction of a ligand in multiple conformations using a Markov Chain Monte Carlo (MCMC) approach is presented. This method yields a metric that quantifies the influence on overall ligand affinity of ligand binding to multiple, distinct sites within a protein binding region. This metric is essentially a measure of dispersion in equilibrium ligand binding and depends on both the number of potential sites of interaction and the distribution of their individual predicted affinities. Analysis of test cases indicates that, for some ligand/protein pairs involving transporters and carrier proteins, diffuse binding contributes greatly to total affinity, whereas in other cases the influence is modest. This approach may be useful for studying situations where "nonspecific" interactions contribute to biological function.

  5. Penetration of naphthalene, n-hexadecane, and 2,4-dinitrotoluene into southern yellow pine under conditions modeling spills and floods

    Treesearch

    I.E. Popova; M.K. Beklemishev; C.R. Frihart; W.S. Seames; T.J. Sundstrom; E.I. Kozliak

    2006-01-01

    This paper investigates the penetration of three common contaminants into building grade southern yellow pine wood samples under the conditions experienced during chemical spills. Contaminants (n-hexadecane, naphthalene, and 2,4-dinitrotoluene) were applied in their 14C-labeled forms to 5-to 9-cm-long pieces of southern yellow pine at ambient conditions. The impact of...

  6. Reduction of benzene and naphthalene mass transfer from crude oils by aging-induced interfacial films.

    PubMed

    Ghoshal, Subhasis; Pasion, Catherine; Alshafie, Mohammed

    2004-04-01

    Semi-rigid films or skins form at the interface of crude oil and water as a result of the accumulation of asphaltene and resin fractions when the water-immiscible crude oil is contacted with water for a period of time or "aged". The time varying patterns of area-independent mass transfer coefficients of two compounds, benzene and naphthalene, for dissolution from crude oil and gasoline were determined. Aqueous concentrations of the compounds were measured in the eluent from flow-through reactors, where a nondispersed oil phase and constant oil-water interfacial area were maintained. For Brent Blend crude oil and for gasoline amended with asphaltenes and resins, a rapid decrease in both benzene and naphthalene mass transfer coefficients over the first few days of aging was observed. The mass transfer coefficients of the two target solutes were reduced by up to 80% over 35 d although the equilibrium partition coefficients were unchanged. Aging of gasoline, which has negligible amounts of asphaltene and resin, did not result in a change in the solute mass transfer coefficients. The study demonstrates that formation of crude oil-water interfacial films comprised of asphaltenes and resins contribute to time-dependent decreases in rates of release of environmentally relevant solutes from crude oils and may contribute to the persistence of such solutes at crude oil-contaminated sites. It is estimated that the interfacial film has an extremely low film mass transfer coefficient in the range of 10(-6) cm/min.

  7. Multiple ligand simultaneous docking: orchestrated dancing of ligands in binding sites of protein.

    PubMed

    Li, Huameng; Li, Chenglong

    2010-07-30

    Present docking methodologies simulate only one single ligand at a time during docking process. In reality, the molecular recognition process always involves multiple molecular species. Typical protein-ligand interactions are, for example, substrate and cofactor in catalytic cycle; metal ion coordination together with ligand(s); and ligand binding with water molecules. To simulate the real molecular binding processes, we propose a novel multiple ligand simultaneous docking (MLSD) strategy, which can deal with all the above processes, vastly improving docking sampling and binding free energy scoring. The work also compares two search strategies: Lamarckian genetic algorithm and particle swarm optimization, which have respective advantages depending on the specific systems. The methodology proves robust through systematic testing against several diverse model systems: E. coli purine nucleoside phosphorylase (PNP) complex with two substrates, SHP2NSH2 complex with two peptides and Bcl-xL complex with ABT-737 fragments. In all cases, the final correct docking poses and relative binding free energies were obtained. In PNP case, the simulations also capture the binding intermediates and reveal the binding dynamics during the recognition processes, which are consistent with the proposed enzymatic mechanism. In the other two cases, conventional single-ligand docking fails due to energetic and dynamic coupling among ligands, whereas MLSD results in the correct binding modes. These three cases also represent potential applications in the areas of exploring enzymatic mechanism, interpreting noisy X-ray crystallographic maps, and aiding fragment-based drug design, respectively. 2010 Wiley Periodicals, Inc.

  8. Electronic absorption spectra of hydrogenated protonated naphthalene and proflavine

    NASA Astrophysics Data System (ADS)

    Bonaca, A.; Bilalbegović, G.

    2011-09-01

    We study hydrogenated cations of two polycyclic hydrocarbon molecules as models of hydrogenated organic species that form in the interstellar medium. Optical spectra of the hydrogenated naphthalene cation Hn-C10H+8 for n= 1, 2 and 10, as well as the astrobiologically interesting hydrogenated proflavine cation Hn-C13H11N+3 for n= 1 and 14, are calculated. The pseudopotential time-dependent density functional theory is used. It is found that the fully hydrogenated proflavine cation H14-C13H11N+3 shows a broad spectrum in which the positions of individual lines are almost lost. The positions, shapes and intensities of lines change in hydronaphthalene and hydroproflavine cations, showing that hydrogen additions induce substantially different optical spectra in comparison with base polycyclic hydrocarbon cations. One calculated line in the visible spectrum of H10-C10H+8 and one in the visible spectrum of H-C13H11N+3 are close to the measured diffuse interstellar bands. We also present the positions of near-ultraviolet lines.

  9. Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction.

    PubMed

    Yang, Chao-Yie; Sun, Haiying; Chen, Jianyong; Nikolovska-Coleska, Zaneta; Wang, Shaomeng

    2009-09-30

    Accurate prediction of the binding affinities of small-molecule ligands to their biological targets is fundamental for structure-based drug design but remains a very challenging task. In this paper, we have performed computational studies to predict the binding models of 31 small-molecule Smac (the second mitochondria-derived activator of caspase) mimetics to their target, the XIAP (X-linked inhibitor of apoptosis) protein, and their binding affinities. Our results showed that computational docking was able to reliably predict the binding models, as confirmed by experimentally determined crystal structures of some Smac mimetics complexed with XIAP. However, all the computational methods we have tested, including an empirical scoring function, two knowledge-based scoring functions, and MM-GBSA (molecular mechanics and generalized Born surface area), yield poor to modest prediction for binding affinities. The linear correlation coefficient (r(2)) value between the predicted affinities and the experimentally determined affinities was found to be between 0.21 and 0.36. Inclusion of ensemble protein-ligand conformations obtained from molecular dynamic simulations did not significantly improve the prediction. However, major improvement was achieved when the free-energy change for ligands between their free- and bound-states, or "ligand-reorganization free energy", was included in the MM-GBSA calculation, and the r(2) value increased from 0.36 to 0.66. The prediction was validated using 10 additional Smac mimetics designed and evaluated by an independent group. This study demonstrates that ligand reorganization free energy plays an important role in the overall binding free energy between Smac mimetics and XIAP. This term should be evaluated for other ligand-protein systems and included in the development of new scoring functions. To our best knowledge, this is the first computational study to demonstrate the importance of ligand reorganization free energy for the

  10. Enhanced Ligand Sampling for Relative Protein–Ligand Binding Free Energy Calculations

    PubMed Central

    2016-01-01

    Free energy calculations are used to study how strongly potential drug molecules interact with their target receptors. The accuracy of these calculations depends on the accuracy of the molecular dynamics (MD) force field as well as proper sampling of the major conformations of each molecule. However, proper sampling of ligand conformations can be difficult when there are large barriers separating the major ligand conformations. An example of this is for ligands with an asymmetrically substituted phenyl ring, where the presence of protein loops hinders the proper sampling of the different ring conformations. These ring conformations become more difficult to sample when the size of the functional groups attached to the ring increases. The Adaptive Integration Method (AIM) has been developed, which adaptively changes the alchemical coupling parameter λ during the MD simulation so that conformations sampled at one λ can aid sampling at the other λ values. The Accelerated Adaptive Integration Method (AcclAIM) builds on AIM by lowering potential barriers for specific degrees of freedom at intermediate λ values. However, these methods may not work when there are very large barriers separating the major ligand conformations. In this work, we describe a modification to AIM that improves sampling of the different ring conformations, even when there is a very large barrier between them. This method combines AIM with conformational Monte Carlo sampling, giving improved convergence of ring populations and the resulting free energy. This method, called AIM/MC, is applied to study the relative binding free energy for a pair of ligands that bind to thrombin and a different pair of ligands that bind to aspartyl protease β-APP cleaving enzyme 1 (BACE1). These protein–ligand binding free energy calculations illustrate the improvements in conformational sampling and the convergence of the free energy compared to both AIM and AcclAIM. PMID:25906170

  11. Perylene-Diimide Based Donor-Acceptor-Donor Type Small-Molecule Acceptors for Solution-Processable Organic Solar Cells

    NASA Astrophysics Data System (ADS)

    Ganesamoorthy, Ramasamy; Vijayaraghavan, Rajagopalan; Sakthivel, Pachagounder

    2017-12-01

    Development of nonfullerene acceptors plays an important role in the commercial availability of plastic solar cells. We report herein synthesis of bay-substituted donor-acceptor-donor (D-A-D)-type perylene diimide (PDI)-based small molecules (SM-1 to SM-4) by Suzuki coupling method and their use as acceptors in bulk heterojunction organic solar cells (BHJ-OSCs) with poly(3-hexylthiophene) (P3HT) polymer donor. We varied the number of electron-rich thiophene units and the solubilizing side chains and also evaluated the optical and electrochemical properties of the small molecules. The synthesized small molecules were confirmed by Fourier-transform infrared (FT-IR) spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, and high-resolution mass spectroscopy (HR-MS). The small molecules showed extensive and strong absorption in the ultraviolet-visible (UV-Vis) region up to 750 nm, with bandgap (E_{{g}}^{{opt}} ) reduced below <2 eV. The energy levels of small molecules SM-1 to SM-4 were suitable for use as electron-accepting materials. The small molecules showed good thermal stability up to 300°C. BHJ-OSCs with SM-1 and P3HT polymer donor showed maximum power conversion efficiency (PCE) of 0.19% with V oc of 0.30 V, J sc of 1.72 mA cm-2, and fill factor (FF) of 37%. The PCE decreased with the number of thiophene units. The PCE of SM-2 was lower than that of SM-1. This difference in PCE can be explained by the higher aggregation tendency of the bithiophene compared with the thiophene unit. Introduction of the solubilizing group in the bay position increased the aggregation property, leading to much lower PCE than for the small molecules without solubilizing group.

  12. Synthesis and characterization of a series of transition metal complexes with a new symmetrical polyoxaaza macroacyclic Schiff base ligand: X-ray crystal structure of cobalt(II) and nickel(II) complexes and their antibacterial properties

    NASA Astrophysics Data System (ADS)

    Keypour, Hassan; Shayesteh, Maryam; Rezaeivala, Majid; Chalabian, Firoozeh; Valencia, Laura

    2013-01-01

    A new symmetrical [N4O2] hexadentate Schiff base ligand, (E)-N-(pyridin-2-ylmethylene)-2-(3-(2-((E)-pyridin-2-lmethyleneamino)phenoxy)naphthalen-2-yloxy)benzenamine, abbreviated to L, and its complexes of Ni(II), Cu(II), Zn(II), Co(II), Cd(II) and Mn(II) have been synthesized in the presence of metal ions. The complexes were structurally characterized by elemental analyses, IR, UV-Vis, NMR and molar conductivity. The crystal structures of two complexes, [NiL(ONO2)2]·2H2O and [CoLCl2]CH3OH·0.5H2O, have been determined by a single crystal X-ray diffraction study. In these complexes, the ligand is coordinated in a neutral form via pyridine and azomethine nitrogen atoms. The metal ions complete their six coordination with two coordinated nitrate or chloride ions, forming a distorted octahedral geometry. The synthesized compounds have antibacterial activity against the three Gram-positive bacteria: Enterococcus faecalis, Bacillus cereus and Staphylococcus epid and also against the three Gram-negative bacteria: Citrobacter freundii, Enterobacter aerogenes and Salmonella typhi. The activity data show that the complexes are more potent antibacterials than the parent Schiff base.

  13. Binding constant of cell adhesion receptors and substrate-immobilized ligands depends on the distribution of ligands

    NASA Astrophysics Data System (ADS)

    Li, Long; Hu, Jinglei; Xu, Guangkui; Song, Fan

    2018-01-01

    Cell-cell adhesion and the adhesion of cells to tissues and extracellular matrix, which are pivotal for immune response, tissue development, and cell locomotion, depend sensitively on the binding constant of receptor and ligand molecules anchored on the apposing surfaces. An important question remains of whether the immobilization of ligands affects the affinity of binding with cell adhesion receptors. We have investigated the adhesion of multicomponent membranes to a flat substrate coated with immobile ligands using Monte Carlo simulations of a statistical mesoscopic model with biologically relevant parameters. We find that the binding of the adhesion receptors to ligands immobilized on the substrate is strongly affected by the ligand distribution. In the case of ligand clusters, the receptor-ligand binding constant can be significantly enhanced due to the less translational entropy loss of lipid-raft domains in the model cell membranes upon the formation of additional complexes. For ligands randomly or uniformly immobilized on the substrate, the binding constant is rather decreased since the receptors localized in lipid-raft domains have to pay an energetic penalty in order to bind ligands. Our findings help to understand why cell-substrate adhesion experiments for measuring the impact of lipid rafts on the receptor-ligand interactions led to contradictory results.

  14. EGF receptor ligands: recent advances.

    PubMed

    Singh, Bhuminder; Carpenter, Graham; Coffey, Robert J

    2016-01-01

    Seven ligands bind to and activate the mammalian epidermal growth factor (EGF) receptor (EGFR/ERBB1/HER1): EGF, transforming growth factor-alpha (TGFA), heparin-binding EGF-like growth factor (HBEGF), betacellulin (BTC), amphiregulin (AREG), epiregulin (EREG), and epigen (EPGN). Of these, EGF, TGFA, HBEGF, and BTC are thought to be high-affinity ligands, whereas AREG, EREG, and EPGN constitute low-affinity ligands. This focused review is meant to highlight recent studies related to actions of the individual EGFR ligands, the interesting biology that has been uncovered, and relevant advances related to ligand interactions with the EGFR.

  15. EGF receptor ligands: recent advances

    PubMed Central

    Singh, Bhuminder; Carpenter, Graham; Coffey, Robert J.

    2016-01-01

    Seven ligands bind to and activate the mammalian epidermal growth factor (EGF) receptor (EGFR/ERBB1/HER1): EGF, transforming growth factor-alpha (TGFA), heparin-binding EGF-like growth factor (HBEGF), betacellulin (BTC), amphiregulin (AREG), epiregulin (EREG), and epigen (EPGN). Of these, EGF, TGFA, HBEGF, and BTC are thought to be high-affinity ligands, whereas AREG, EREG, and EPGN constitute low-affinity ligands. This focused review is meant to highlight recent studies related to actions of the individual EGFR ligands, the interesting biology that has been uncovered, and relevant advances related to ligand interactions with the EGFR. PMID:27635238

  16. Attaching naphthalene derivatives onto BODIPY for generating excited triplet state and singlet oxygen: Tuning PET-based photosensitizer by electron donors

    NASA Astrophysics Data System (ADS)

    Zhang, Xian-Fu; Feng, Nan

    2018-01-01

    meso-Naphthalene substituted BODIPY compounds were prepared in a facile one pot reaction. The naphthalene functionalization of BODIPY leads up to a 5-fold increase in the formation efficiency of excited triplet state and singlet oxygen in polar solvents. Steady state and time resolved fluorescence, laser flash photolysis, and quantum chemistry methods were used to reveal the mechanism. All measured data and quantum chemical results suggest that these systems can be viewed as electron donor-acceptor (D-A) pair (BODIPY acts as the acceptor), photoinduced charge transfer (PCT) or photoinduced electron transfer (PET) occurs upon photo excitation (D-A + hν → Dδ +-Aδ -, 0 < δ ≤ 1), and the charge recombination induced the formation of triplet state (Dδ +-Aδ - → D-A (T1). These novel PCT- or PET-based photosensitizers (PSs) show different features from traditional PSs, such as the strong tunability by facile structural modification and good selectivity upon medium polarity. The new character for this type of PSs can lead to important applications in organic oxygenation reactions and photodynamic therapy of tumors.

  17. Developing Ligands for Palladium(II)-Catalyzed C–H Functionalization: Intimate Dialogue between Ligand and Substrate

    PubMed Central

    Engle, Keary M.; Yu, Jin-Quan

    2013-01-01

    Homogeneous transition metal–catalyzed reactions are indispensable to all facets of modern chemical synthesis. It is thus difficult to imagine that for much of the early 20th century, the reactivity and selectivity of all known homogeneous metal catalysts paled in comparison to their heterogeneous and biological counterparts. In the intervening decades, advances in ligand design bridged this divide, such that today some of the most demanding bond-forming events are mediated by ligand-supported homogeneous metal species. While ligand design has propelled many areas of homogeneous catalysis, in the field of Pd(II)-catalyzed C–H functionalization, suitable ligand scaffolds are lacking, which has hampered the development of broadly practical transformations based on C–H functionalization logic. In this review, we offer an account of our research employing three ligand scaffolds, mono-N-protected amino acids, 2,6-disubstituted pyridines, and 2,2′-bipyridines, to address challenges posed by several synthetically versatile substrate classes. Drawing on this work, we discuss principles of ligand design, such as the need to match a ligand to a particular substrate class, and how ligand traits such as tunability and modularity can be advantageous in reaction discovery. PMID:23565982

  18. Novel leads from Heliotropium ovalifolium, 4,7,8-trimethoxy-naphthalene-2-carboxylic acid and 6-hydroxy-5,7-dimethoxy-naphthalene-2-carbaldehyde show specific IL-6 inhibitory activity in THP-1 cells and primary human monocytes.

    PubMed

    Kulkarni-Almeida, Asha; Suthar, Ashish; Goswami, Hitesh; Vishwakarma, Ram; Chauhan, Vijay Singh; Balakrishnan, Arun; Sharma, Somesh

    2008-12-01

    From our screening program, we identified the anti-inflammatory effects of the extracts of Heliotropium ovalifolium in its ability to inhibit specific cytokines. The H. ovalifolium extract was found to be moderately active with an IC(50) equaling 10 microg/ml for inhibition of interleukin-6 (IL-6) in a human monocytic cell line. Interleukin-6 is a pleiotropic cytokine with implications in the regulation of the immune response, inflammation and hematopoiesis. This prompted us to examine and identify the active molecules that are responsible for the bioactivity in THP-1 cells. Bioassay guided fractionation identified two compounds 4,7,8-trimethoxy-naphthalene-2-carboxylic acid and 6-hydroxy-5,7-dimethoxy-naphthalene-2-carbaldehyde with an IC(50) of 2.4 and 2.0 microM for IL-6 inhibition and an IC(50) of 15.6 and 7.0 microM for tumor necrosis factor-alpha (TNF-alpha) inhibition in THP-1 cells. The protein expression data were supported by the inhibitory effect on mRNA gene expression. The compounds isolated from H. ovalifolium were also non-toxic in human peripheral blood monocytes from normal donors and the activity profile was similar to that obtained on THP-1 cells. Thus, we believe that these scaffolds may be of interest to develop leads for treating rheumatoid arthritis, psoriasis, ulcerative colitis, Crohn's disease and other inflammatory disorders. However, more detailed investigations need to be carried out to explain the efficacy of these compounds as drugs.

  19. Degradation of phenanthrene by Burkholderia sp. C3: initial 1,2- and 3,4-dioxygenation and meta- and ortho-cleavage of naphthalene-1,2-diol.

    PubMed

    Seo, Jong-Su; Keum, Young-Soo; Hu, Yuting; Lee, Sung-Eun; Li, Qing X

    2007-02-01

    Burkholderia sp. C3 was isolated from a polycyclic aromatic hydrocarbon (PAH)-contaminated site in Hilo, Hawaii, USA, and studied for its degradation of phenanthrene as a sole carbon source. The initial 3,4-C dioxygenation was faster than 1,2-C dioxygenation in the first 3-day culture. However, 1-hydroxy-2-naphthoic acid derived from 3,4-C dioxygenation degraded much slower than 2-hydroxy-1-naphthoic acid derived from 1,2-C dioxygenation. Slow degradation of 1-hydroxy-2-naphthoic acid relative to 2-hydroxy-1-naphthoic acid may trigger 1,2-C dioxygenation faster after 3 days of culture. High concentrations of 5,6- and 7,8-benzocoumarins indicated that meta-cleavage was the major degradation mechanism of phenanthrene-1,2- and -3,4-diols. Separate cultures with 2-hydroxy-1-naphthoic acid and 1-hydroxy-2-naphthoic acid showed that the degradation rate of the former to naphthalene-1,2-diol was much faster than that of the latter. The two upper metabolic pathways of phenanthrene are converged into naphthalene-1,2-diol that is further metabolized to 2-carboxycinnamic acid and 2-hydroxybenzalpyruvic acid by ortho- and meta-cleavages, respectively. Transformation of naphthalene-1,2-diol to 2-carboxycinnamic acid by this strain represents the first observation of ortho-cleavage of two rings-PAH-diols by a Gram-negative species.

  20. Structures and Binding Energies of the Naphthalene Dimer in Its Ground and Excited States.

    PubMed

    Dubinets, N O; Safonov, A A; Bagaturyants, A A

    2016-05-05

    Possible structures of the naphthalene dimer corresponding to local energy minima in the ground and excited (excimer) electronic states are comprehensively investigated using DFT-D and TDDFT-D methods with a special accent on the excimer structures. The corresponding binding and electronic transition energies are calculated, and the nature of the electronic states in different structures is analyzed. Several parallel (stacked) and T-shaped structures were found in both the ground and excited (excimer) states in a rather narrow energy range. The T-shaped structure with the lowest energy in the excited state exhibits a marked charge transfer from the upright molecule to the base one.

  1. Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach

    NASA Astrophysics Data System (ADS)

    Lam, Polo C.-H.; Abagyan, Ruben; Totrov, Maxim

    2018-01-01

    Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace.

  2. Synthetic bioactive novel ether based Schiff bases and their copper(II) complexes

    NASA Astrophysics Data System (ADS)

    Shabbir, Muhammad; Akhter, Zareen; Ismail, Hammad; Mirza, Bushra

    2017-10-01

    Novel ether based Schiff bases (HL1- HL4) were synthesized from 5-chloro-2-hydroxy benzaldehyde and primary amines (1-amino-4-phenoxybenzene, 4-(4-aminophenyloxy) biphenyl, 1-(4-aminophenoxy) naphthalene and 2-(4-aminophenoxy) naphthalene). From these Schiff bases copper(II) complexes (Cu(L1)2-Cu(L4)2)) were synthesized and characterized by elemental analysis and spectroscopic (FTIR, NMR) techniques. The synthesized Schiff bases and copper(II) complexes were further assessed for various biological studies. In brine shrimp assay the copper(II) complexes revealed 4-fold higher activity (LD50 3.8 μg/ml) as compared with simple ligands (LD50 12.4 μg/ml). Similar findings were observed in potato disc antitumor assay with higher activities for copper(II) complexes (IC50 range 20.4-24.1 μg/ml) than ligands (IC50 range 40.5-48.3 μg/ml). DPPH assay was performed to determine the antioxidant potential of the compounds. Significant antioxidant activity was shown by the copper(II) complexes whereas simple ligands have shown no activity. In DNA protection assay significant protection behavior was exhibited by simple ligand molecules while copper(II) complexes showed neutral behavior (neither protective nor damaging).

  3. ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites.

    PubMed

    Konc, Janez; Janežič, Dušanka

    2014-07-01

    The ProBiS-ligands web server predicts binding of ligands to a protein structure. Starting with a protein structure or binding site, ProBiS-ligands first identifies template proteins in the Protein Data Bank that share similar binding sites. Based on the superimpositions of the query protein and the similar binding sites found, the server then transposes the ligand structures from those sites to the query protein. Such ligand prediction supports many activities, e.g. drug repurposing. The ProBiS-ligands web server, an extension of the ProBiS web server, is open and free to all users at http://probis.cmm.ki.si/ligands. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Linear and Non-Linear Thermal Lens Signal of the Fifth C-H Vibrational Overtone of Naphthalene in Liquid Solutions of Hexane

    NASA Astrophysics Data System (ADS)

    Manzanares, Carlos; Diaz, Marlon; Barton, Ann; Nyaupane, Parashu R.

    2017-06-01

    The thermal lens technique is applied to vibrational overtone spectroscopy of solutions of naphthalene in n-hexane. The pump and probe thermal lens technique is found to be very sensitive for detecting samples of low composition (ppm) in transparent solvents. In this experiment two different probe lasers: one at 488 nm and another 568 nm were used. The C-H fifth vibrational overtone spectrum of benzene is detected at room temperature for different concentrations. A plot of normalized integrated intensity as a function of concentration of naphthalene in solution reveals a non-linear behavior at low concentrations when using the 488 nm probe and a linear behavior over the entire range of concentrations when using the 568 nm probe. The non-linearity cannot be explained assuming solvent enhancement at low concentrations. A two color absorption model that includes the simultaneous absorption of the pump and probe lasers could explain the enhanced magnitude and the non-linear behavior of the thermal lens signal. Other possible mechanisms will also be discussed.

  5. Dissociation of Multisubunit Protein-Ligand Complexes in the Gas Phase. Evidence for Ligand Migration

    NASA Astrophysics Data System (ADS)

    Zhang, Yixuan; Deng, Lu; Kitova, Elena N.; Klassen, John S.

    2013-10-01

    The results of collision-induced dissociation (CID) experiments performed on gaseous protonated and deprotonated ions of complexes of cholera toxin B subunit homopentamer (CTB5) with the pentasaccharide (β-D-Gal p-(1→3)-β-D-Gal pNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Gal p-(1→4)-β-D-Glc p (GM1)) and corresponding glycosphingolipid (β-D-Gal p-(1→3)-β-D-Gal pNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Gal p-(1→4)-β-D-Glc p-Cer (GM1-Cer)) ligands, and the homotetramer streptavidin (S4) with biotin (B) and 1,2-dipalmitoyl- sn-glycero-3-phosphoethanolamine-N-(biotinyl) (Btl), are reported. The protonated (CTB5 + 5GM1)n+ ions dissociated predominantly by the loss of a single subunit, with the concomitant migration of ligand to another subunit. The simultaneous loss of ligand and subunit was observed as a minor pathway. In contrast, the deprotonated (CTB5 + 5GM1)n- ions dissociated preferentially by the loss of deprotonated ligand; the loss of ligand-bound and ligand-free subunit were minor pathways. The presence of ceramide (Cer) promoted ligand migration and the loss of subunit. The main dissociation pathway for the protonated and deprotonated (S4 + 4B)n+/- ions, as well as for deprotonated (S4 + 4Btl)n- ions, was loss of the ligand. However, subunit loss from the (S4 + 4B)n+ ions was observed as a minor pathway. The (S4 + 4Btl)n+ ions dissociated predominantly by the loss of free and ligand-bound subunit. The charge state of the complex and the collision energy were found to have little effect on the relative contribution of the different dissociation channels. Thermally-driven ligand migration between subunits was captured in the results of molecular dynamics simulations performed on protonated (CTB5 + 5GM1)15+ ions (with a range of charge configurations) at 800 K. Notably, the migration pathway was found to be highly dependent on the charge configuration of the ion. The main conclusion of this study is that the dissociation pathways of multisubunit protein-ligand

  6. Ligand-induced Epitope Masking

    PubMed Central

    Mould, A. Paul; Askari, Janet A.; Byron, Adam; Takada, Yoshikazu; Jowitt, Thomas A.; Humphries, Martin J.

    2016-01-01

    We previously demonstrated that Arg-Gly-Asp (RGD)-containing ligand-mimetic inhibitors of integrins are unable to dissociate pre-formed integrin-fibronectin complexes (IFCs). These observations suggested that amino acid residues involved in integrin-fibronectin binding become obscured in the ligand-occupied state. Because the epitopes of some function-blocking anti-integrin monoclonal antibodies (mAbs) lie near the ligand-binding pocket, it follows that the epitopes of these mAbs may become shielded in the ligand-occupied state. Here, we tested whether function-blocking mAbs directed against α5β1 can interact with the integrin after it forms a complex with an RGD-containing fragment of fibronectin. We showed that the anti-α5 subunit mAbs JBS5, SNAKA52, 16, and P1D6 failed to disrupt IFCs and hence appeared unable to bind to the ligand-occupied state. In contrast, the allosteric anti-β1 subunit mAbs 13, 4B4, and AIIB2 could dissociate IFCs and therefore were able to interact with the ligand-bound state. However, another class of function-blocking anti-β1 mAbs, exemplified by Lia1/2, could not disrupt IFCs. This second class of mAbs was also distinguished from 13, 4B4, and AIIB2 by their ability to induce homotypic cell aggregation. Although the epitope of Lia1/2 was closely overlapping with those of 13, 4B4, and AIIB2, it appeared to lie closer to the ligand-binding pocket. A new model of the α5β1-fibronectin complex supports our hypothesis that the epitopes of mAbs that fail to bind to the ligand-occupied state lie within, or very close to, the integrin-fibronectin interface. Importantly, our findings imply that the efficacy of some therapeutic anti-integrin mAbs could be limited by epitope masking. PMID:27484800

  7. Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system.

    PubMed

    Kantardjiev, Alexander A

    2012-07-01

    Quantum.Ligand.Dock (protein-ligand docking with graphic processing unit (GPU) quantum entanglement refinement on a GPU system) is an original modern method for in silico prediction of protein-ligand interactions via high-performance docking code. The main flavour of our approach is a combination of fast search with a special account for overlooked physical interactions. On the one hand, we take care of self-consistency and proton equilibria mutual effects of docking partners. On the other hand, Quantum.Ligand.Dock is the the only docking server offering such a subtle supplement to protein docking algorithms as quantum entanglement contributions. The motivation for development and proposition of the method to the community hinges upon two arguments-the fundamental importance of quantum entanglement contribution in molecular interaction and the realistic possibility to implement it by the availability of supercomputing power. The implementation of sophisticated quantum methods is made possible by parallelization at several bottlenecks on a GPU supercomputer. The high-performance implementation will be of use for large-scale virtual screening projects, structural bioinformatics, systems biology and fundamental research in understanding protein-ligand recognition. The design of the interface is focused on feasibility and ease of use. Protein and ligand molecule structures are supposed to be submitted as atomic coordinate files in PDB format. A customization section is offered for addition of user-specified charges, extra ionogenic groups with intrinsic pK(a) values or fixed ions. Final predicted complexes are ranked according to obtained scores and provided in PDB format as well as interactive visualization in a molecular viewer. Quantum.Ligand.Dock server can be accessed at http://87.116.85.141/LigandDock.html.

  8. Zero-point fluctuations in naphthalene and their effect on charge transport parameters.

    PubMed

    Kwiatkowski, Joe J; Frost, Jarvist M; Kirkpatrick, James; Nelson, Jenny

    2008-09-25

    We calculate the effect of vibronic coupling on the charge transport parameters in crystalline naphthalene, between 0 and 400 K. We find that nuclear fluctuations can cause large changes in both the energy of a charge on a molecule and on the electronic coupling between molecules. As a result, nuclear fluctuations cause wide distributions of both energies and couplings. We show that these distributions have a small temperature dependence and that, even at high temperatures, vibronic coupling is dominated by the effect of zero-point fluctuations. Because of the importance of zero-point fluctuations, we find that the distributions of energies and couplings have substantial width, even at 0 K. Furthermore, vibronic coupling with high energy modes may be significant, even though these modes are never thermally activated. Our results have implications for the temperature dependence of charge mobilities in organic semiconductors.

  9. Effects of methoxy and formyl substituents on the energetics and reactivity of α-naphthalenes: a calorimetric and computational study.

    PubMed

    Silva, Ana L R; Freitas, Vera L S; Ribeiro da Silva, Maria D M C

    2014-07-01

    A combined experimental and computational study was developed to evaluate and understand the energetics and reactivity of formyl and methoxy α-naphthalene derivatives. Static bomb combustion calorimetry and the Calvet microcalorimetry were the experimental techniques used to determine the standard (p(o)=0.1 MPa) molar enthalpies of formation, in the liquid phase, ΔfHm(o)(l), and of vaporization, Δl(g)Hm(o), at T=298.15K, respectively, of the two liquid naphthalene derivatives. Those experimental values were used to derive the values of the experimental standard molar enthalpies of formation, in the gaseous phase, ΔfHm(o)(g), of 1-methoxynaphthalene, (-3.0 ± 3.1)kJmol(-1), and of 1-formylnaphthalene, (36.3 ± 4.1)kJ mol(-1). High-level quantum chemical calculations at the composite G3(MP2)//B3LYP level were performed to estimate the values of the ΔfHm(o)(g) of the two compounds studied resulting in values in very good agreement with experimental ones. Natural bond orbital (NBO) calculations were also performed to determine more about the structure and reactivity of this class of compounds. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Thermogravimetric study of thermal decontamination of soils polluted by hexachlorobenzene, 4-chlorobiphenyl, naphthalene, or n-decane.

    PubMed

    Risoul, V; Pichon, C; Trouvé, G; Peters, W A; Gilot, P; Prado, G

    1999-02-15

    To determine decontamination behavior as affected by temperature, shallow beds of a clay-rich, a calcerous, and a sedimentary soil, artificially polluted with hexachlorobenzene, 4-chlorobiphenyl, naphthalene, or n-decane, were separately heated at 5 degrees C min-1 in a thermogravimetric analyzer. Temperatures for deep cleaning of the calcerous and the sedimentary soil increased with increasing boiling point (bp) of the aromatic contaminants, but removal efficiencies still approached 100% well below the bp. Decontamination rates were therefore modelled according to a pollutant evaporation-diffusion transport model. For the calcerous and sedimentary soils, this model reasonably correlated removal of roughly the first 2/3 of the naphthalene, but gave only fair predictions for hexachlorobenzene and 4-chlorobiphenyl. It was necessary to heat the clay soil above the aromatics bp to achieve high decontamination efficiencies. Weight loss data imply that for temperatures from near ambient to as much as 150 degrees C, interactions of each aromatic with the clay soil, or its decomposition products, result in lower net volatilization of the contaminated vs. neat clay. A similar effect was observed in heating calcerous soil polluted with hexachlorobenzene from near ambient to about 140 degrees C. Decontamination mechanisms remain to be established, although the higher temperatures needed to remove aromatics from the clay may reflect a more prominent role for surface desorption than evaporation. This would be consistent with our estimates that the clay can accommodate all of the initial pollutant loadings within a single surface monolayer, whereas the calcerous and sedimentary soils cannot.

  11. The formation of SOA and chemical tracer compounds from the photooxidation of naphthalene and its methyl analogs in the presence and absence of nitrogen oxides

    EPA Science Inventory

    Laboratory smog chamber experiments have been carried out to investigate secondary organic aerosol (SOA)formation from the photooxidation of naphthalene and its methyl analogs, 1- and 2-methylnaphthalene (1-MN and 2- MN, respectively). Laboratory smog chamber irradiations were co...

  12. Amino acid ionic liquids as chiral ligands in ligand-exchange chiral separations.

    PubMed

    Liu, Qian; Wu, Kangkang; Tang, Fei; Yao, Lihua; Yang, Fei; Nie, Zhou; Yao, Shouzhuo

    2009-09-28

    Recently, amino acid ionic liquids (AAILs) have attracted much research interest. In this paper, we present the first application of AAILs in chiral separation based on the chiral ligand exchange principle. By using 1-alkyl-3-methylimidazolium L-proline (L-Pro) as a chiral ligand coordinated with copper(II), four pairs of underivatized amino acid enantiomers-dl-phenylalanine (dl-Phe), dl-histidine (dl-His), dl-tryptophane (dl-Trp), and dl-tyrosine (dl-Tyr)-were successfully separated in two major chiral separation techniques, HPLC and capillary electrophoresis (CE), with higher enantioselectivity than conventionally used amino acid ligands (resolution (R(s))=3.26-10.81 for HPLC; R(s)=1.34-4.27 for CE). Interestingly, increasing the alkyl chain length of the AAIL cation remarkably enhanced the enantioselectivity. It was inferred that the alkylmethylimidazolium cations and L-Pro form ion pairs on the surface of the stationary phase or on the inner surface of the capillary. The ternary copper complexes with L-Pro are consequently attached to the support surface, thus inducing an ion-exchange type of retention for the dl-enantiomers. Therefore, the AAIL cation plays an essential role in the separation. This work demonstrates that AAILs are good alternatives to conventional amino acid ligands for ligand-exchange-based chiral separation. It also reveals the tremendous application potential of this new type of task-specific ILs.

  13. Mode-of-Action Uncertainty for Dual-Mode Carcinogens:Lower Bounds for Naphthalene-Induced Nasal Tumors in Rats Implied byPBPK and 2-Stage Stochastic Cancer Risk Models

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

    Bogen, K T

    2007-01-30

    As reflected in the 2005 USEPA Guidelines for Cancer Risk Assessment, some chemical carcinogens may have a site-specific mode of action (MOA) that is dual, involving mutation in addition to cell-killing induced hyperplasia. Although genotoxicity may contribute to increased risk at all doses, the Guidelines imply that for dual MOA (DMOA) carcinogens, judgment be used to compare and assess results obtained using separate ''linear'' (genotoxic) vs. ''nonlinear'' (nongenotoxic) approaches to low-level risk extrapolation. However, the Guidelines allow the latter approach to be used only when evidence is sufficient to parameterize a biologically based model that reliably extrapolates risk to lowmore » levels of concern. The Guidelines thus effectively prevent MOA uncertainty from being characterized and addressed when data are insufficient to parameterize such a model, but otherwise clearly support a DMOA. A bounding factor approach--similar to that used in reference dose procedures for classic toxicity endpoints--can address MOA uncertainty in a way that avoids explicit modeling of low-dose risk as a function of administered or internal dose. Even when a ''nonlinear'' toxicokinetic model cannot be fully validated, implications of DMOA uncertainty on low-dose risk may be bounded with reasonable confidence when target tumor types happen to be extremely rare. This concept was illustrated for the rodent carcinogen naphthalene. Bioassay data, supplemental toxicokinetic data, and related physiologically based pharmacokinetic and 2-stage stochastic carcinogenesis modeling results all clearly indicate that naphthalene is a DMOA carcinogen. Plausibility bounds on rat-tumor-type specific DMOA-related uncertainty were obtained using a 2-stage model adapted to reflect the empirical link between genotoxic and cytotoxic effects of the most potent identified genotoxic naphthalene metabolites, 1,2- and 1,4-naphthoquinone. Resulting bounds each provided the basis for a corresponding

  14. Synthesis, characterization, DFT calculations and biological studies of Mn(II), Fe(II), Co(II) and Cd(II) complexes based on a tetradentate ONNO donor Schiff base ligand

    NASA Astrophysics Data System (ADS)

    Abdel-Rahman, Laila H.; Ismail, Nabawia M.; Ismael, Mohamed; Abu-Dief, Ahmed M.; Ahmed, Ebtehal Abdel-Hameed

    2017-04-01

    This study highlights synthesis and characterization of a tetradentate ONNO Schiff base ligand namely (1, 1‧- (pyridine-2, 3-dimethyliminomethyl) naphthalene-2, 2‧-diol) and hereafter denotes as "HNDAP″ and selected metal complexes including Mn(II), Fe(II), Co(II) and Cd(II) as a central metal. HNDAP was synthesized from 1:2 M ratio condensation of 2, 3-diaminopyridine and 2- hydroxy-1-naphthaldhyde, respectively. The stoichiometric ratios of the prepared complexes were estimated using complementary techniques such as; elemental analyses (-C, H, N), FT-IR, magnetic measurements and molar conductivity. Furthermore, their physicochemical studies were carried out using thermal TGA, DTA and kinetic-thermodynamic studies along with DFT calculations. The results of elemental analyses showed that these complexes are present in a 1:1 metal-to- ligand molar ratio. Moreover, the magnetic susceptibilities values at room temperature revealed that Mn(II), Fe(II) and Co(II) complexes are paramagnetic in nature and have an octahedral (Oh) geometry. In contrast, Cd(II) is diamagnetic and stabilizes in square planar sites. The molar conductivity measurements indicated that all complexes are nonelectrolytes in dimethyl formamide. Spectral data suggested that the ligand is as tetradentate and coordinated with Co(II) ion through two phenolic OH and two azomethine nitrogen. However, for Mn(II), Fe(II) and Cd(II) complexes, the coordination occurred through two phenolic oxygen and two azomethine nitrogen with deprotonation of OH groups. The proposed chemical structures have been validated by quantum mechanics calculations. Antimicrobial activities of both the HNDAP Schiff base ligand and its metal complexes were tested against strains of Gram (-ve) E. coli and Gram (+ve) B. subtilis and S. aureus bacteria and C. albicans, A. flavus and T. rubrum fungi. All the prepared compounds showed good results of inhibition against the selected pathogenic microorganisms. The investigated

  15. Comparison of the Morphology Development of Polymer-Fullerene and Polymer-Polymer Solar Cells during Solution-Shearing Blade Coating

    DOE PAGES

    Gu, Xiaodan; Yan, Hongping; Kurosawa, Tadanori; ...

    2016-08-22

    Here in this work, the detailed morphology studies of polymer poly(3-hexylthiophene-2,5-diyl) (P3HT):fullerene(PCBM) and polymer(P3HT):polymer naphthalene diimide thiophene (PNDIT) solar cell are presented to understand the challenge for getting high performance all-polymer solar cells. The in situ X-ray scattering and optical interferometry and ex situ hard and soft X-ray scattering and imaging techniques are used to characterize the bulk heterojunction (BHJ) ink during drying and in dried state. The crystallization of P3HT polymers in P3HT:PCBM bulk heterojunction shows very different behavior compared to that of P3HT:PNDIT BHJ due to different mobilities of P3HT in the donor:acceptor glass. Supplemented by the exmore » situ grazing incidence X-ray diffraction and soft X-ray scattering, PNDIT has a lower tendency to form a mixed phase with P3HT than PCBM, which may be the key to inhibit the donor polymer crystallization process, thus creating preferred small phase separation between the donor and acceptor polymer.« less

  16. An alternate binding site for PPARγ ligands

    PubMed Central

    Hughes, Travis S.; Giri, Pankaj Kumar; de Vera, Ian Mitchelle S.; Marciano, David P.; Kuruvilla, Dana S.; Shin, Youseung; Blayo, Anne-Laure; Kamenecka, Theodore M.; Burris, Thomas P.; Griffin, Patrick R.; Kojetin, Douglas J.

    2014-01-01

    PPARγ is a target for insulin sensitizing drugs such as glitazones, which improve plasma glucose maintenance in patients with diabetes. Synthetic ligands have been designed to mimic endogenous ligand binding to a canonical ligand-binding pocket to hyperactivate PPARγ. Here we reveal that synthetic PPARγ ligands also bind to an alternate site, leading to unique receptor conformational changes that impact coregulator binding, transactivation and target gene expression. Using structure-function studies we show that alternate site binding occurs at pharmacologically relevant ligand concentrations, and is neither blocked by covalently bound synthetic antagonists nor by endogenous ligands indicating non-overlapping binding with the canonical pocket. Alternate site binding likely contributes to PPARγ hyperactivation in vivo, perhaps explaining why PPARγ full and partial or weak agonists display similar adverse effects. These findings expand our understanding of PPARγ activation by ligands and suggest that allosteric modulators could be designed to fine tune PPARγ activity without competing with endogenous ligands. PMID:24705063

  17. INFRARED STUDY OF UV/EUV IRRADIATION OF NAPHTHALENE IN H2O+NH3 ICE

    NASA Astrophysics Data System (ADS)

    Chen, Y.-J.; Nuevo, M.; Yeh, F.-C.; Yih, T.-S.; Sun, W.-H.; Ip, W.-H.; Fung, H.-S.; Lee, Y.-Y.; Wu, C.-Y. R.

    We have carried out photon irradiation study of naphthalene (C10H8), the smallest polycyclic aromatic hydrocarbon (PAH) in water and ammonia ice mixtures. Photons provided by a synchrotron radiation light source in two broad-band energy ranges in the ultraviolet/near extreme ultraviolet (4-20 eV) and the extreme ultraviolet (13-45 eV) ranges were used for the irradiation of H2O+NH3+C10H8 = 1:1:1 ice mixtures at 15K. We could identify several photo-products, namely CH4, C2H6, C3H8, CO, CO2, HNCO, OCN-, and probably quinoline (C9H7N) and phenanthridine (C13H9N). We found that the light hydrocarbons are preferably produced for the ice mixture subjected to 4-20 eV photons. However, the production yields of CO, CO2, and OCN- species seem to be higher for the mixture subjected to EUV photons (13-45 eV). Therefore, naphthalene and its photo-products appear to be more efficiently destroyed when high energy photons (E > 20 eV) are used. This has important consequences on the photochemical evolution of PAHs in astrophysical environments.

  18. A general ligand design for gold catalysis allowing ligand-directed anti-nucleophilic attack of alkynes.

    PubMed

    Wang, Yanzhao; Wang, Zhixun; Li, Yuxue; Wu, Gongde; Cao, Zheng; Zhang, Liming

    2014-04-07

    Most homogenous gold catalyses demand ≥ 0.5 mol% catalyst loading. Owing to the high cost of gold, these reactions are unlikely to be applicable in medium- or large-scale applications. Here we disclose a novel ligand design based on the privileged (1,1'-biphenyl)-2-ylphosphine framework that offers a potentially general approach to dramatically lowering catalyst loading. In this design, an amide group at the 3'-position of the ligand framework directs and promotes nucleophilic attack at the ligand gold complex-activated alkyne, which is unprecedented in homogenous gold catalysis considering the spatial challenge of using ligand to reach anti-approaching nucleophile in a linear P-Au-alkyne centroid structure. With such a ligand, the gold(I) complex becomes highly efficient in catalysing acid addition to alkynes, with a turnover number up to 99,000. Density functional theory calculations support the role of the amide moiety in directing the attack of carboxylic acid via hydrogen bonding.

  19. A General Ligand Design for Gold Catalysis allowing Ligand-Directed Anti Nucleophilic Attack of Alkynes

    PubMed Central

    Wang, Yanzhao; Wang, Zhixun; Li, Yuxue; Wu, Gongde; Cao, Zheng; Zhang, Liming

    2014-01-01

    Most homogenous gold catalyses demand ≥0.5 mol % catalyst loading. Due to the high cost of gold, these reactions are unlikely to be applicable in medium or large scale applications. Here we disclose a novel ligand design based on the privileged biphenyl-2-phosphine framework that offers a potentially general approach to dramatically lowering catalyst loading. In this design, an amide group at the 3’ position of the ligand framework directs and promotes nucleophilic attack at the ligand gold complex-activated alkyne, which is unprecedented in homogeneous gold catalysis considering the spatial challenge of using ligand to reach antiapproaching nucleophile in a linear P-Au-alkyne centroid structure. With such a ligand, the gold(I) complex becomes highly efficient in catalyzing acid addition to alkynes, with a turnover number up to 99,000. Density functional theory calculations support the role of the amide moiety in directing the attack of carboxylic acid via hydrogen bonding. PMID:24704803

  20. Genome Sequences of Two Naphthalene-Degrading Strains of Pseudomonas balearica, Isolated from Polluted Marine Sediment and from an Oil Refinery Site.

    PubMed

    Salvà-Serra, Francisco; Jakobsson, Hedvig E; Busquets, Antonio; Gomila, Margarita; Jaén-Luchoro, Daniel; Seguí, Carolina; Aliaga-Lozano, Francisco; García-Valdés, Elena; Lalucat, Jorge; Moore, Edward R B; Bennasar-Figueras, Antoni

    2017-04-06

    The genome sequences of Pseudomonas balearica strains LS401 (CCUG 66666) and st101 (CCUG 66667) have been determined. The strains were isolated as naphthalene degraders from polluted marine sediment and from a sample from an oil refinery site, respectively. These genomes provide essential data about the biodegradation capabilities and the ecological implications of P. balearica . Copyright © 2017 Salvà-Serra et al.

  1. Electronic absorption spectroscopy of matrix-isolated polycyclic aromatic hydrocarbon cations. I - The naphthalene cation (C10H8/+/)

    NASA Technical Reports Server (NTRS)

    Salama, F.; Allamandola, L. J.

    1991-01-01

    The ultraviolet, visible, and near-infrared absorption spectra of naphthalene (C10H8) and its radical ion (C10H8/+/), formed by vacuum ultraviolet irradiation, were measured in argon and neon matrices at 4.2 K. The associated vibronic band systems and their spectroscopic assignments are discussed together with the physical and chemical conditions governing ion production in the solid phase. The absorption coefficients were calculated for the ion and found lower than previous values, presumably due to the low polarizability of the neon matrix.

  2. Stereospecific oxidation of (R)- and (S)-1-indanol by naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4.

    PubMed Central

    Lee, K; Resnick, S M; Gibson, D T

    1997-01-01

    A recombinant Escherichia coli strain which expresses naphthalene dioxygenase (NDO) from Pseudomonas sp. strain NCIB 9816-4 oxidized (S)-1-indanol to trans-(1S,3S)-indan-1,3-diol (95.5%) and (R)-3-hydroxy-1-indanone (4.5%). The same cells oxidized (R)-1-indanol to cis-1,3-indandiol (71%), (R)-3-hydroxy-1-indanone (18.2%), and cis-1,2,3-indantriol (10.8%). Purified NDO oxidized (S)-1-indenol to both syn- and anti-2,3-dihydroxy-1-indanol. PMID:9143136

  3. Stereospecific oxidation of (R)- and (S)-1-indanol by naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4.

    PubMed

    Lee, K; Resnick, S M; Gibson, D T

    1997-05-01

    A recombinant Escherichia coli strain which expresses naphthalene dioxygenase (NDO) from Pseudomonas sp. strain NCIB 9816-4 oxidized (S)-1-indanol to trans-(1S,3S)-indan-1,3-diol (95.5%) and (R)-3-hydroxy-1-indanone (4.5%). The same cells oxidized (R)-1-indanol to cis-1,3-indandiol (71%), (R)-3-hydroxy-1-indanone (18.2%), and cis-1,2,3-indantriol (10.8%). Purified NDO oxidized (S)-1-indenol to both syn- and anti-2,3-dihydroxy-1-indanol.

  4. Acute and chronic liver toxicity resulting from exposure to chlorinated naphthalenes at a cable manufacturing plant during World War II.

    PubMed

    Ward, E M; Ruder, A M; Suruda, A; Smith, A B; Fessler-Flesch, C A; Zahm, S H

    1996-08-01

    Historical records were used to reconstruct an outbreak of chlorance and acute liver toxicity due to chlorinated naphthalene exposure at a New York State plant which manufactured "Navy cables" during World War II. A cohort mortality study was conducted of the population (n = 9,028) employed at the plant from 1940 to 1944. Vital status was followed through December 31, 1985. The study found an excess of deaths from cirrhosis of the liver [observed (OBS) = 150; standardized mortality ratio (SMR) = 1.84; 95% confidence interval (CI) = 1.56-2.16]; cirrhosis deaths were elevated to a similar degree in the 460 individuals who had chlorance (OBS = 8; SMR = 1.51; CI = 0.65-2.98). The SMR for "non-alcoholic cirrhosis" (OBS = 83; SMR = 1.67; CI = 1.33-2.07) was similar to the SMR for "alcoholic cirrhosis" (OBS = 59; SMR = 1.96; CI = 1.49-2.53). There was no evidence for increased alcoholism in the overall cohort based on mortality from alcohol-related causes of death other than cirrhosis (SMR for esophageal cancer = 1.01 and for deaths from alcoholism = 0.99). We conclude that the excess mortality from cirrhosis of the liver observed in this cohort is due to the chronic effect of chlorinated naphthalene exposure.

  5. Synthesis, characterization, crystal structure, superoxide dismutase and biological activities of nickel (II) complexes with bidentate ligands possessing N and O donor atoms

    NASA Astrophysics Data System (ADS)

    Sangeeta, S.; Ahmad, K.; Noorussabah, N.; Bharti, S.; Mishra, M. K.; Sharma, S. R.; Choudhary, M.

    2017-12-01

    Two new Schiff bases 2-((E)-(4-bromo-2-chlorophenylimino)methyl)-4-bromophenol(HL1) and1-((E)-(4-bromo-2-chlorophenylimino)methyl)naphthalene-2-ol (HL2) and their new nickel (II) complexes [Ni(L1)2]·DMF(1) and [Ni(L2)2] (2) have been synthesized and characterized by various physico- chemical and spectroscopic methods. The solid-state structures of synthesized compounds were determined by single crystal X-ray crystallography, which revealed square planar geometry around Ni (II) ion. Infrared spectra, UV-Vis, thermal analysis and magnetic susceptibility measurements agreed with the observed crystal structures. The ligand (HL1) crystallized in the Orthorhombic system of the space group Pbca,a = 7.5485(4)Å, b = 11.5514(5) Å, c = 30.1370(14)Å, α = 90°, β = 90°, γ = 90°and Z = 8. Complex[Ni(L1)2]·DMF(1) crystallized in the Triclinic system of the space group P-1, a = 8.9954(3) Å, b = 9.4593(4) Å, c = 13.2657(5) Å, α = 101.478°, β = 99.595°, γ = 117.651°and Z = 2, whereas complex [Ni(L2)2]·(2) crystallized in the Monoclinic system of the space group P21/c, a = 9.301(9)Å, b = 12.149(8)Å, c = 13.792(10)Å, α = 90°, β = 106.35(4).°, γ = 90°and Z = 2. The Schiff bases (HL1and HL2) behaved as monobasic bidentate ligands possessing N and O donor atoms. The SOD activities of HL1 and its Ni (II) complex[Ni(L1)2]·DMF(1) have been measured using xanthine-xanthine oxidase as a source of superoxide radical and NBT assay as O2- scavenger. In vitro antimicrobial activities of the Ni(II) complexes (1) and (2)against Bacillus cereus and Staphylococcus aureus as Gram + ve and Salmonella typhi, Klebsiella pneumonia and Escherichia coli as Gram-ve species have been investigated comparing with the Schiff base ligands (HL1and HL2).

  6. Highly sensitive detection of naphthalene in solvent vapor using a functionalized PBG refractive index sensor.

    PubMed

    Girschikofsky, Maiko; Rosenberger, Manuel; Belle, Stefan; Brutschy, Malte; Waldvogel, Siegfried R; Hellmann, Ralf

    2012-01-01

    We report an optical refractive index sensor system based on a planar Bragg grating which is functionalized by substituted γ-cyclodextrin to determine low concentrations of naphthalene in solvent vapor. The sensor system exhibits a quasi-instantaneous shift of the Bragg wavelength and is therefore capable for online detection. The overall shift of the Bragg wavelength reveals a linear relationship to the analyte concentration with a gradient of 12.5 ± 1.5 pm/ppm. Due to the spectral resolution and repeatability of the interrogation system, this corresponds to acquisition steps of 80 ppb. Taking into account the experimentally detected signal noise a minimum detection limit of 0.48 ± 0.05 ppm is deduced.

  7. Ligand cluster-based protein network and ePlatton, a multi-target ligand finder.

    PubMed

    Du, Yu; Shi, Tieliu

    2016-01-01

    Small molecules are information carriers that make cells aware of external changes and couple internal metabolic and signalling pathway systems with each other. In some specific physiological status, natural or artificial molecules are used to interact with selective biological targets to activate or inhibit their functions to achieve expected biological and physiological output. Millions of years of evolution have optimized biological processes and pathways and now the endocrine and immune system cannot work properly without some key small molecules. In the past thousands of years, the human race has managed to find many medicines against diseases by trail-and-error experience. In the recent decades, with the deepening understanding of life and the progress of molecular biology, researchers spare no effort to design molecules targeting one or two key enzymes and receptors related to corresponding diseases. But recent studies in pharmacogenomics have shown that polypharmacology may be necessary for the effects of drugs, which challenge the paradigm, 'one drug, one target, one disease'. Nowadays, cheminformatics and structural biology can help us reasonably take advantage of the polypharmacology to design next-generation promiscuous drugs and drug combination therapies. 234,591 protein-ligand interactions were extracted from ChEMBL. By the 2D structure similarity, 13,769 ligand emerged from 156,151 distinct ligands which were recognized by 1477 proteins. Ligand cluster- and sequence-based protein networks (LCBN, SBN) were constructed, compared and analysed. For assisting compound designing, exploring polypharmacology and finding possible drug combination, we integrated the pathway, disease, drug adverse reaction and the relationship of targets and ligand clusters into the web platform, ePlatton, which is available at http://www.megabionet.org/eplatton. Although there were some disagreements between the LCBN and SBN, communities in both networks were largely the same

  8. Two three-dimensional coordination polymers of lead(II) with iminodiacetate and naphthalene-dicarboxylate anions: Synthesis, characterization and luminescence behavior

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

    Hazari, Debdoot; Jana, Swapan Kumar; Fleck, Michel

    2014-11-15

    Two lead(II) compounds [Pb{sub 3}(idiac){sub 3}(phen){sub 2}(H{sub 2}O)]·2(H{sub 2}O) (1) and [Pb(ndc)]{sub n} (2), where H{sub 2}idiac=iminodiacetic acid, phen=1,10-phenanthroline and H{sub 2}ndc=naphthalene-2,6-dicarboxylic acid, have been synthesized and structurally characterized. Single crystal X-ray diffraction analysis showed that compound 1 is a discrete trinuclear complex (of two-fold symmetry) which evolves to a supramolecular 3D network via π–π interactions, while in compound 2 the naphthalene dicarboxylate anion act as a linker to form a three dimensional architecture, where the anion adopts a bis-(bidentate bridging) coordination mode connecting four Pb(II) centers. The photoluminescence property of the two complexes has been studied. - graphical abstract:more » Two new topologically different 1D coordination polymers formed by Pb{sub 4} clusters have been synthesized and characterized by x-ray analysis. The luminescence and thermal properties have been studied. - Highlights: • 1 is a trinuclear complex of Pb(II) growing to 3D network via weak interactions. • In 1, layers of (4,4) rhomboidal topology are identified. • In 2, the ndc anion adopts interesting bis-(bidentate bridging) coordination. • In 2, network is reinforced by C–H…π-ring interactions between the ndc rings.« less

  9. Assessment of bile fluorescence patterns in a tropical fish, Nile tilapia (Oreochromis niloticus) exposed to naphthalene, phenanthrene, pyrene and chrysene using fixed wavelength fluorescence and synchronous fluorescence spectrometry.

    PubMed

    Pathiratne, A; Hemachandra, C K; Pathiratne, K A S

    2010-05-01

    Bile fluorescence patterns in Nile tilapia, a potential fish for biomonitoring tropical water pollution were assessed following exposure to selected polycyclic aromatic hydrocarbons (PAHs): naphthalene, phenanthrene, pyrene and chrysene. Non-normalized fixed wavelength fluorescence signals in the fish exposed to these PAHs reflected dose and/or time response relationships of their metabolism. Normalizing signals to biliverdin introduced deviations to these response patterns. The optimal wavelength pairs (excitation/emission) for synchronous fluorescence scanning measurements of bile metabolites of naphthalene, phenanthrene, pyrene and chrysene were identified as 284/326, 252/357, 340/382 and 273/382 respectively. This study supports the use of bile fluorescence in Nile tilapia by fixed wavelength fluorescence and synchronous fluorescence spectrometry with non-normalized data as a simple method for screening bioavailability of these PAHs.

  10. Chemistry of Marine Ligands and Siderophores

    PubMed Central

    Vraspir, Julia M.; Butler, Alison

    2011-01-01

    Marine microorganisms are presented with unique challenges to obtain essential metal ions required to survive and thrive in the ocean. The production of organic ligands to complex transition metal ions is one strategy to both facilitate uptake of specific metals, such as iron, and to mitigate the potential toxic effects of other metal ions, such as copper. A number of important trace metal ions are complexed by organic ligands in seawater, including iron, cobalt, nickel, copper, zinc, and cadmium, thus defining the speciation of these metal ions in the ocean. In the case of iron, siderophores have been identified and structurally characterized. Siderophores are low molecular weight iron-binding ligands produced by marine bacteria. Although progress has been made toward the identity of in situ iron-binding ligands, few compounds have been identified that coordinate the other trace metals. Deciphering the chemical structures and production stimuli of naturally produced organic ligands and the organisms they come from is fundamental to understanding metal speciation and bioavailability. The current evidence for marine ligands, with an emphasis on siderophores, and discussion of the importance and implications of metal-binding ligands in controlling metal speciation and cycling within the world’s oceans are presented. PMID:21141029

  11. Perfluorinated Ligands in Organometallic Chemistry

    DTIC Science & Technology

    1989-12-12

    C49t00ooVER ,or C M’ AD"OV’~mDecember 12) 199IFinal 1/1/86 to 8/31/89C smuS. FUNOING NUMgIERS cJ Perfluorinated Ligands in Organometallic Chemistry 612...compounds, stabilized by tridentate perfluorinated ligands. Dinuclear rhodium complexes of OFCOT undergo a selective C-F bond activation reaction...hexafluorocyclooctatrieneyne ligand. Stereospecific cleavage of a fluorinated C-C bond,#-bond in perfluorocyclopropene by platinum and iridium complexes has been achieved

  12. Effect of Energy Alignment, Electron Mobility, and Film Morphology of Perylene Diimide Based Polymers as Electron Transport Layer on the Performance of Perovskite Solar Cells.

    PubMed

    Guo, Qiang; Xu, Yingxue; Xiao, Bo; Zhang, Bing; Zhou, Erjun; Wang, Fuzhi; Bai, Yiming; Hayat, Tasawar; Alsaedi, Ahmed; Tan, Zhan'ao

    2017-03-29

    For organic-inorganic perovskite solar cells (PerSCs), the electron transport layer (ETL) plays a crucial role in efficient electron extraction and transport for high performance PerSCs. Fullerene and its derivatives are commonly used as ETL for p-i-n structured PerSCs. However, these spherical small molecules are easy to aggregate with high annealing temperature and thus induce morphology stability problems. N-type conjugated polymers are promising candidates to overcome these problems due to the tunable energy levels, controllable aggregation behaviors, and good film formation abilities. Herein, a series of perylene diimide (PDI) based polymers (PX-PDIs), which contain different copolymeried units (X), including vinylene (V), thiophene (T), selenophene (Se), dibenzosilole (DBS), and cyclopentadithiophene (CPDT), are introduced as ETL for p-i-n structured PerSCs. The effect of energy alignment, electron mobility, and film morphology of these ETLs on the photovoltaic performance of the PerSCs are fully investigated. Among the PX-PDIs, PV-PDI demonstrates the deeper LUMO energy level, the highly delocalized LUMO electron density, and a better planar structure, making it the best electron transport material for PerSCs. The planar heterojunction PerSC with PV-PDI as ETL achieves a power conversion efficiency (PCE) of 10.14%, among the best values for non-fullerene based PerSCs.

  13. Structural Analysis of Chemokine Receptor–Ligand Interactions

    PubMed Central

    2017-01-01

    This review focuses on the construction and application of structural chemokine receptor models for the elucidation of molecular determinants of chemokine receptor modulation and the structure-based discovery and design of chemokine receptor ligands. A comparative analysis of ligand binding pockets in chemokine receptors is presented, including a detailed description of the CXCR4, CCR2, CCR5, CCR9, and US28 X-ray structures, and their implication for modeling molecular interactions of chemokine receptors with small-molecule ligands, peptide ligands, and large antibodies and chemokines. These studies demonstrate how the integration of new structural information on chemokine receptors with extensive structure–activity relationship and site-directed mutagenesis data facilitates the prediction of the structure of chemokine receptor–ligand complexes that have not been crystallized. Finally, a review of structure-based ligand discovery and design studies based on chemokine receptor crystal structures and homology models illustrates the possibilities and challenges to find novel ligands for chemokine receptors. PMID:28165741

  14. The fluorescently responsive 3-(naphthalen-1-ylethynyl)-3-deaza-2'-deoxyguanosine discriminates cytidine via the DNA minor groove.

    PubMed

    Suzuki, Azusa; Yanagi, Masaki; Takeda, Takuya; Hudson, Robert H E; Saito, Yoshio

    2017-09-26

    A new environmentally responsive fluorescent nucleoside, 3-(naphthalen-1-ylethynyl)-3-deaza-2'-deoxyguanosine ( 3nz G), has been synthesized. The nucleoside, 3nz G, exhibited solvatochromic properties and when introduced into ODN probes it was able to recognize 2'-deoxycytidine in target strands by a distinct change in its emission wavelength through probing microenvironmental changes in the DNA minor groove. Thus, 3nz G has the potential for use as a fluorescent probe molecule for micro-structural studies of nucleic acids including the detection of single-base alterations in target DNA sequences.

  15. A fluorescent 3,7-bis-(naphthalen-1-ylethynylated)-2'-deoxyadenosine analogue reports thymidine in complementary DNA by a large emission Stokes shift.

    PubMed

    Yanagi, Masaki; Suzuki, Azusa; Hudson, Robert H E; Saito, Yoshio

    2018-02-28

    The new environmentally responsive fluorescent nucleosides, 3,7-bis-(naphthalen-1-ylethynyl)-8-aza-3,7-dideaza-2'-deoxyadenosine (3n7nzA, 1) and 7-(naphthalen-1-ylethynyl)-8-aza-3,7-dideaza-2'-deoxyadenosine (37nzA, 2), have been synthesized. Both 3n7nzA (1) and 37nzA (2) possess large π-conjugated systems which extend into both the minor and major grooves or the major groove alone, respectively. The nucleosides exhibited large solvatochromic shifts (3n7nzA: Δλ = 45 nm, 37nzA: Δλ = 78 nm) and were examined for their ability to fluorimetrically report hybridization events. When incorporated into ODN probes, the bis-substituted 3n7nzA (1) selectively recognized thymidine on target strands which was reported by a distinct change in its emission wavelength in the long wavelength region, whereas 37nzA (2) showed a preference for pairing to cytidine and a smaller wavelength shift. Thus, 3n7nzA (1) has the potential for use as a fluorescent probe for structural studies of DNAs/RNAs including the detection of single-base alterations in target DNA sequences.

  16. Integrating computational and chemical biology tools in the discovery of antiangiogenic small molecule ligands of FGF2 derived from endogenous inhibitors

    PubMed Central

    Foglieni, Chiara; Pagano, Katiuscia; Lessi, Marco; Bugatti, Antonella; Moroni, Elisabetta; Pinessi, Denise; Resovi, Andrea; Ribatti, Domenico; Bertini, Sabrina; Ragona, Laura; Bellina, Fabio; Rusnati, Marco; Colombo, Giorgio; Taraboletti, Giulia

    2016-01-01

    The FGFs/FGFRs system is a recognized actionable target for therapeutic approaches aimed at inhibiting tumor growth, angiogenesis, metastasis, and resistance to therapy. We previously identified a non-peptidic compound (SM27) that retains the structural and functional properties of the FGF2-binding sequence of thrombospondin-1 (TSP-1), a major endogenous inhibitor of angiogenesis. Here we identified new small molecule inhibitors of FGF2 based on the initial lead. A similarity-based screening of small molecule libraries, followed by docking calculations and experimental studies, allowed selecting 7 bi-naphthalenic compounds that bound FGF2 inhibiting its binding to both heparan sulfate proteoglycans and FGFR-1. The compounds inhibit FGF2 activity in in vitro and ex vivo models of angiogenesis, with improved potency over SM27. Comparative analysis of the selected hits, complemented by NMR and biochemical analysis of 4 newly synthesized functionalized phenylamino-substituted naphthalenes, allowed identifying the minimal stereochemical requirements to improve the design of naphthalene sulfonates as FGF2 inhibitors. PMID:27000667

  17. Secondary ligand-directed assembly of Co(II) coordination polymers based on a pyridine carboxylate ligand

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

    Cao, Ke-Li; Zhang, Yi-Ping; Cai, Yi-Ni

    2014-07-01

    To investigate the influence of hydrogen bonds and secondary ligands on the structures and properties of the resulting frameworks, five new Co(II) compounds have been synthesized by the reactions of Co(II) salts and 3,5-bis(pyridin-4-ylmethoxy)benzoic acid (HL) with four rationally selected dicarboxylic acid ligands. Without secondary ligand, we got one compound [CoL{sub 2}(H{sub 2}O){sub 2}]{sub n}·2nH{sub 2}O (1), which possesses a 1D chain structure. In the presence of ancillary ligands, namely, 1,3-adamantanedicarboxylic acid (H{sub 2}adbc), terephthalic acid (H{sub 2}tpa), thiophene-2,5-dicarboxylic acid (H{sub 2}tdc) and 1,4-benzenedithioacetic acid (H{sub 2}bdtc), four 3D structures [Co{sub 2}L{sub 2}(adbc)]{sub n}·nH{sub 2}O (2), [Co{sub 2}L{sub 2}(tpa)]{sub n}more » (3), [Co{sub 2}L{sub 2}(tdc)]{sub n} (4), [Co{sub 2}L{sub 2}(bdtc)(H{sub 2}O)]{sub n} (5) were obtained, respectively. It can be observed from the architectures of 1–5 that hydrogen bonds and secondary ligands both have great effects on the spatial connective fashions, resulting in the formation of various dimensional compounds. The XRPD, TGA data of title polymers and the magnetic properties for 2 and 5 have also been investigated. - Graphical abstract: The structural differences show that the ancillary ligands have great effects on the spatial connective fashions, resulting in the formation of various dimensional compounds. - Highlights: • Five new Co(II) coordination polymers have been synthesized by solvothermal reactions based on 3,5-bis(pyridin-4-ylmethoxy)benzoic acid (HL). • The long-flexible ligand (HL) is a good candidate to produce interpenetrating architectures. • The secondary dicarboxylic acid ligands play important roles in the spatial connective fashions and the formation of various dimensional compounds. • The magnetism studies show that both 2 and 5 exhibit antiferromagnetic interactions.« less

  18. Designing ligands to bind proteins

    PubMed Central

    Whitesides, George M.; Krishnamurthy, Vijay M.

    2009-01-01

    The ability to design drugs (so-called ‘rational drug design’) has been one of the long-term objectives of chemistry for 50 years. It is an exceptionally difficult problem, and many of its parts lie outside the expertise of chemistry. The much more limited problem – how to design tight-binding ligands (rational ligand design) – would seem to be one that chemistry could solve, but has also proved remarkably recalcitrant. The question is ‘Why is it so difficult?’ and the answer is ‘We still don't entirely know’. This perspective discusses some of the technical issues – potential functions, protein plasticity, enthalpy/entropy compensation, and others – that contribute, and suggests areas where fundamental understanding of protein–ligand interactions falls short of what is needed. It surveys recent technological developments (in particular, isothermal titration calorimetry) that will, hopefully, make now the time for serious progress in this area. It concludes with the calorimetric examination of the association of a series of systematically varied ligands with a model protein. The counterintuitive thermodynamic results observed serve to illustrate that, even in relatively simple systems, understanding protein–ligand association is challenging. PMID:16817982

  19. Multisubstrate biodegradation kinetics of naphthalene, phenanthrene, and pyrene mixtures

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

    Guha, S.; Peters, C.A.; Jaffe, P.R.

    Biodegradation kinetics of naphthalene, phenanthrene and pyrene were studied in sole-substrate systems, and in binary and ternary mixtures to examine substrate interactions. The experiments were conducted in aerobic batch aqueous systems inoculated with a mixed culture that had been isolated from soils contaminated with polycyclic aromatic hydrocarbons (PAHs). Monod kinetic parameters and yield coefficients for the individual parameters and yield coefficients for the individual compounds were estimated from substrate depletion and CO{sub 2} evolution rate data in sole-substrate experiments. In all three binary mixture experiments, biodegradation kinetics were comparable to the sole-substrate kinetics. In the ternary mixture, biodegradation of naphthalenemore » was inhibited and the biodegradation rates of phenanthrene and pyrene were enhanced. A multisubstrate form of the Monod kinetic model was found to adequately predict substrate interactions in the binary and ternary mixtures using only the parameters derived from sole-substrate experiments. Numerical simulations of biomass growth kinetics explain the observed range of behaviors in PAH mixtures. In general, the biodegradation rates of the more degradable and abundant compounds are reduced due to competitive inhibition, but enhanced biodegradation of the more recalcitrant PAHs occurs due to simultaneous biomass growth on multiple substrates. In PAH-contaminated environments, substrate interactions may be very large due to additive effects from the large number of compounds present.« less

  20. Crystallization of bi-functional ligand protein complexes.

    PubMed

    Antoni, Claudia; Vera, Laura; Devel, Laurent; Catalani, Maria Pia; Czarny, Bertrand; Cassar-Lajeunesse, Evelyn; Nuti, Elisa; Rossello, Armando; Dive, Vincent; Stura, Enrico Adriano

    2013-06-01

    Homodimerization is important in signal transduction and can play a crucial role in many other biological systems. To obtaining structural information for the design of molecules able to control the signalization pathways, the proteins involved will have to be crystallized in complex with ligands that induce dimerization. Bi-functional drugs have been generated by linking two ligands together chemically and the relative crystallizability of complexes with mono-functional and bi-functional ligands has been evaluated. There are problems associated with crystallization with such ligands, but overall, the advantages appear to be greater than the drawbacks. The study involves two matrix metalloproteinases, MMP-12 and MMP-9. Using flexible and rigid linkers we show that it is possible to control the crystal packing and that by changing the ligand-enzyme stoichiometric ratio, one can toggle between having one bi-functional ligand binding to two enzymes and having the same ligand bound to each enzyme. The nature of linker and its point of attachment on the ligand can be varied to aid crystallization, and such variations can also provide valuable structural information about the interactions made by the linker with the protein. We report here the crystallization and structure determination of seven ligand-dimerized complexes. These results suggest that the use of bi-functional drugs can be extended beyond the realm of protein dimerization to include all drug design projects. Copyright © 2013 Elsevier Inc. All rights reserved.

  1. Autocrine signal transmission with extracellular ligand degradation

    NASA Astrophysics Data System (ADS)

    Muratov, C B; Posta, F; Shvartsman, S Y

    2009-03-01

    Traveling waves of cell signaling in epithelial layers orchestrate a number of important processes in developing and adult tissues. These waves can be mediated by positive feedback autocrine loops, a mode of cell signaling where binding of a diffusible extracellular ligand to a cell surface receptor can lead to further ligand release. We formulate and analyze a biophysical model that accounts for ligand-induced ligand release, extracellular ligand diffusion and ligand-receptor interaction. We focus on the case when the main mode for ligand degradation is extracellular and analyze the problem with the sharp threshold positive feedback nonlinearity. We derive expressions that link the speed of propagation and other characteristics of traveling waves to the parameters of the biophysical processes, such as diffusion rates, receptor expression level, etc. Analyzing the derived expressions we found that traveling waves in such systems can exhibit a number of unusual properties, e.g. non-monotonic dependence of the speed of propagation on ligand diffusivity. Our results for the fully developed traveling fronts can be used to analyze wave initiation from localized perturbations, a scenario that frequently arises in the in vitro models of epithelial wound healing, and guide future modeling studies of cell communication in epithelial layers.

  2. Cell-specific targeting by heterobivalent ligands.

    PubMed

    Josan, Jatinder S; Handl, Heather L; Sankaranarayanan, Rajesh; Xu, Liping; Lynch, Ronald M; Vagner, Josef; Mash, Eugene A; Hruby, Victor J; Gillies, Robert J

    2011-07-20

    Current cancer therapies exploit either differential metabolism or targeting to specific individual gene products that are overexpressed in aberrant cells. The work described herein proposes an alternative approach--to specifically target combinations of cell-surface receptors using heteromultivalent ligands ("receptor combination approach"). As a proof-of-concept that functionally unrelated receptors can be noncovalently cross-linked with high avidity and specificity, a series of heterobivalent ligands (htBVLs) were constructed from analogues of the melanocortin peptide ligand ([Nle(4), dPhe(7)]-α-MSH) and the cholecystokinin peptide ligand (CCK-8). Binding of these ligands to cells expressing the human Melanocortin-4 receptor and the Cholecystokinin-2 receptor was analyzed. The MSH(7) and CCK(6) were tethered with linkers of varying rigidity and length, constructed from natural and/or synthetic building blocks. Modeling data suggest that a linker length of 20-50 Å is needed to simultaneously bind these two different G-protein coupled receptors (GPCRs). These ligands exhibited up to 24-fold enhancement in binding affinity to cells that expressed both (bivalent binding), compared to cells with only one (monovalent binding) of the cognate receptors. The htBVLs had up to 50-fold higher affinity than that of a monomeric CCK ligand, i.e., Ac-CCK(6)-NH(2). Cell-surface targeting of these two cell types with labeled heteromultivalent ligand demonstrated high avidity and specificity, thereby validating the receptor combination approach. This ability to noncovalently cross-link heterologous receptors and target individual cells using a receptor combination approach opens up new possibilities for specific cell targeting in vivo for therapy or imaging.

  3. Cell-Specific Targeting by Heterobivalent Ligands

    PubMed Central

    Josan, Jatinder S.; Handl, Heather L.; Sankaranarayanan, Rajesh; Xu, Liping; Lynch, Ronald M.; Vagner, Josef; Mash, Eugene A.; Hruby, Victor J.; Gillies, Robert J.

    2012-01-01

    Current cancer therapies exploit either differential metabolism or targeting to specific individual gene products that are overexpressed in aberrant cells. The work described herein proposes an alternative approach—to specifically target combinations of cell-surface receptors using heteromultivalent ligands (“receptor combination approach”). As a proof-of-concept that functionally unrelated receptors can be noncovalently cross-linked with high avidity and specificity, a series of heterobivalent ligands (htBVLs) were constructed from analogues of the melanocortin peptide ligand ([Nle4, DPhe7]-α-MSH) and the cholecystokinin peptide ligand (CCK-8). Binding of these ligands to cells expressing the human Melanocortin-4 receptor and the Cholecystokinin-2 receptor was analyzed. The MSH(7) and CCK(6) were tethered with linkers of varying rigidity and length, constructed from natural and/or synthetic building blocks. Modeling data suggest that a linker length of 20–50 Å is needed to simultaneously bind these two different G-protein coupled receptors (GPCRs). These ligands exhibited up to 24-fold enhancement in binding affinity to cells that expressed both (bivalent binding), compared to cells with only one (monovalent binding) of the cognate receptors. The htBVLs had up to 50-fold higher affinity than that of a monomeric CCK ligand, i.e., Ac-CCK(6)-NH2. Cell-surface targeting of these two cell types with labeled heteromultivalent ligand demonstrated high avidity and specificity, thereby validating the receptor combination approach. This ability to noncovalently cross-link heterologous receptors and target individual cells using a receptor combination approach opens up new possibilities for specific cell targeting in vivo for therapy or imaging. PMID:21639139

  4. Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands

    NASA Astrophysics Data System (ADS)

    Costanzi, Stefano; Tikhonova, Irina G.; Harden, T. Kendall; Jacobson, Kenneth A.

    2009-11-01

    Accurate in silico models for the quantitative prediction of the activity of G protein-coupled receptor (GPCR) ligands would greatly facilitate the process of drug discovery and development. Several methodologies have been developed based on the properties of the ligands, the direct study of the receptor-ligand interactions, or a combination of both approaches. Ligand-based three-dimensional quantitative structure-activity relationships (3D-QSAR) techniques, not requiring knowledge of the receptor structure, have been historically the first to be applied to the prediction of the activity of GPCR ligands. They are generally endowed with robustness and good ranking ability; however they are highly dependent on training sets. Structure-based techniques generally do not provide the level of accuracy necessary to yield meaningful rankings when applied to GPCR homology models. However, they are essentially independent from training sets and have a sufficient level of accuracy to allow an effective discrimination between binders and nonbinders, thus qualifying as viable lead discovery tools. The combination of ligand and structure-based methodologies in the form of receptor-based 3D-QSAR and ligand and structure-based consensus models results in robust and accurate quantitative predictions. The contribution of the structure-based component to these combined approaches is expected to become more substantial and effective in the future, as more sophisticated scoring functions are developed and more detailed structural information on GPCRs is gathered.

  5. Modeling Conformational Transitions and Energetics of Ligand Binding with the Glutamate Receptor Ligand Binding Domain

    NASA Astrophysics Data System (ADS)

    Kurnikova, Maria

    2009-03-01

    Understanding of protein motion and energetics of conformational transitions is crucial to understanding protein function. The glutamate receptor ligand binding domain (GluR2 S1S2) is a two lobe protein, which binds ligand at the interface of two lobes and undergoes conformational transition. The cleft closure conformational transition of S1S2 has been implicated in gating of the ion channel formed by the transmembrane domain of the receptor. In this study we present a composite multi-faceted theoretical analysis of the detailed mechanism of this conformational transition based on rigid cluster decomposition of the protein structure [1] and identifying hydrogen bonds that are responsible for stabilizing the closed conformation [2]. Free energy of the protein reorganization upon ligand binding was calculated using combined Thermodynamic Integration (TI) and Umbrella Sampling (US) simulations [3]. Ligand -- protein interactions in the binding cleft were analyzed using Molecular Dynamics, continuum electrostatics and QM/MM models [4]. All model calculations compare well with corresponding experimental measurements. [4pt] [1] Protein Flexibility using Constraints from Molecular Dynamics Simulations T. Mamonova, B. Hespenheide, R. Straub, M. F. Thorpe, M. G. Kurnikova , Phys. Biol., 2, S137 (2005)[0pt] [2] Theoretical Study of the Glutamate Receptor Ligand Binding Domain Flexibility and Conformational Reorganization T. Mamonova, K. Speranskiy, and M. Kurnikova , Prot.: Struct., Func., Bioinf., 73,656 (2008)[0pt] [3] Energetics of the cleft closing transition and glutamate binding in the Glutamate Receptor ligand Binding Domain T. Mamonova, M. Yonkunas, and M. Kurnikova Biochemistry 47, 11077 (2008)[0pt] [4] On the Binding Determinants of the Glutamate Agonist with the Glutamate Receptor Ligand Binding Domain K. Speranskiy and M. Kurnikova Biochemistry 44, 11208 (2005)

  6. Mixed-ligand Pt(II) dithione-dithiolato complexes: influence of the dicyanobenzodithiolato ligand on the second-order NLO properties.

    PubMed

    Espa, Davide; Pilia, Luca; Marchiò, Luciano; Artizzu, Flavia; Serpe, Angela; Mercuri, Maria Laura; Simão, Dulce; Almeida, Manuel; Pizzotti, Maddalena; Tessore, Francesca; Deplano, Paola

    2012-03-28

    The mixed-ligand dithiolene complex [Pt(Bz(2)pipdt)(dcbdt)] (1) bearing the two ligands Bz(2)pipdt = 1,4-dibenzyl-piperazine-3,2-dithione and dcbdt = dicyanobenzodithiolato, has been synthesized, characterized and studied to evaluate its second-order optical nonlinearity. The dithione/dithiolato character of the two ligands gives rise to an asymmetric distribution of the charge in the molecule. This is reflected by structural data showing that in the C(2)S(2)PtS(2)C(2) dithiolene core the four sulfur atoms define a square-planar coordination environment of the metal where the Pt-S bond distances involving the two ligands are similar, while the C-S bond distances in the C(2)S(2) units exhibit a significant difference in Bz(2)pipdt (dithione) and dcbdt (dithiolato). 1 shows a moderately strong absorption peak in the visible region, which can be related to a HOMO-LUMO transition, where the dcbdt ligand (dithiolato) contributes mostly to the HOMO, and the Bz(2)pipdt one (dithione) mostly to the LUMO. Thus this transition has ligand-to-ligand charge transfer (CT) character with some contribution of the metal and undergoes negative solvatochromism and molecular quadratic optical nonlinearity (μβ(0) = -1296 × 10(-48) esu), which was determined by the EFISH (electric-field-induced second-harmonic generation) technique and compared with the values of similar complexes on varying the dithiolato ligand (mnt = maleonitriledithiolato, dmit = 2-thioxo-1,3-dithiole-4,5-dithiolato). Theoretical calculations help to elucidate the role of the dithiolato ligands in affecting the molecular quadratic optical nonlinearity of these complexes.

  7. Role of ligands in permanganate oxidation of organics.

    PubMed

    Jiang, Jin; Pang, Su-Yan; Ma, Jun

    2010-06-01

    We previously demonstrated that several ligands such as phosphate, pyrophosphate, EDTA, and humic acid could significantly enhance permanganate oxidation of triclosan (one phenolic biocide), which was explained by the contribution of ligand-stabilized reactive manganese intermediates in situ formed upon permanganate reduction. To further understand the underlying mechanism, we comparatively investigated the influence of ligands on permanganate oxidation of bisphenol A (BPA, one phenolic endocrine-disrupting chemical), carbamazepine (CBZ, a pharmaceutical containing the olefinic group), and methyl p-tolyl sulfoxide (TMSO, a typical oxygen-atom acceptor). Selected ligands exerted oxidation enhancement for BPA but had negligible influence for CBZ and TMSO. This was mainly attributed to the effects of identified Mn(III) complexes, which would otherwise disproportionate spontaneously in the absence of ligands. The one-electron oxidant Mn(III) species exhibited no reactivity toward CBZ and TMSO for which the two-electron oxygen donation may be the primary oxidation mechanism but readily oxidized BPA. The latter case was a function of pH, the complexing ligand, and the molar [Mn(III)]:[ligand] ratio, generally consistent with the patterns of ligand-affected permanganate oxidation. Moreover, the combination of the one-electron reduction of Mn(III) (Mn(III) + e(-) -->Mn(II)) and the Mn(VII)/Mn(II) reaction in excess ligands (Mn(VII) + 4Mn(II) ----> (ligands) 5Mn(III)) suggested a catalytic role of the Mn(III)/Mn(II) pair in permanganate oxidation of some phenolics in the presence of ligands.

  8. Characterization of a Naphthalene Dioxygenase Endowed with an Exceptionally Broad Substrate Specificity Toward Polycyclic Aromatic Hydrocarbons

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

    Jouanneau,Y.; Meyer, C.; Jakoncic, J.

    In Sphingomonas CHY-1, a single ring-hydroxylating dioxygenase is responsible for the initial attack of a range of polycyclic aromatic hydrocarbons (PAHs) composed of up to five rings. The components of this enzyme were separately purified and characterized. The oxygenase component (ht-PhnI) was shown to contain one Rieske-type [2Fe-2S] cluster and one mononuclear Fe center per {alpha} subunit, based on EPR measurements and iron assay. Steady-state kinetic measurements revealed that the enzyme had a relatively low apparent Michaelis constant for naphthalene (K{sub m} = 0.92 {+-} 0.15 {mu}M) and an apparent specificity constant of 2.0 {+-} 0.3 M{sup -1} s{sup -1}.more » Naphthalene was converted to the corresponding 1,2-dihydrodiol with stoichiometric oxidation of NADH. On the other hand, the oxidation of eight other PAHs occurred at slower rates and with coupling efficiencies that decreased with the enzyme reaction rate. Uncoupling was associated with hydrogen peroxide formation, which is potentially deleterious to cells and might inhibit PAH degradation. In single turnover reactions, ht-PhnI alone catalyzed PAH hydroxylation at a faster rate in the presence of organic solvent, suggesting that the transfer of substrate to the active site is a limiting factor. The four-ring PAHs chrysene and benz[a]anthracene were subjected to a double ring-dihydroxylation, giving rise to the formation of a significant proportion of bis-cis-dihydrodiols. In addition, the dihydroxylation of benz[a]anthracene yielded three dihydrodiols, the enzyme showing a preference for carbons in positions 1,2 and 10,11. This is the first characterization of a dioxygenase able to dihydroxylate PAHs made up of four and five rings.« less

  9. Doped Tricalcium Phosphate Scaffolds by Thermal Decomposition of Naphthalene: Mechanical Properties and In vivo Osteogenesis in a Rabbit Femur Model

    PubMed Central

    Ke, Dongxu; Dernell, William; Bandyopadhyay, Amit; Bose, Susmita

    2015-01-01

    Tricalcium phosphate (TCP) is a bioceramic that is widely used in orthopedic and dental applications. TCP structures show excellent biocompatibility as well as biodegradability. In this study, porous β-TCP scaffolds were prepared by thermal decomposition of naphthalene. Scaffolds with 57.64 ± 3.54 % density and a maximum pore size around 100 μm were fabricated via removing 30% naphthalene at 1150°C. The compressive strength for these scaffolds was 32.85 ± 1.41 MPa. Furthermore, by mixing 1 wt % SrO and 0.5 wt % SiO2, pore interconnectivity improved, but the compressive strength decreased to 22.40 ± 2.70 MPa. However, after addition of polycaprolactone (PCL) coating layers, the compressive strength of doped scaffolds increased to 29.57 ± 3.77 MPa. Porous scaffolds were implanted in rabbit femur defects to evaluate their biological property. The addition of dopants triggered osteoinduction by enhancing osteoid formation, osteocalcin expression and bone regeneration, especially at the interface of the scaffold and host bone. This study showed processing flexibility to make interconnected porous scaffolds with different pore size and volume fraction porosity with high compressive mechanical strength and better bioactivity. Results show that SrO/SiO2 doped porous TCP scaffolds have excellent potential to be used in bone tissue engineering applications. PMID:25504889

  10. Electronic spectra and photophysics of platinum(II) complexes with alpha-diimine ligands - Solid-state effects. I - Monomers and ligand pi dimers

    NASA Technical Reports Server (NTRS)

    Miskowski, Vincent M.; Houlding, Virginia H.

    1989-01-01

    Two types of emission behavior for Pt(II) complexes containing alpha-diimine ligands have been observed in dilute solution. If the complex also has weak field ligands such as chloride, ligand field (d-d) excited states become the lowest energy excited states. If only strong field ligands are present, a diimine 3(pi-pi/asterisk/) state becomes the lowest. In none of the cases studied did metal-to-ligand charge transfer excited state lie lowest.

  11. Flexible ligand docking using a genetic algorithm

    NASA Astrophysics Data System (ADS)

    Oshiro, C. M.; Kuntz, I. D.; Dixon, J. Scott

    1995-04-01

    Two computational techniques have been developed to explore the orientational and conformational space of a flexible ligand within an enzyme. Both methods use the Genetic Algorithm (GA) to generate conformationally flexible ligands in conjunction with algorithms from the DOCK suite of programs to characterize the receptor site. The methods are applied to three enzyme-ligand complexes: dihydrofolate reductase-methotrexate, thymidylate synthase-phenolpthalein and HIV protease-thioketal haloperidol. Conformations and orientations close to the crystallographically determined structures are obtained, as well as alternative structures with low energy. The potential for the GA method to screen a database of compounds is also examined. A collection of ligands is evaluated simultaneously, rather than docking the ligands individually into the enzyme.

  12. Identifying Marine Copper-Binding Ligands in Seawater

    NASA Astrophysics Data System (ADS)

    Whitby, H.; Hollibaugh, J. T.; Maldonado, M. T.; Ouchi, S.; van den Berg, S. M.

    2016-02-01

    Complexation reactions are important because they affect the bioavailability of trace metals such as copper and iron. For example, organic complexation can determine whether copper is a limiting or a toxic micronutrient at natural levels. Copper competes with iron for complexing ligands, and when iron is limiting, copper can also substitute for iron in some metabolic pathways. The speciation of copper can be measured using complexing capacity titrations, which provide the concentration of individual ligand classes (L1, L2 etc.) and the complex stabilities (log K). Using methods recently developed in our laboratory, we show that the ligands within these classes can be measured independently of titrations, thus confirming the titration method and simultaneously identifying the ligands within each class. Thiols were identified as the L1 ligand class and humic compounds as the weaker L2 class in samples from coastal Georgia, USA, collected monthly from April to December. Log K values of the ligand complexes were consistent with values expected for thiols and humic substances. Recent results from culture studies and from samples collected along Line P, a coastal - oceanic transect in the HNLC region of the NE subarctic Pacific, will be presented in comparison to the estuarine results. This comparison will help to broaden our perspective on copper complexation and the ligands responsible, furthering our understanding of ligand sources and life cycles.

  13. Structures of undecagold clusters: Ligand effect

    NASA Astrophysics Data System (ADS)

    Spivey, Kasi; Williams, Joseph I.; Wang, Lichang

    2006-12-01

    The most stable structure of undecagold, or Au 11, clusters was predicted from our DFT calculations to be planar [L. Xiao, L. Wang, Chem. Phys. Lett. 392 (2004) 452; L. Xiao, B. Tollberg, X. Hu, L. Wang, J. Chem. Phys. 124 (2005) 114309.]. The structures of ligand protected undecagold clusters were shown to be three-dimensional experimentally. In this work, we used DFT calculations to study the ligand effect on the structures of Au 11 clusters. Our results show that the most stable structure of Au 11 is in fact three-dimensional when SCH 3 ligands are attached. This indicates that the structures of small gold clusters are altered substantially in the presence of ligands.

  14. Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.

    PubMed

    Gill, Samuel C; Lim, Nathan M; Grinaway, Patrick B; Rustenburg, Ariën S; Fass, Josh; Ross, Gregory A; Chodera, John D; Mobley, David L

    2018-05-31

    Accurately predicting protein-ligand binding affinities and binding modes is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like ligand in a receptor, and the populations of the multiple binding modes which may be relevant. This problem is important in its own right, but is even more timely given the recent success of alchemical free energy calculations. Alchemical calculations are increasingly used to predict binding free energies of ligands to receptors. However, the accuracy of these calculations is dependent on proper sampling of the relevant ligand binding modes. Unfortunately, ligand binding modes may often be uncertain, hard to predict, and/or slow to interconvert on simulation time scales, so proper sampling with current techniques can require prohibitively long simulations. We need new methods which dramatically improve sampling of ligand binding modes. Here, we develop and apply a nonequilibrium candidate Monte Carlo (NCMC) method to improve sampling of ligand binding modes. In this technique, the ligand is rotated and subsequently allowed to relax in its new position through alchemical perturbation before accepting or rejecting the rotation and relaxation as a nonequilibrium Monte Carlo move. When applied to a T4 lysozyme model binding system, this NCMC method shows over 2 orders of magnitude improvement in binding mode sampling efficiency compared to a brute force molecular dynamics simulation. This is a first step toward applying this methodology to pharmaceutically relevant binding of fragments and, eventually, drug-like molecules. We are making this approach available via our new Binding modes of ligands using enhanced sampling (BLUES) package which is freely available on GitHub.

  15. Assessment of automatic ligand building in ARP/wARP.

    PubMed

    Evrard, Guillaume X; Langer, Gerrit G; Perrakis, Anastassis; Lamzin, Victor S

    2007-01-01

    The efficiency of the ligand-building module of ARP/wARP version 6.1 has been assessed through extensive tests on a large variety of protein-ligand complexes from the PDB, as available from the Uppsala Electron Density Server. Ligand building in ARP/wARP involves two main steps: automatic identification of the location of the ligand and the actual construction of its atomic model. The first step is most successful for large ligands. The second step, ligand construction, is more powerful with X-ray data at high resolution and ligands of small to medium size. Both steps are successful for ligands with low to moderate atomic displacement parameters. The results highlight the strengths and weaknesses of both the method of ligand building and the large-scale validation procedure and help to identify means of further improvement.

  16. Defining the property space for chromatographic ligands from a homologous series of mixed-mode ligands.

    PubMed

    Woo, James A; Chen, Hong; Snyder, Mark A; Chai, Yiming; Frost, Russell G; Cramer, Steven M

    2015-08-14

    A homologous ligand library based on the commercially-available Nuvia cPrime ligand was generated to systematically explore various features of a multimodal cation-exchange ligand and to identify structural variants that had significantly altered chromatographic selectivity. Substitution of the polar amide bond with more hydrophobic chemistries was found to enhance retention while remaining hydrophobically-selective for aromatic residues. In contrast, increasing the solvent exposure of the aromatic ring was observed to strengthen the ligand affinity for both types of hydrophobic residues. An optimal linker length between the charged and hydrophobic moieties was also observed to enhance retention, balancing the steric accessibility of the hydrophobic moiety with its ability to interact independently of the charged group. The weak pKa of the carboxylate charge group was found to have a notable impact on protein retention on Nuvia cPrime at lower pH, increasing hydrophobic interactions with the protein. Substituting the charged group with a sulfonic acid allowed this strong MM ligand to retain its electrostatic-dominant character in this lower pH range. pH gradient experiments were also carried out to further elucidate this pH dependent behavior. A single QSAR model was generated using this accumulated experimental data to predict protein retention across a range of multimodal and ion exchange systems. This model could correctly predict the retention of proteins on resins that were not included in the original model and could prove quite powerful as an in silico approach toward designing more effective and differentiated multimodal ligands. Copyright © 2015. Published by Elsevier B.V.

  17. Scoring ligand similarity in structure-based virtual screening.

    PubMed

    Zavodszky, Maria I; Rohatgi, Anjali; Van Voorst, Jeffrey R; Yan, Honggao; Kuhn, Leslie A

    2009-01-01

    Scoring to identify high-affinity compounds remains a challenge in virtual screening. On one hand, protein-ligand scoring focuses on weighting favorable and unfavorable interactions between the two molecules. Ligand-based scoring, on the other hand, focuses on how well the shape and chemistry of each ligand candidate overlay on a three-dimensional reference ligand. Our hypothesis is that a hybrid approach, using ligand-based scoring to rank dockings selected by protein-ligand scoring, can ensure that high-ranking molecules mimic the shape and chemistry of a known ligand while also complementing the binding site. Results from applying this approach to screen nearly 70 000 National Cancer Institute (NCI) compounds for thrombin inhibitors tend to support the hypothesis. EON ligand-based ranking of docked molecules yielded the majority (4/5) of newly discovered, low to mid-micromolar inhibitors from a panel of 27 assayed compounds, whereas ranking docked compounds by protein-ligand scoring alone resulted in one new inhibitor. Since the results depend on the choice of scoring function, an analysis of properties was performed on the top-scoring docked compounds according to five different protein-ligand scoring functions, plus EON scoring using three different reference compounds. The results indicate that the choice of scoring function, even among scoring functions measuring the same types of interactions, can have an unexpectedly large effect on which compounds are chosen from screening. Furthermore, there was almost no overlap between the top-scoring compounds from protein-ligand versus ligand-based scoring, indicating the two approaches provide complementary information. Matchprint analysis, a new addition to the SLIDE (Screening Ligands by Induced-fit Docking, Efficiently) screening toolset, facilitated comparison of docked molecules' interactions with those of known inhibitors. The majority of interactions conserved among top-scoring compounds for a given scoring

  18. Ligand structure and mechanical properties of single-nanoparticle-thick membranes.

    PubMed

    Salerno, K Michael; Bolintineanu, Dan S; Lane, J Matthew D; Grest, Gary S

    2015-06-01

    The high mechanical stiffness of single-nanoparticle-thick membranes is believed to result from the local structure of ligand coatings that mediate interactions between nanoparticles. These ligand structures are not directly observable experimentally. We use molecular dynamics simulations to observe variations in ligand structure and simultaneously measure variations in membrane mechanical properties. We have shown previously that ligand end group has a large impact on ligand structure and membrane mechanical properties. Here we introduce and apply quantitative molecular structure measures to these membranes and extend analysis to multiple nanoparticle core sizes and ligand lengths. Simulations of nanoparticle membranes with a nanoparticle core diameter of 4 or 6 nm, a ligand length of 11 or 17 methylenes, and either carboxyl (COOH) or methyl (CH(3)) ligand end groups are presented. In carboxyl-terminated ligand systems, structure and interactions are dominated by an end-to-end orientation of ligands. In methyl-terminated ligand systems large ordered ligand structures form, but nanoparticle interactions are dominated by disordered, partially interdigitated ligands. Core size and ligand length also affect both ligand arrangement within the membrane and the membrane's macroscopic mechanical response, but are secondary to the role of the ligand end group. Moreover, the particular end group (COOH or CH(3)) alters the nature of how ligand length, in turn, affects the membrane properties. The effect of core size does not depend on the ligand end group, with larger cores always leading to stiffer membranes. Asymmetry in the stress and ligand density is observed in membranes during preparation at a water-vapor interface, with the stress asymmetry persisting in all membranes after drying.

  19. Ligand structure and mechanical properties of single-nanoparticle thick membranes

    DOE PAGES

    Salerno, Kenneth Michael; Bolintineanu, Dan S.; Lane, J. Matthew D.; ...

    2015-06-16

    We believe that the high mechanical stiffness of single-nanoparticle-thick membranes is the result of the local structure of ligand coatings that mediate interactions between nanoparticles. These ligand structures are not directly observable experimentally. We use molecular dynamics simulations to observe variations in ligand structure and simultaneously measure variations in membrane mechanical properties. We have shown previously that ligand end group has a large impact on ligand structure and membrane mechanical properties. Here we introduce and apply quantitative molecular structure measures to these membranes and extend analysis to multiple nanoparticle core sizes and ligand lengths. Simulations of nanoparticle membranes with amore » nanoparticle core diameter of 4 or 6 nm, a ligand length of 11 or 17 methylenes, and either carboxyl (COOH) or methyl (CH 3) ligand end groups are presented. In carboxyl-terminated ligand systems, structure and interactions are dominated by an end-to-end orientation of ligands. In methyl-terminated ligand systems large ordered ligand structures form, but nanoparticle interactions are dominated by disordered, partially interdigitated ligands. Core size and ligand length also affect both ligand arrangement within the membrane and the membrane's macroscopic mechanical response, but are secondary to the role of the ligand end group. Additionally, the particular end group (COOH or CH 3) alters the nature of how ligand length, in turn, affects the membrane properties. The effect of core size does not depend on the ligand end group, with larger cores always leading to stiffer membranes. Asymmetry in the stress and ligand density is observed in membranes during preparation at a water-vapor interface, with the stress asymmetry persisting in all membranes after drying.« less

  20. High-throughput screening of dye-ligands for chromatography.

    PubMed

    Kumar, Sunil; Punekar, Narayan S

    2014-01-01

    Dye-ligand-based chromatography has become popular after Cibacron Blue, the first reactive textile dye, found application for protein purification. Many other textile dyes have since been successfully used to purify a number of proteins and enzymes. While the exact nature of their interaction with target proteins is often unclear, dye-ligands are thought to mimic the structural features of their corresponding substrates, cofactors, etc. The dye-ligand affinity matrices are therefore considered pseudo-affinity matrices. In addition, dye-ligands may simply bind with proteins due to electrostatic, hydrophobic, and hydrogen-bonding interactions. Because of their low cost, ready availability, and structural stability, dye-ligand affinity matrices have gained much popularity. Choice of a large number of dye structures offers a range of matrices to be prepared and tested. When presented in the high-throughput screening mode, these dye-ligand matrices provide a formidable tool for protein purification. One could pick from the list of dye-ligands already available or build a systematic library of such structures for use. A high-throughput screen may be set up to choose best dye-ligand matrix as well as ideal conditions for binding and elution, for a given protein. The mode of operation could be either manual or automated. The technology is available to test the performance of dye-ligand matrices in small volumes in an automated liquid-handling workstation. Screening a systematic library of dye-ligand structures can help establish a structure-activity relationship. While the origins of dye-ligand chromatography lay in exploiting pseudo-affinity, it is now possible to design very specific biomimetic dye structures. High-throughput screening will be of value in this endeavor as well.

  1. Fluorescence decay of naphthalene studied in an electrostatic storage ring, the Mini-Ring

    NASA Astrophysics Data System (ADS)

    Martin, S.; Matsumoto, J.; Kono, N.; Ji, M.-C.; Brédy, R.; Bernard, J.; Cassimi, A.; Chen, L.

    2017-10-01

    The cooling of naphthalene cations (C10H8)+ has been studied in a compact electrostatic ion storage ring, the Mini-Ring. A nano second laser pulse of 532 nm (2.33 eV) was used to probe the internal energy distribution every millisecond during the storage time up to 5 ms. The evolution of the internal energy distribution of the stored ions was simulated with a model taking into account the dissociation and the radiative decay processes. Calculated decay curves were fitted to the corresponding laser induced neutral decays. For a laser power of 200 μJ/pulse, a good agreement between experiment and modeling was found using an initial Gaussian energy distribution centered to 5.9 eV and a fluorescence decay rate varying from 200 to 300 s-1 in the energy range from 6 to 7 eV. This fast decay was attributed to the delayed Poincaré fluorescence process.

  2. Azulene-to-naphthalene rearrangement: the Car-Parrinello metadynamics method explores various reaction mechanisms.

    PubMed

    Stirling, András; Iannuzzi, Marcella; Laio, Alessandro; Parrinello, Michele

    2004-10-18

    We studied the thermal intramolecular and radical rearrangement of azulene to naphthalene by employing a novel metadynamics method based on Car-Parrinello molecular dynamics. We demonstrate that relatively short simulations can provide us with several possible reaction mechanisms for the rearrangement. We show that different choices of the collective coordinates can steer the reaction along different pathways, thus offering the possibility of choosing the most probable mechanism. We consider herein three intramolecular mechanisms and two radical pathways. We found the norcaradiene pathway to be the preferable intramolecular mechanism, whereas the spiran mechanism is the favored radical route. We obtained high activation energies for all the intramolecular pathways (81.5-98.6 kcal mol(-1)), whereas the radical routes have activation energies of 24-39 kcal mol(-1). The calculations have also resulted in elementary steps and intermediates not yet considered. A few attractive features of the metadynamics method in studying chemical reactions are pointed out.

  3. Synthesis, spectral, thermal and biological studies of mixed ligand complexes with newly prepared Schiff base and 1,10-phenanthroline ligands

    NASA Astrophysics Data System (ADS)

    Abd El-Halim, Hanan F.; Mohamed, Gehad G.; Khalil, Eman A. M.

    2017-10-01

    A series of mixed ligand complexes were prepared from the Schiff base (L1) as a primary ligand, prepared by condensation of oxamide and furan-2-carbaldehyde, and 1,10-phenanthroline (1,10-phen) as a secondary ligand. The Schiff base ligand and its mixed ligand chelates were characterized based on elemental analysis, IR, 1H NMR, thermal analysis, UV-Visible, mass, molar conductance, magnetic moment. X-ray diffraction, solid reflectance and ESR also have been studied. The mixed ligand complexes were found to have the formulae of [M(L1) (1,10-phen)]Clm.nH2O (M = Cr(III) and Fe(III) (m = 3) (n = 0); M = Mn(II), Cu(II) and Cd(II) (m = 2) (n = 0); and M = Co(II) (m = 2) (n = 1), Ni(II) (m = 2) (n = 2) and Zn(II) (m = 2) (n = 3)) and that the geometrical structure of the complexes were octahedral. The parameters of thermodynamic using Coats-Redfern and Horowitz-Metzger equations were calculated. The synthesized Schiff base ligand, 1,10-phenanthroline ligand and Their mixed ligand complexes were also investigated for their antibacterial and antifungal activity against bacterial species (Gram-Ve bacteria: Pseudomonas aeruginosa and Escherichia coli) and (Gram + Ve bacteria: Bacillus subtilis and Streptococcus pneumonia) and fungi (Aspergillus fumigates and Candida albicans). The anticancer activity of the new compounds had been tested against breast (MFC7) and colon (HCT-116) cell lines. The results showed high activity for the synthesized compounds.

  4. Ligand-Induced Conformational Change in the α7 Nicotinic Receptor Ligand Binding Domain

    PubMed Central

    Henchman, Richard H.; Wang, Hai-Long; Sine, Steven M.; Taylor, Palmer; McCammon, J. Andrew

    2005-01-01

    Molecular dynamics simulations of a homology model of the ligand binding domain of the α7 nicotinic receptor are conducted with a range of bound ligands to induce different conformational states. Four simulations of 15 ns each are run with no ligand, antagonist d-tubocurarine (dTC), agonist acetylcholine (ACh), and agonist ACh with potentiator Ca2+, to give insight into the conformations of the active and inactive states of the receptor and suggest the mechanism for conformational change. The main structural factor distinguishing the active and inactive states is that a more open, symmetric arrangement of the five subunits arises for the two agonist simulations, whereas a more closed and asymmetric arrangement results for the apo and dTC cases. Most of the difference arises in the lower portion of the ligand binding domain near its connection to the adjacent transmembrane domain. The transfer of the more open state to the transmembrane domain could then promote ion flow through the channel. Variation in how subunits pack together with no ligand bound appears to give rise to asymmetry in the apo case. The presence of dTC expands the receptor but induces rotations in alternate directions in adjacent subunits that lead to an asymmetric arrangement as in the apo case. Ca2+ appears to promote a slightly greater expansion in the subunits than ACh alone by stabilizing the C-loop and ACh positions. Although the simulations are unlikely to be long enough to view the full conformational changes between open and closed states, a collection of different motions at a range of length scales are observed that are likely to participate in the conformational change. PMID:15665135

  5. Phytoremediation of BTEX and Naphthalene from produced-water spill sites using Poaceae.

    PubMed

    Shores, Amanda Rose; Hethcock, Brittany; Laituri, Melinda

    2018-07-03

    Surface spills of water produced from hydraulic fracturing can expose soil and groundwater to organics such as BTEX and naphthalene (BTEX&N) as well as high concentrations of salt. As an alternative to soil excavation, we evaluated the effectiveness of BTEX&N soil remediation using 2 grasses present in Colorado. Perennial ryegrass and foxtail barley were grown separately in pots in the greenhouse and exposed to salt or a synthesized produced-water slurry containing relevant levels of salt and BTEX&N. Plant biomass was measured 14 days post-spill, and levels of BTEX&N were quantified using GC/MS for soil, roots, and shoots at day 7 and 14 post-spill. Foxtail barley shoot growth was limited by BTEX&N, whereas perennial ryegrass shoot growth was enhanced by salt but not BTEX&N. While BTEX&N in soil associated with foxtail barley mainly decreased over time, the soil associated with perennial ryegrass mainly saw an increase in BTEX&N with time. However, further research is needed to determine the fate of BTEX&N within grasses and soil.

  6. Preparation and isolation of dithiolene thiophosphoryl molecules as stable, protected forms of dithiolene ligands.

    PubMed

    Arumugam, Kuppuswamy; Bollinger, James E; Fink, Mark; Donahue, James P

    2007-04-16

    The reaction of P4S10 with acyloins, RC(O)CH(OH)R, in refluxing dioxane, followed by the addition of alkylating agents, forms dithiolene thiophosphoryl thiolate compounds, (R2C2S2)P(S)(SR'), which are readily isolated and purified. The compounds that have been prepared and identified spectroscopically are those with R = p-anisyl, R' = Me (1); R = p-anisyl, R' = Bz (2); R = Ph, R' = Me (4); R = Et, R' = Bz (5). Compounds 1, 2, and 4 were structurally characterized by X-ray crystallography and found to possess a tetrahedral coordination geometry about the phosphorus atom, with overall Cs symmetry. In each case, the mirror plane bisects the dithiolene S-P-S chelate and contains the thiophosphoryl bond, which ranges in length from 1.9241(8) to 1.9361(7) A. The use of 2-(bromomethyl)naphthalene as organic electrophile in the P4S10/acyloin reaction produced bis(2-methylnaphthalenyl) disulfide as the only identifiable product. The substitution of Lawesson's reagent for P4S10 in reactions with acyloins produced deoxy acyloin rather than products resulting from chalcogen exchange. Compounds 1-2 and 4-5 are Group 5 analogues of 1,3-dithiol-2-ones, (R2C2S2)C=O, and undergo a similar hydrolysis in aqueous base to liberate ene-1,2-dithiolate dianions from which corresponding metal dithiolene complexes may be prepared. Deprotection of 1 in MeO-/MeOH, followed by the addition of NiCl2.6H2O and then I2, produces square planar [Ni(S2C2(C6H4-p-OCH3)2)2] (8) in 93% yield. A high-resolution structure of 8 (P) reveals dithiolene C-C and C-S bond lengths that are clearly indicative of the thionyl radical monoanionic nature of the ligand. The use of isolated (R2C2S2)P(S)(SR') compounds as a dithiolene ligand source for the preparation of metal dithiolene complexes offers the advantages of clean reactivity and high yield.

  7. PDBToSDF: Create ligand structure files from PDB file.

    PubMed

    Muppalaneni, Naresh Babu; Rao, Allam Appa

    2011-01-01

    Protein Data Bank (PDB) file contains atomic data for protein and ligand in protein-ligand complexes. Structure data file (SDF) contains data for atoms, bonds, connectivity and coordinates of molecule for ligands. We describe PDBToSDF as a tool to separate the ligand data from pdb file for the calculation of ligand properties like molecular weight, number of hydrogen bond acceptors, hydrogen bond receptors easily.

  8. Three closely related 1-(naphthalen-2-yl)prop-2-en-1-ones: pseudosymmetry, disorder and supramoleular assembly mediated by C-H...π and C-Br...π interactions.

    PubMed

    Girisha, Marisiddaiah; Sagar, Belakavadi K; Yathirajan, Hemmige S; Rathore, Ravindranath S; Glidewell, Christopher

    2017-02-01

    It has been observed that when electron-rich naphthyl rings are present in chalcones they can participate in π-π stacking interactions, and this can play an important role in orientating inhibitors within the active sites of enzymes, while chalcones containing heterocyclic substituents additionally exhibit fungistatic and fungicidal properties. With these considerations in mind, three new chalcones containing 2-naphthyl substituents were prepared. 3-(4-Fluorophenyl)-1-(naphthalen-2-yl)prop-2-en-1-one, C 19 H 13 FO, (I), crystallizes with Z' = 2 in the space group P-1 and the four molecules in the unit cell adopt an arrangement which resembles that in the space group P2 1 /a. Although 3-(4-bromophenyl)-1-(naphthalen-2-yl)prop-2-en-1-one, C 19 H 13 BrO, (II), with Z' = 1, is not isostructural with (I), the molecules of (I) and (II) adopt very similar conformations. In 1-(naphthalen-2-yl)-3-(thiophen-2-yl)prop-2-en-1-one, C 17 H 12 OS, (III), the thiophene unit is disordered over two sets of atomic sites, with occupancies of 0.780 (3) and 0.220 (3), which are related by a near 180° rotation of the thiophene unit about its exocyclic C-C bond. The molecules of compound (I) are linked by three independent C-H...π(arene) hydrogen bonds to form centrosymmetric octamolecular aggregates, whereas the molecules of compound (II) are linked into molecular ladders by a combination of C-H...π(arene) and C-Br...π(arene) interactions, and those of compound (III) are linked into centrosymmetric dimers by C-H...π(thiophene) interactions.

  9. All-inorganic Germanium nanocrystal films by cationic ligand exchange

    DOE PAGES

    Wheeler, Lance M.; Nichols, Asa W.; Chernomordik, Boris D.; ...

    2016-01-21

    In this study, we introduce a new paradigm for group IV nanocrystal surface chemistry based on room temperature surface activation that enables ionic ligand exchange. Germanium nanocrystals synthesized in a gas-phase plasma reactor are functionalized with labile, cationic alkylammonium ligands rather than with traditional covalently bound groups. We employ Fourier transform infrared and 1H nuclear magnetic resonance spectroscopies to demonstrate the alkylammonium ligands are freely exchanged on the germanium nanocrystal surface with a variety of cationic ligands, including short inorganic ligands such as ammonium and alkali metal cations. This ionic ligand exchange chemistry is used to demonstrate enhanced transport inmore » germanium nanocrystal films following ligand exchange as well as the first photovoltaic device based on an all-inorganic germanium nanocrystal absorber layer cast from solution. This new ligand chemistry should accelerate progress in utilizing germanium and other group IV nanocrystals for optoelectronic applications.« less

  10. Dye-ligand affinity systems.

    PubMed

    Denizli, A; Pişkin, E

    2001-10-30

    Dye-ligands have been considered as one of the important alternatives to natural counterparts for specific affinity chromatography. Dye-ligands are able to bind most types of proteins, in some cases in a remarkably specific manner. They are commercially available, inexpensive, and can easily be immobilized, especially on matrices bearing hydroxyl groups. Although dyes are all synthetic in nature, they are still classified as affinity ligands because they interact with the active sites of many proteins mimicking the structure of the substrates, cofactors, or binding agents for those proteins. A number of textile dyes, known as reactive dyes, have been used for protein purification. Most of these reactive dyes consist of a chromophore (either azo dyes, anthraquinone, or phathalocyanine), linked to a reactive group (often a mono- or dichlorotriazine ring). The interaction between the dye ligand and proteins can be by complex combination of electrostatic, hydrophobic, hydrogen bonding. Selection of the supporting matrix is the first important consideration in dye-affinity systems. There are several methods for immobilization of dye molecules onto the support matrix, in which usually several intermediate steps are followed. Both the adsorption and elution steps should carefully be optimized/designed for a successful separation. Dye-affinity systems in the form of spherical sorbents or as affinity membranes have been used in protein separation.

  11. Glucagon-Like Peptide-1 Receptor Ligand Interactions: Structural Cross Talk between Ligands and the Extracellular Domain

    PubMed Central

    West, Graham M.; Willard, Francis S.; Sloop, Kyle W.; Showalter, Aaron D.; Pascal, Bruce D.; Griffin, Patrick R.

    2014-01-01

    Activation of the glucagon-like peptide-1 receptor (GLP-1R) in pancreatic β-cells potentiates insulin production and is a current therapeutic target for the treatment of type 2 diabetes mellitus (T2DM). Like other class B G protein-coupled receptors (GPCRs), the GLP-1R contains an N-terminal extracellular ligand binding domain. N-terminal truncations on the peptide agonist generate antagonists capable of binding to the extracellular domain, but not capable of activating full length receptor. The main objective of this study was to use Hydrogen/deuterium exchange (HDX) to identify how the amide hydrogen bonding network of peptide ligands and the extracellular domain of GLP-1R (nGLP-1R) were altered by binding interactions and to then use this platform to validate direct binding events for putative GLP-1R small molecule ligands. The HDX studies presented here for two glucagon-like peptide-1 receptor (GLP-1R) peptide ligands indicates that the antagonist exendin-4[9-39] is significantly destabilized in the presence of nonionic detergents as compared to the agonist exendin-4. Furthermore, HDX can detect stabilization of exendin-4 and exendin-4[9-39] hydrogen bonding networks at the N-terminal helix [Val19 to Lys27] upon binding to the N-terminal extracellular domain of GLP-1R (nGLP-1R). In addition we show hydrogen bonding network stabilization on nGLP-1R in response to ligand binding, and validate direct binding events with the extracellular domain of the receptor for putative GLP-1R small molecule ligands. PMID:25180755

  12. New singlet oxygen donors based on naphthalenes: synthesis, physical chemical data, and improved stability.

    PubMed

    Klaper, Matthias; Linker, Torsten

    2015-06-01

    Singlet oxygen donors are of current interest for medical applications, but suffer from a short half-life leading to low singlet oxygen yields and problems with storage. We have synthesized more than 25 new singlet oxygen donors based on differently substituted naphthalenes in only a few steps. The influence of functional groups on the reaction rate of the photooxygenations, thermolysis, half-life, and singlet oxygen yield has been thoroughly studied. We determined various thermodynamic data and compared them with density functional calculations. Interestingly, remarkable stabilities of functional groups during the photooxygenations and stabilizing effects for some endoperoxides during the thermolysis have been found. Furthermore, we give evidence for a partly concerted and partly stepwise thermolysis mechanism leading to singlet and triplet oxygen, respectively. Our results might be interesting for "dark oxygenations" and future applications in medicine. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Sensitization of Nanocrystalline Metal Oxides with a Phosphonate-Functionalized Perylene Diimide for Photoelectrochemical Water Oxidation with a CoOx Catalyst.

    PubMed

    Kirner, Joel T; Finke, Richard G

    2017-08-23

    A planar organic thin film composed of a perylene diimide dye (N,N'-bis(phosphonomethyl)-3,4,9,10-perylenediimide, PMPDI) with photoelectrochemically deposited cobalt oxide (CoO x ) catalyst was previously shown to photoelectrochemically oxidize water (DOI: 10.1021/am405598w). Herein, the same PMPDI dye is studied for the sensitization of different nanostructured metal oxide (nano-MO x ) films in a dye-sensitized photoelectrochemical cell architecture. Dye adsorption kinetics and saturation decreases in the order TiO 2 > SnO 2 ≫ WO 3 . Despite highest initial dye loading on TiO 2 films, photocurrent with hydroquinone (H 2 Q) sacrificial reductant in pH 7 aqueous solution is much higher on SnO 2 films, likely due to a higher driving force for charge injection into the more positive conduction band energy of SnO 2 . Dyeing conditions and SnO 2 film thickness were subsequently optimized to achieve light-harvesting efficiency >99% at the λ max of the dye, and absorbed photon-to-current efficiency of 13% with H 2 Q, a 2-fold improvement over the previous thin-film architecture. A CoO x water-oxidation catalyst was photoelectrochemically deposited, allowing for photoelectrochemical water oxidation with a faradaic efficiency of 31 ± 7%, thus demonstrating the second example of a water-oxidizing, dye-sensitized photoelectrolysis cell composed entirely of earth-abundant materials. However, deposition of CoO x always results in lower photocurrent due to enhanced recombination between catalyst and photoinjected electrons in SnO 2 , as confirmed by open-circuit photovoltage measurements. Possible future studies to enhance photoanode performance are discussed, including alternative catalyst deposition strategies or structural derivatization of the perylene dye.

  14. Thermal behavior and catalytic activity in naphthalene destruction of Ce-, Zr- and Mn-containing oxide layers on titanium

    NASA Astrophysics Data System (ADS)

    Vasilyeva, Marina S.; Rudnev, Vladimir S.; Wiedenmann, Florian; Wybornov, Svetlana; Yarovaya, Tatyana P.; Jiang, Xin

    2011-11-01

    The present paper is devoted to studies of the composition and surface structure, including those after annealing at high temperatures, and catalytic activity in the reaction of naphthalene destruction of Ce-, Zr- and Mn-containing oxide layers on titanium obtained by means of the plasma electrolytic oxidation (PEO) method. The composition and structure of the obtained systems were investigated using the methods of X-ray phase and energy dispersive analysis and scanning electron microscopy (SEM). It was demonstrated that Ce- and Zr- containing structures had relatively high thermal stability: their element and phase compositions and surface structure underwent virtually no changes after annealing in the temperature range 600-800 °C. Annealing of Ce- and Zr-containing coatings in the temperature range 850-900 °C resulted in substantial changes of their surface composition and structure: a relatively homogeneous and porous surface becomes coated by large pole-like crystals. The catalytic studies showed rather high activity of Ce- and Zr-containing coatings in the reaction of naphthalene destruction at temperatures up to 850 °C. Mn-containing structures of the type MnOx + SiO2 + TiO2/Ti have a well-developed surface coated by “nano-whiskers”. The phase composition and surface structure of manganese-containing layers changes dramatically in the course of thermal treatment. After annealing above 600 °C nano-whiskers vanish with formation of molten structures on the surface. The Mn-containing oxide systems demonstrated lower conversion degrees than the Ce- and Zr-containing coatings, which can be attributed to substantial surface modification and formation of molten manganese silicates at high temperatures.

  15. Chelating ligands for nanocrystals' surface functionalization.

    PubMed

    Querner, Claudia; Reiss, Peter; Bleuse, Joël; Pron, Adam

    2004-09-22

    A new family of ligands for the surface functionalization of CdSe nanocrystals is proposed, namely alkyl or aryl derivatives of carbodithioic acids (R-C(S)SH). The main advantages of these new ligands are as follows: they nearly quantitatively exchange the initial surface ligands (TOPO) in very mild conditions; they significantly improve the resistance of nanocrystals against photooxidation because of their ability of strong chelate-type binding to metal atoms; their relatively simple preparation via Grignard intermediates facilitates the development of new bifunctional ligands containing, in addition to the anchoring carbodithioate group, a second function, which enables the grafting of molecules or macromolecules of interest on the nanocrystal surface. To give an example of this approach, we report, for the first time, the grafting of an electroactive oligomer from the polyaniline family-aniline tetramer-on CdSe nanocrystals after their functionalization with 4-formyldithiobenzoic acid. The grafting proceeds via a condensation reaction between the aldehyde group of the ligand and the terminal primary amine group of the tetramer. The resulting organic/inorganic hybrid exhibits complete extinction of the fluorescence of its constituents, indicating efficient charge or energy transfer between the organic and the inorganic semiconductors.

  16. A new window towards multidimensional sensing of transition metal cations through dual mode sensing ability of N-benzyl-(3-hydoxy-2-naphthalene): Emission enhancement coupled remarkable spectral shift

    NASA Astrophysics Data System (ADS)

    Paul, Bijan Kumar; Mahanta, Subrata; Singh, Rupashree Balia; Guchhait, Nikhil

    2011-06-01

    A structurally simple Schiff base N-benzyl-(3-hydroxy-2-naphthalene) (NBHN32) has been synthesized and characterized by 1H NMR, 13C NMR, and DEPT spectroscopy. The photophysical behaviour of NBHN32 in response to the presence of various transition metal cations has been explored by means of steady-state absorption, emission and time-resolved emission spectroscopy techniques. Efficient through space intramolecular photoinduced electron transfer (PET) between the naphthalene fluorophore and the imine group has been argued for extremely low fluorescence yield of NBHN32 compared to the parent molecule 3-hydroxy-2-naphthaldehyde (HN32) containing the same fluorophore but lacking the receptor moiety. Transition metal ion-induced emission enhancement is thus addressed on the lexicon of perturbation of the PET by the metal ions. Apart from fluorescence enhancement, transition metal ion imparts remarkable shift of the emission maxima of NBHN32, which is another unique aspect on the proposed ability of NBHN32 to function as a fluorescence chemosensor.

  17. Synthesis and characterization β-ketoamine ligands

    NASA Astrophysics Data System (ADS)

    Zaid, Nurzati Amani Mohamed; Hassan, Nur Hasyareeda; Karim, Nurul Huda Abd

    2018-04-01

    β-ketoamine ligands are important members of heterodonor ligand because of their ease of preparation and modification of both steric and/or electronic effects. Complexes with β-ketoamine has received much less attention and there has been no study about this complex with β-ketoamine in ionic liquid reported. Two type of β-ketoamine ligands which are 4-amino-3-pentene-2-onato (A) and 3-amino-2-butenoic acid methyl ester (B) have been synthesized in this work. The resulting compound formed was characterized using standard spectroscopic and structural techniques which includes 1H and 13C, NMR spectroscopy and FTIR spectroscopy. The 1H and 13C NMR spectrum displayed all the expected signals with correct integration and multiplicity. And it is proved that there are some differences between two ligands as observed in NMR and FTIR spectrum.

  18. Estimation of affinities of ligands in mixtures via magnetic recovery of target-ligand complexes and chromatographic analyses: chemometrics and an experimental model

    PubMed Central

    2011-01-01

    Abstract Background The combinatorial library strategy of using multiple candidate ligands in mixtures as library members is ideal in terms of cost and efficiency, but needs special screening methods to estimate the affinities of candidate ligands in such mixtures. Herein, a new method to screen candidate ligands present in unknown molar quantities in mixtures was investigated. Results The proposed method involves preparing a processed-mixture-for-screening (PMFS) with each mixture sample and an exogenous reference ligand, initiating competitive binding among ligands from the PMFS to a target immobilized on magnetic particles, recovering target-ligand complexes in equilibrium by magnetic force, extracting and concentrating bound ligands, and analyzing ligands in the PMFS and the concentrated extract by chromatography. The relative affinity of each candidate ligand to its reference ligand is estimated via an approximation equation assuming (a) the candidate ligand and its reference ligand bind to the same site(s) on the target, (b) their chromatographic peak areas are over five times their intercepts of linear response but within their linear ranges, (c) their binding ratios are below 10%. These prerequisites are met by optimizing primarily the quantity of the target used and the PMFS composition ratio. The new method was tested using the competitive binding of biotin derivatives from mixtures to streptavidin immobilized on magnetic particles as a model. Each mixture sample containing a limited number of candidate biotin derivatives with moderate differences in their molar quantities were prepared via parallel-combinatorial-synthesis (PCS) without purification, or via the pooling of individual compounds. Some purified biotin derivatives were used as reference ligands. This method showed resistance to variations in chromatographic quantification sensitivity and concentration ratios; optimized conditions to validate the approximation equation could be applied to

  19. fac-Re(CO)3L complexes containing tridentate monoanionic ligands (L-) with a seldom-studied sulfonamido group as one terminal ligating group.

    PubMed

    Christoforou, Anna Maria; Fronczek, Frank R; Marzilli, Patricia A; Marzilli, Luigi G

    2007-08-20

    To achieve a net-neutral coordination unit in radiopharmaceuticals with a fac-M(CO)3+ core (M = Tc, Re), facially coordinated monoanionic tridentate ligands are needed. New neutral fac-Re(CO)3L complexes were obtained by treating fac-[Re(CO)3(H2O)3]+ with unsymmetrical tridentate NNN donor ligands (LH) based primarily on a diethylenetriamine (dien) moiety with an aromatic group linked to a terminal nitrogen through a sulfonamide. LHs contain 2,4,6-trimethylbenzenesulfonyl (tmbSO2) and 5-(dimethylamino)naphthalene-1-sulfonyl (DNS) groups. X-ray crystallographic and NMR analyses confirm that in both the solid and the solution states all L- in fac-Re(CO)3L complexes are bound in a tridentate fashion with one donor being nitrogen from a deprotonated sulfonamido group. Another fundamental property that is important in radiopharmaceuticals is shape, which in turn depends on ring pucker. For L- = tmbSO2-dien-, tmbSO2-N'-Medien-, and tmbSO2-N,N-Me2dien-, the two chelate rings have a different pucker chirality, as is commonly found for a broad range of metal complexes. However, for fac-Re(CO)3(DNS-dien), both chelate rings have the same pucker chirality because the sulfonamido ring has an unusual pucker for the absolute configuration at Re; a finding that is attributable to intramolecular and intermolecular hydrogen bonds from the sulfonamido oxygens to the NH2 groups. Averaging of tmb NMR signals, even at -90 degrees C for Re(CO)3(tmbSO2-N,N-Me2dien), indicates rapid dynamic motion in the complexes with this group. However, examination of the structures suggests that free rotation about the S-C(tmb) bond is not possible but that concerted coupled rotations about the N-S and the S-C bonds can explain the NMR data.

  20. Clinical Use of PPARγ Ligands in Cancer

    PubMed Central

    Hatton, Jennifer L.; Yee, Lisa D.

    2008-01-01

    The role of PPARγ in adipocyte differentiation has fueled intense interest in the function of this steroid nuclear receptor for regulation of malignant cell growth and differentiation. Given the antiproliferative and differentiating effects of PPARγ ligands on liposarcoma cells, investigation of PPARγ expression and ligand activation in other solid tumors such as breast, colon, and prostate cancers ensued. The anticancer effects of PPARγ ligands in cell culture and rodent models of a multitude of tumor types suggest broad applicability of these agents to cancer therapy. This review focuses on the clinical use of PPARγ ligands, specifically the thiazolidinediones, for the treatment and prevention of cancer. PMID:19125177

  1. Luminescence of ytterbium(III) in mixed-ligand compounds with cinnamic acid and neutral phosphorus-containing ligands

    NASA Astrophysics Data System (ADS)

    Kalinovskaya, I. V.

    2014-09-01

    The luminescence spectral characteristics of mixed-ligand compounds of ytterbium(III) with cinnamic acid and neutral phosphorus-containing ligands were studied by luminescence spectroscopy. The intensity of luminescence of the compounds was determined. The highest intensity of luminescence was found for the ytterbium(III) compound with triphenylphosphine oxide.

  2. Modulation of protein function by exogenous ligands in protein cavities: CO binding to a myoglobin cavity mutant containing unnatural proximal ligands.

    PubMed

    Decatur, S M; DePillis, G D; Boxer, S G

    1996-04-02

    A variety of heterocyclic ligands can be exchanged into the proximal cavity of sperm whale myoglobin mutant H93G, providing a simple method for introduction of the equivalent of unnatural amino acid side chains into a functionally critical location in this protein. These modified proteins bind CO on the distal side. 1H NMR data on H93G(Im)CO, where Im is imidazole, demonstrate that the structure of the distal heme pocket in H93G(Im)CO is very similar to that of wild type; thus, the effects of the proximal ligand's properties on CO binding can be studied with minimal perturbation of distal pocket structure. The exogenous proximal ligands used in this study include imidazole (Im), 4-methylimidazole (4-MeIm), 4-bromoimidazole (4-BrIm), N-methylimidazole (N-MeIm), pyridine (Pyr), and 3-fluoropyridine (3-FPyr). Substitution of the proximal ligand is found to produce substantial changes in the CO on and off rates, the equilibrium binding constant, and the vibrational stretch frequency of CO. Many of the changes are as large as those reported for distal pocket mutants prepared by site-directed mutagenesis. The ability to systematically vary the nature of the proximal ligand is exploited to test the effects of particular properties of the proximal ligand on CO binding. For example, 4-MeIm and 4-BrIm are similar in size and shape but differ significantly in pKa. The same relationship is true for Pyr and 3-FPyr. By comparison of the IR spectra and CO recombination kinetics of these complexes, the effects of proximal ligand pKa on the CO binding are assessed. Likewise, N-MeIm and 4-MeIm are similar in size and pKa but differ in their ability to hydrogen bond to amino acid residues in the proximal cavity. Comparisons of IR spectra and CO binding kinetics in these complexes reveal that proximal ligand conformation and hydrogen bonding affect the kinetics of CO binding. The mechanism of proximal ligand exchange between solution and the proximal cavity in CO complexes was

  3. Interactions between alkaline earth cations and oxo ligands. DFT study of the affinity of the Mg²+ cation for phosphoryl ligands.

    PubMed

    da Costa, Leonardo Moreira; de Mesquita Carneiro, José Walkimar; Paes, Lilian Weitzel Coelho

    2011-08-01

    DFT (B3LYP/6-31+G(d)) calculations of Mg(2+) affinities for a set of phosphoryl ligands were performed. Two types of ligands were studied: a set of trivalent [O = P(R)] and a set of pentavalent phosphoryl ligands [O = P(R)(3)] (R = H, F, Cl, Br, OH, OCH(3), CH(3), CN, NH(2) and NO(2)), with R either bound directly to the phosphorus atom or to the para position of a phenyl ring. The affinity of the Mg(2+) cation for the ligands was quantified by means of the enthalpy for the substitution of one water molecule in the [Mg(H(2)O)(6)](2+) complex for a ligand. The enthalpy of substitution was correlated with electronic and geometric parameters. Electron-donor groups increase the interaction between the cation and the ligand, while electron-acceptor groups decrease the interaction enthalpy.

  4. Identifying tips for intramolecular NC-AFM imaging via in situ fingerprinting

    NASA Astrophysics Data System (ADS)

    Sang, Hongqian; Jarvis, Samuel P.; Zhou, Zhichao; Sharp, Peter; Moriarty, Philip; Wang, Jianbo; Wang, Yu; Kantorovich, Lev

    2014-10-01

    A practical experimental strategy is proposed that could potentially enable greater control of the tip apex in non-contact atomic force microscopy experiments. It is based on a preparation of a structure of interest alongside a reference surface reconstruction on the same sample. Our proposed strategy is as follows. Spectroscopy measurements are first performed on the reference surface to identify the tip apex structure using a previously collected database of responses of different tips to this surface. Next, immediately following the tip identification protocol, the surface of interest is studied (imaging, manipulation and/or spectroscopy). The prototype system we choose is the mixed Si(111)-7×7 and surface which can be prepared on the same sample with a controlled ratio of reactive and passivated regions. Using an ``in silico'' approach based on ab initio density functional calculations and a set of tips with varying chemical reactivities, we show how one can perform tip fingerprinting using the Si(111)-7×7 reference surface. Then it is found by examining the imaging of a naphthalene tetracarboxylic diimide (NTCDI) molecule adsorbed on surface that negatively charged tips produce the best intramolecular contrast attributed to the enhancement of repulsive interactions.

  5. Semiconductor Quantum Dots with Photoresponsive Ligands.

    PubMed

    Sansalone, Lorenzo; Tang, Sicheng; Zhang, Yang; Thapaliya, Ek Raj; Raymo, Françisco M; Garcia-Amorós, Jaume

    2016-10-01

    Photochromic or photocaged ligands can be anchored to the outer shell of semiconductor quantum dots in order to control the photophysical properties of these inorganic nanocrystals with optical stimulations. One of the two interconvertible states of the photoresponsive ligands can be designed to accept either an electron or energy from the excited quantum dots and quench their luminescence. Under these conditions, the reversible transformations of photochromic ligands or the irreversible cleavage of photocaged counterparts translates into the possibility to switch luminescence with external control. As an alternative to regulating the photophysics of a quantum dot via the photochemistry of its ligands, the photochemistry of the latter can be controlled by relying on the photophysics of the former. The transfer of excitation energy from a quantum dot to a photocaged ligand populates the excited state of the species adsorbed on the nanocrystal to induce a photochemical reaction. This mechanism, in conjunction with the large two-photon absorption cross section of quantum dots, can be exploited to release nitric oxide or to generate singlet oxygen under near-infrared irradiation. Thus, the combination of semiconductor quantum dots and photoresponsive ligands offers the opportunity to assemble nanostructured constructs with specific functions on the basis of electron or energy transfer processes. The photoswitchable luminescence and ability to photoinduce the release of reactive chemicals, associated with the resulting systems, can be particularly valuable in biomedical research and can, ultimately, lead to the realization of imaging probes for diagnostic applications as well as to therapeutic agents for the treatment of cancer.

  6. Shedding Light on Anesthetic Mechanisms: Application of Photoaffinity Ligands

    PubMed Central

    Woll, Kellie A.; Dailey, William P.; Brannigan, Grace; Eckenhoff, Roderic G.

    2016-01-01

    Anesthetic photoaffinity ligands have had an increasing presence within anesthesiology research. These ligands mimic parent general anesthetics, and allow investigators to study anesthetic interactions with receptors and enzymes; identify novel targets; and determine distribution within biological systems. To date nearly all general anesthetics used in medicine have a corresponding photoaffinity ligand represented in the literature. In this review we examine all aspects of the current methodologies, including ligand design, characterization and deployment. Finally we offer points of consideration and highlight the future outlook as more photoaffinity ligands emerge within the field. PMID:27464974

  7. Shedding Light on Anesthetic Mechanisms: Application of Photoaffinity Ligands.

    PubMed

    Woll, Kellie A; Dailey, William P; Brannigan, Grace; Eckenhoff, Roderic G

    2016-11-01

    Anesthetic photoaffinity ligands have had an increasing presence within anesthesiology research. These ligands mimic parent general anesthetics and allow investigators to study anesthetic interactions with receptors and enzymes; identify novel targets; and determine distribution within biological systems. To date, nearly all general anesthetics used in medicine have a corresponding photoaffinity ligand represented in the literature. In this review, we examine all aspects of the current methodologies, including ligand design, characterization, and deployment. Finally we offer points of consideration and highlight the future outlook as more photoaffinity ligands emerge within the field.

  8. Sensing multiple ligands with single receptor

    NASA Astrophysics Data System (ADS)

    Singh, Vijay; Nemenman, Ilya

    2015-03-01

    Cells use surface receptors to measure concentrations of external ligand molecules. Limits on the accuracy of such sensing are well-known for the scenario where concentration of one molecular species is being determined by one receptor [Endres]. However, in more realistic scenarios, a cognate (high-affinity) ligand competes with many non-cognate (low-affinity) ligands for binding to the receptor. We analyze effects of this competition on the accuracy of sensing. We show that maximum-likelihood statistical inference allows determination of concentrations of multiple ligands, cognate and non-cognate, by the same receptor concurrently. While it is unclear if traditional biochemical circuitry downstream of the receptor can implement such inference exactly, we show that an approximate inference can be performed by coupling the receptor to a kinetic proofreading cascade. We characterize the accuracy of such kinetic proofreading sensing in comparison to the exact maximum-likelihood approach. We acknowledge the support from the James S. McDonnell Foundation and the Human Frontier Science Program.

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

    PubMed

    Lin, Ying-Ting

    2013-04-30

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

  10. Synthesis and photophysical properties of a series of cyclopenta[b]naphthalene solvatochromic fluorophores.

    PubMed

    Benedetti, Erica; Kocsis, Laura S; Brummond, Kay M

    2012-08-01

    The synthesis and photophysical properties of a series of naphthalene-containing solvatochromic fluorophores are described within. These novel fluorophores are prepared using a microwave-assisted dehydrogenative Diels-Alder reaction of styrene, followed by a palladium-catalyzed cross coupling reaction to install an electron donating amine group. The new fluorophores are structurally related to Prodan. Photophysical properties of the new fluorophores were studied and intriguing solvatochromic behavior was observed. For most of these fluorophores, high quantum yields (60-99%) were observed in methylene chloride in addition to large Stokes shifts (95-226 nm) in this same solvent. As the solvent polarity increased, so did the observed Stokes shift with one derivative displaying a Stokes shift of ~300 nm in ethanol. All fluorophore emission maxima, and nearly all absorption maxima were significantly red-shifted when compared to Prodan. Shifting the absorption and emission maxima of a fluorophore into the visible region increases its utility in biological applications. Moreover, the cyclopentane portion of the fluorophore structure provides an attachment point for biomolecules that will minimize disruptions of the photophysical properties.

  11. Visualizing ligand molecules in Twilight electron density.

    PubMed

    Weichenberger, Christian X; Pozharski, Edwin; Rupp, Bernhard

    2013-02-01

    Three-dimensional models of protein structures determined by X-ray crystallography are based on the interpretation of experimentally derived electron-density maps. The real-space correlation coefficient (RSCC) provides an easily comprehensible, objective measure of the residue-based fit of atom coordinates to electron density. Among protein structure models, protein-ligand complexes are of special interest, given their contribution to understanding the molecular underpinnings of biological activity and to drug design. For consumers of such models, it is not trivial to determine the degree to which ligand-structure modelling is biased by subjective electron-density interpretation. A standalone script, Twilight, is presented for the analysis, visualization and annotation of a pre-filtered set of 2815 protein-ligand complexes deposited with the PDB as of 15 January 2012 with ligand RSCC values that are below a threshold of 0.6. It also provides simplified access to the visualization of any protein-ligand complex available from the PDB and annotated by the Uppsala Electron Density Server. The script runs on various platforms and is available for download at http://www.ruppweb.org/twilight/.

  12. Engineering death receptor ligands for cancer therapy.

    PubMed

    Wajant, Harald; Gerspach, Jeannette; Pfizenmaier, Klaus

    2013-05-28

    CD95, TNFR1, TRAILR1 and TRAILR2 belong to a subgroup of TNF receptors which is characterized by a conserved cell death-inducing protein domain that connects these receptors to the apoptotic machinery of the cell. Activation of death receptors in malignant cells attracts increasing attention as a principle to fight cancer. Besides agonistic antibodies the major way to stimulate death receptors is the use of their naturally occurring "death ligands" CD95L, TNF and TRAIL. However, dependent from the concept followed to develop a death ligand-based therapy various limiting aspects have to be taken into consideration on the way to a "bedside" usable drug. Problems arise in particular from the cell associated transmembrane nature of the death ligands, the poor serum half life of the soluble fragments derived from the transmembrane ligands, the ubiquitous expression of the death receptors and the existence of additional non-death receptors of the death ligands. Here, we summarize strategies how these limitations can be overcome by genetic engineering. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  13. Receptor-ligand binding sites and virtual screening.

    PubMed

    Hattotuwagama, Channa K; Davies, Matthew N; Flower, Darren R

    2006-01-01

    Within the pharmaceutical industry, the ultimate source of continuing profitability is the unremitting process of drug discovery. To be profitable, drugs must be marketable: legally novel, safe and relatively free of side effects, efficacious, and ideally inexpensive to produce. While drug discovery was once typified by a haphazard and empirical process, it is now increasingly driven by both knowledge of the receptor-mediated basis of disease and how drug molecules interact with receptors and the wider physiome. Medicinal chemistry postulates that to understand a congeneric ligand series, or set thereof, is to understand the nature and requirements of a ligand binding site. Likewise, structural molecular biology posits that to understand a binding site is to understand the nature of ligands bound therein. Reality sits somewhere between these extremes, yet subsumes them both. Complementary to rules of ligand design, arising through decades of medicinal chemistry, structural biology and computational chemistry are able to elucidate the nature of binding site-ligand interactions, facilitating, at both pragmatic and conceptual levels, the drug discovery process.

  14. Thermometric titration studies of mixed ligand complexes of thorium.

    PubMed

    Kugler, G C; Carey, G H

    1970-10-01

    Mixed-ligand chelates consisting of two different multidentate ligands linked to a central thorium(IV) ion have been prepared in aqueous solution and their heats of formation studied thermo metrically. Pyrocatechol, tiron, chromotropic acid, potassium hydrogen phthalate, 8-hydroxyquinoline-S-sulphonic acid, iminodiacetic acid, 5-sulphosalicylic acid and salicylic acid were used as the secondary ligands, while ethylenediaminetetra-acetate and 1, 2-diaminocyclohexane-N,N,N',N'-tetra-acetate were used as primary ligands. DeltaH values for the overall reactions are given, and where possible, the DeltaH and DeltaS values for the specific secondary ligand addition were calculated. The overall stability of the mixed-ligand chelates and the enhanced stability of EDTA mixed chelates relative to the analogous DCTA chelates were found to be due to entropy rather than enthalpy effects.

  15. Calculating the mean time to capture for tethered ligands and its effect on the chemical equilibrium of bound ligand pairs.

    PubMed

    Shen, Lu; Decker, Caitlin G; Maynard, Heather D; Levine, Alex J

    2016-09-01

    We present here the calculation of the mean time to capture of a tethered ligand to the receptor. This calculation is then used to determine the shift in the partitioning between (1) free, (2) singly bound, and (3) doubly bound ligands in chemical equilibrium as a function of the length of the tether. These calculations are used in the research article Fibroblast Growth Factor 2 Dimer with Superagonist in vitro Activity Improves Granulation Tissue Formation During Wound Healing (Decker et al., in press [1]) to explain quantitatively how changes in polymeric linker length in the ligand dimers modifies the efficacy of these molecules relative to that of free ligands.

  16. Predicting receptor-ligand pairs through kernel learning

    PubMed Central

    2011-01-01

    Background Regulation of cellular events is, often, initiated via extracellular signaling. Extracellular signaling occurs when a circulating ligand interacts with one or more membrane-bound receptors. Identification of receptor-ligand pairs is thus an important and specific form of PPI prediction. Results Given a set of disparate data sources (expression data, domain content, and phylogenetic profile) we seek to predict new receptor-ligand pairs. We create a combined kernel classifier and assess its performance with respect to the Database of Ligand-Receptor Partners (DLRP) 'golden standard' as well as the method proposed by Gertz et al. Among our findings, we discover that our predictions for the tgfβ family accurately reconstruct over 76% of the supported edges (0.76 recall and 0.67 precision) of the receptor-ligand bipartite graph defined by the DLRP "golden standard". In addition, for the tgfβ family, the combined kernel classifier is able to relatively improve upon the Gertz et al. work by a factor of approximately 1.5 when considering that our method has an F-measure of 0.71 while that of Gertz et al. has a value of 0.48. Conclusions The prediction of receptor-ligand pairings is a difficult and complex task. We have demonstrated that using kernel learning on multiple data sources provides a stronger alternative to the existing method in solving this task. PMID:21834994

  17. Importance of the pharmacological profile of the bound ligand in enrichment on nuclear receptors: toward the use of experimentally validated decoy ligands.

    PubMed

    Lagarde, Nathalie; Zagury, Jean-François; Montes, Matthieu

    2014-10-27

    The evaluation of virtual ligand screening methods is of major importance to ensure their reliability. Taking into account the agonist/antagonist pharmacological profile should improve the quality of the benchmarking data sets since ligand binding can induce conformational changes in the nuclear receptor structure and such changes may vary according to the agonist/antagonist ligand profile. We indeed found that splitting the agonist and antagonist ligands into two separate data sets for a given nuclear receptor target significantly enhances the quality of the evaluation. The pharmacological profile of the ligand bound in the binding site of the target structure was also found to be an additional critical parameter. We also illustrate that active compound data sets for a given pharmacological activity can be used as a set of experimentally validated decoy ligands for another pharmacological activity to ensure a reliable and challenging evaluation of virtual screening methods.

  18. Sensitization of Nanocrystalline Metal Oxides with a Phosphonate-Functionalized Perylene Diimide for Photoelectrochemical Water Oxidation with a CoO x Catalyst

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

    Kirner, Joel T.; Finke, Richard G.

    A planar organic thin film composed of a perylene diimide dye (N,N'-bis(phosphonomethyl)-3,4,9,10-perylenediimide, PMPDI) with photoelectrochemically deposited cobalt oxide (CoO x) catalyst was previously shown to photoelectrochemically oxidize water (DOI: 10.1021/am405598w). Herein, the same PMPDI dye is studied for the sensitization of different nanostructured metal oxide (nano-MO x) films in a dye-sensitized photoelectrochemical cell architecture. Dye adsorption kinetics and saturation decreases in the order TiO 2 > SnO 2 >> WO 3. Despite highest initial dye loading on TiO 2 films, photocurrent with hydroquinone (H 2Q) sacrificial reductant in pH 7 aqueous solution is much higher on SnO 2 films, likelymore » due to a higher driving force for charge injection into the more positive conduction band energy of SnO 2. Dyeing conditions and SnO 2 film thickness were subsequently optimized to achieve light-harvesting efficiency >99% at the λmax of the dye, and absorbed photon-to-current efficiency of 13% with H 2Q, a 2-fold improvement over the previous thin-film architecture. A CoO x water-oxidation catalyst was photoelectrochemically deposited, allowing for photoelectrochemical water oxidation with a faradaic efficiency of 31 ± 7%, thus demonstrating the second example of a water-oxidizing, dye-sensitized photoelectrolysis cell composed entirely of earth-abundant materials. However, deposition of CoO x always results in lower photocurrent due to enhanced recombination between catalyst and photoinjected electrons in SnO 2, as confirmed by open-circuit photovoltage measurements. Possible future studies to enhance photoanode performance are also discussed, including alternative catalyst deposition strategies or structural derivatization of the perylene dye.« less

  19. Sensitization of Nanocrystalline Metal Oxides with a Phosphonate-Functionalized Perylene Diimide for Photoelectrochemical Water Oxidation with a CoO x Catalyst

    DOE PAGES

    Kirner, Joel T.; Finke, Richard G.

    2017-07-20

    A planar organic thin film composed of a perylene diimide dye (N,N'-bis(phosphonomethyl)-3,4,9,10-perylenediimide, PMPDI) with photoelectrochemically deposited cobalt oxide (CoO x) catalyst was previously shown to photoelectrochemically oxidize water (DOI: 10.1021/am405598w). Herein, the same PMPDI dye is studied for the sensitization of different nanostructured metal oxide (nano-MO x) films in a dye-sensitized photoelectrochemical cell architecture. Dye adsorption kinetics and saturation decreases in the order TiO 2 > SnO 2 >> WO 3. Despite highest initial dye loading on TiO 2 films, photocurrent with hydroquinone (H 2Q) sacrificial reductant in pH 7 aqueous solution is much higher on SnO 2 films, likelymore » due to a higher driving force for charge injection into the more positive conduction band energy of SnO 2. Dyeing conditions and SnO 2 film thickness were subsequently optimized to achieve light-harvesting efficiency >99% at the λmax of the dye, and absorbed photon-to-current efficiency of 13% with H 2Q, a 2-fold improvement over the previous thin-film architecture. A CoO x water-oxidation catalyst was photoelectrochemically deposited, allowing for photoelectrochemical water oxidation with a faradaic efficiency of 31 ± 7%, thus demonstrating the second example of a water-oxidizing, dye-sensitized photoelectrolysis cell composed entirely of earth-abundant materials. However, deposition of CoO x always results in lower photocurrent due to enhanced recombination between catalyst and photoinjected electrons in SnO 2, as confirmed by open-circuit photovoltage measurements. Possible future studies to enhance photoanode performance are also discussed, including alternative catalyst deposition strategies or structural derivatization of the perylene dye.« less

  20. Design of a Hole Trapping Ligand

    DOE PAGES

    La Croix, Andrew D.; O’Hara, Andrew; Reid, Kemar R.; ...

    2017-01-18

    A new ligand that covalently attaches to the surface of colloidal CdSe/ CdS nanorods and can simultaneously chelate a molecular metal center is described. The dithiocarbamate$-$bipyridine ligand system facilitates hole transfer through energetic overlap at the inorganic$-$organic interface and conjugation through the organic ligand to a chelated metal center. Density functional theory calculations show that the coordination of the free ligand to a CdS surface causes the formation of two hybridized molecular states that lie in the band gap of CdS. The further chelation of Fe(II) to the bipyridine moiety causes the presence of seven midgap states. Hole transfer frommore » the CdS valence band to the midgap states is dipole allowed and occurs at a faster rate than what is experimentally known for the CdSe/CdS band-edge radiative recombination. In the case of the ligand bound with iron, a two-step process emerges that places the hole on the iron, again at rates much faster than band gap recombination. The system was experimentally assembled and characterized via UV$-$vis absorbance spectroscopy, fluorescence spectroscopy, time-resolved photoluminescence spectroscopy, and energy dispersive X-ray spectroscopy. Lastly, theoretically predicted red shifts in absorbance were observed experimentally, as well as the expected quench in photoluminescence and lifetimes in time-resolved photoluminescence« less

  1. Design of a Hole Trapping Ligand

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

    La Croix, Andrew D.; O’Hara, Andrew; Reid, Kemar R.

    A new ligand that covalently attaches to the surface of colloidal CdSe/ CdS nanorods and can simultaneously chelate a molecular metal center is described. The dithiocarbamate$-$bipyridine ligand system facilitates hole transfer through energetic overlap at the inorganic$-$organic interface and conjugation through the organic ligand to a chelated metal center. Density functional theory calculations show that the coordination of the free ligand to a CdS surface causes the formation of two hybridized molecular states that lie in the band gap of CdS. The further chelation of Fe(II) to the bipyridine moiety causes the presence of seven midgap states. Hole transfer frommore » the CdS valence band to the midgap states is dipole allowed and occurs at a faster rate than what is experimentally known for the CdSe/CdS band-edge radiative recombination. In the case of the ligand bound with iron, a two-step process emerges that places the hole on the iron, again at rates much faster than band gap recombination. The system was experimentally assembled and characterized via UV$-$vis absorbance spectroscopy, fluorescence spectroscopy, time-resolved photoluminescence spectroscopy, and energy dispersive X-ray spectroscopy. Lastly, theoretically predicted red shifts in absorbance were observed experimentally, as well as the expected quench in photoluminescence and lifetimes in time-resolved photoluminescence« less

  2. Expression of nociceptive ligands in canine osteosarcoma.

    PubMed

    Shor, S; Fadl-Alla, B A; Pondenis, H C; Zhang, X; Wycislo, K L; Lezmi, S; Fan, T M

    2015-01-01

    Canine osteosarcoma (OS) is associated with localized pain as a result of tissue injury from tumor infiltration and peritumoral inflammation. Malignant bone pain is caused by stimulation of peripheral pain receptors, termed nociceptors, which reside in the localized tumor microenvironment, including the periosteal and intramedullary bone cavities. Several nociceptive ligands have been determined to participate directly or indirectly in generating bone pain associated with diverse skeletal abnormalities. Canine OS cells actively produce nociceptive ligands with the capacity to directly or indirectly activate peripheral pain receptors residing in the bone tumor microenvironment. Ten dogs with appendicular OS. Expression of nerve growth factor, endothelin-1, and microsomal prostaglandin E synthase-1 was characterized in OS cell lines and naturally occurring OS samples. In 10 dogs with OS, circulating concentrations of nociceptive ligands were quantified and correlated with subjective pain scores and tumor volume in patients treated with standardized palliative therapies. Canine OS cells express and secrete nerve growth factor, endothelin-1, and prostaglandin E2. Naturally occurring OS samples uniformly express nociceptive ligands. In a subset of OS-bearing dogs, circulating nociceptive ligand concentrations were detectable but failed to correlate with pain status. Localized foci of nerve terminal proliferation were identified in a minority of primary bone tumor samples. Canine OS cells express nociceptive ligands, potentially permitting active participation of OS cells in the generation of malignant bone pain. Specific inhibitors of nociceptive ligand signaling pathways might improve pain control in dogs with OS. Copyright © 2015 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals, Inc. on behalf of American College of Veterinary Internal Medicine.

  3. Bending nanofibers into nanospirals: coordination chemistry as a tool for shaping hydrophobic assemblies.

    PubMed

    Kossoy, Elizaveta; Weissman, Haim; Rybtchinski, Boris

    2015-01-02

    In the current work, we demonstrate how coordination chemistry can be employed to direct self-assembly based on strong hydrophobic interactions. To investigate the influence of coordination sphere geometry on aqueous self-assembly, we synthesized complexes of the amphiphilic perylene diimide terpyridine ligand with the first-row transition-metal centers (zinc, cobalt, and nickel). In aqueous medium, aggregation of these complexes is induced by hydrophobic interactions between the ligands. However, the final shapes of the resulting assemblies depend on the preferred geometry of the coordination spheres typical for the particular metal center. The self-assembly process was characterized by UV/Vis spectroscopy, zeta potential measurements, and cryogenic transmission electron microscopy (cryo-TEM). Coordination of zinc(II) and cobalt(II) leads to the formation of unique nanospiral assemblies, whereas complexation of nickel(II) leads to the formation of straight nanofibers. Notably, coordination bonds are utilized not as connectors between elementary building blocks, but as directing interactions, enabling control over supramolecular geometry. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Vibrational spectroscopic and quantum chemical calculations of (E)-N-Carbamimidoyl-4-((naphthalen-1-yl-methylene)amino)benzene sulfonamide.

    PubMed

    Chandran, Asha; Varghese, Hema Tresa; Mary, Y Sheena; Panicker, C Yohannan; Manojkumar, T K; Van Alsenoy, Christian; Rajendran, G

    2012-02-15

    FT-IR and FT-Raman spectra of (E)-N-Carbamimidoyl-4-((naphthalen-1-yl-methylene)amino)benzene sulfonamide were recorded and analyzed. The vibrational wavenumbers were computing at various levels of theory. The data obtained from theoretical calculations are used to assign vibrational bands obtained experimentally. The results indicate that B3LYP method is able to provide satisfactory results for predicting vibrational frequencies and structural parameters. The calculated first hyperpolarizability is comparable with reported values of similar derivatives and is an attractive object for future studies of non-linear optics. The geometrical parameters of the title compound are in agreement with that of similar derivatives. Copyright © 2011 Elsevier B.V. All rights reserved.

  5. Implicit ligand theory for relative binding free energies

    NASA Astrophysics Data System (ADS)

    Nguyen, Trung Hai; Minh, David D. L.

    2018-03-01

    Implicit ligand theory enables noncovalent binding free energies to be calculated based on an exponential average of the binding potential of mean force (BPMF)—the binding free energy between a flexible ligand and rigid receptor—over a precomputed ensemble of receptor configurations. In the original formalism, receptor configurations were drawn from or reweighted to the apo ensemble. Here we show that BPMFs averaged over a holo ensemble yield binding free energies relative to the reference ligand that specifies the ensemble. When using receptor snapshots from an alchemical simulation with a single ligand, the new statistical estimator outperforms the original.

  6. Superior serum half life of albumin tagged TNF ligands

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

    Mueller, Nicole; Schneider, Britta; Pfizenmaier, Klaus

    2010-06-11

    Due to their immune stimulating and apoptosis inducing properties, ligands of the TNF family attract increasing interest as therapeutic proteins. A general limitation of in vivo applications of recombinant soluble TNF ligands is their notoriously rapid clearance from circulation. To improve the serum half life of the TNF family members TNF, TWEAK and TRAIL, we genetically fused soluble variants of these molecules to human serum albumin (HSA). The serum albumin-TNF ligand fusion proteins were found to be of similar bioactivity as the corresponding HSA-less counterparts. Upon intravenous injection (i.v.), serum half life of HSA-TNF ligand fusion proteins, as determined bymore » ELISA, was around 15 h as compared to approximately 1 h for all of the recombinant control TNF ligands without HSA domain. Moreover, serum samples collected 6 or 24 h after i.v. injection still contained high TNF ligand bioactivity, demonstrating that there is only limited degradation/inactivation of circulating HSA-TNF ligand fusion proteins in vivo. In a xenotransplantation model, significantly less of the HSA-TRAIL fusion protein compared to the respective control TRAIL protein was required to achieve inhibition of tumor growth indicating that the increased half life of HSA-TNF ligand fusion proteins translates into better therapeutic action in vivo. In conclusion, our data suggest that genetic fusion to serum albumin is a powerful and generally applicable mean to improve bioavailability and in vivo activity of TNF ligands.« less

  7. Stabilization of peroxisome proliferator-activated receptor alpha by the ligand.

    PubMed

    Hirotani, M; Tsukamoto, T; Bourdeaux, J; Sadano, H; Osumi, T

    2001-10-19

    Peroxisome proliferator-activated receptor (PPAR) constitutes a subfamily among a large group of ligand-activated transcription factors, the nuclear receptor superfamily. We studied the effects of ligand on the intracellular behaviors of PPARalpha. Although nuclear localization of PPARalpha was not affected by a selective ligand, Wy14643, we observed that exogenously expressed PPARalpha was rapidly degraded in HeLa cells, and the ligand significantly stabilized the protein. The stability of PPARalpha was also improved by coexpression of the heterodimer partner retinoid X receptor (RXR) alpha, and further stabilization was not observed with the ligand. These results indicate that PPARalpha is stabilized through heterodimerization with RXR, and the excess protein unpaired with RXR is rapidly turned over, if not bound by an appropriate ligand. These observations on PPARalpha are in sharp contrast to the ligand-stimulated degradation reported on PPARgamma. The ligand-dependent stabilization would have physiological significance when the synthesis of PPARalpha is elevated exceeding the available level of RXR. Copyright 2001 Academic Press.

  8. Effects of electrostatic interactions on ligand dissociation kinetics

    NASA Astrophysics Data System (ADS)

    Erbaş, Aykut; de la Cruz, Monica Olvera; Marko, John F.

    2018-02-01

    We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics simulations are suggested by single-molecule studies of protein-DNA interactions. We consider univalent salt concentrations spanning roughly a 1000-fold range, together with various concentrations of excess ligands in solution. To reveal the ionic effects on unbinding kinetics of spontaneous and facilitated dissociation mechanisms, we treat electrostatic interactions both at a Debye-Hückel (DH) (or implicit ions, i.e., use of an electrostatic potential with a prescribed decay length) level and by the more precise approach of considering all ionic species explicitly in the simulations. We find that the DH approach systematically overestimates unbinding rates, relative to the calculations where all ion pairs are present explicitly in solution, although many aspects of the two types of calculation are qualitatively similar. For facilitated dissociation (FD) (acceleration of unbinding by free ligands in solution) explicit-ion simulations lead to unbinding at lower free-ligand concentrations. Our simulations predict a variety of FD regimes as a function of free-ligand and ion concentrations; a particularly interesting regime is at intermediate concentrations of ligands where nonelectrostatic binding strength controls FD. We conclude that explicit-ion electrostatic modeling is an essential component to quantitatively tackle problems in molecular ligand dissociation, including nucleic-acid-binding proteins.

  9. [Supercomputer investigation of the protein-ligand system low-energy minima].

    PubMed

    Oferkin, I V; Sulimov, A V; Katkova, E V; Kutov, D K; Grigoriev, F V; Kondakova, O A; Sulimov, V B

    2015-01-01

    The accuracy of the protein-ligand binding energy calculations and ligand positioning is strongly influenced by the choice of the docking target function. This work demonstrates the evaluation of the five different target functions used in docking: functions based on MMFF94 force field and functions based on PM7 quantum-chemical method accounting or without accounting the implicit solvent model (PCM, COSMO or SGB). For these purposes the ligand positions corresponding to the minima of the target function and the experimentally known ligand positions in the protein active site (crystal ligand positions) were compared. Each function was examined on the same test-set of 16 protein-ligand complexes. The new parallelized docking program FLM based on Monte Carlo search algorithm was developed to perform the comprehensive low-energy minima search and to calculate the protein-ligand binding energy. This study demonstrates that the docking target function based on the MMFF94 force field can be used to detect the crystal or near crystal positions of the ligand by the finding the low-energy local minima spectrum of the target function. The importance of solvent accounting in the docking process for the accurate ligand positioning is also shown. The accuracy of the ligand positioning as well as the correlation between the calculated and experimentally determined protein-ligand binding energies are improved when the MMFF94 force field is substituted by the new PM7 method with implicit solvent accounting.

  10. Critical ligand binding reagent preparation/selection: when specificity depends on reagents.

    PubMed

    Rup, Bonita; O'Hara, Denise

    2007-05-11

    Throughout the life cycle of biopharmaceutical products, bioanalytical support is provided using ligand binding assays to measure the drug product for pharmacokinetic, pharmacodynamic, and immunogenicity studies. The specificity and selectivity of these ligand binding assays are highly dependent on the ligand binding reagents. Thus the selection, characterization, and management processes for ligand binding reagents are crucial to successful assay development and application. This report describes process considerations for selection and characterization of ligand binding reagents that are integral parts of the different phases of assay development. Changes in expression, purification, modification, and storage of the ligand binding reagents may have a profound effect on the ligand binding assay performance. Thus long-term management of the critical ligand binding assay reagents is addressed including suggested characterization criteria that allow ligand binding reagents to be used in as consistent a manner as possible. Examples of challenges related to the selection, modification, and characterization of ligand binding reagents are included.

  11. (2E)-3-(6-Meth­oxy­naphthalen-2-yl)-1-[4-(methyl­sulfan­yl)phen­yl]prop-2-en-1-one

    PubMed Central

    Fun, Hoong-Kun; Chia, Tze Shyang; Padaki, Mahesh; Isloor, Arun M.; Ismail, A. F.

    2012-01-01

    The asymmetric unit of the title compound, C21H18O2S, consists of two crystallographically independent mol­ecules (A and B). The mol­ecules exist in a trans conformation with respect to the central C=C bond. The naphthalene ring system makes dihedral angles of 51.62 (12) (mol­ecule A) and 52.69 (12)° (mol­ecule B) with the benzene ring. In mol­ecule A, the prop-2-en-1-one group forms dihedral angles of 22.84 (15) and 29.02 (12)° with the adjacent naphthalene ring system and benzene ring, respectively, whereas the corresponding angles are 30.04 (12) and 23.33 (12)° in mol­ecule B. In the crystal, mol­ecules are linked by inter­molecular C—H⋯O hydrogen bonds into head-to-tail chains along the a axis. The crystal packing also features C—H⋯π inter­actions. The crystal studied was a pseudo-merohedral twin with twin law (100 0-10 00-1) and a refined component ratio of 0.6103 (16):0.3897 (16). PMID:22798922

  12. Ligand.Info small-molecule Meta-Database.

    PubMed

    von Grotthuss, Marcin; Koczyk, Grzegorz; Pas, Jakub; Wyrwicz, Lucjan S; Rychlewski, Leszek

    2004-12-01

    Ligand.Info is a compilation of various publicly available databases of small molecules. The total size of the Meta-Database is over 1 million entries. The compound records contain calculated three-dimensional coordinates and sometimes information about biological activity. Some molecules have information about FDA drug approving status or about anti-HIV activity. Meta-Database can be downloaded from the http://Ligand.Info web page. The database can also be screened using a Java-based tool. The tool can interactively cluster sets of molecules on the user side and automatically download similar molecules from the server. The application requires the Java Runtime Environment 1.4 or higher, which can be automatically downloaded from Sun Microsystems or Apple Computer and installed during the first use of Ligand.Info on desktop systems, which support Java (Ms Windows, Mac OS, Solaris, and Linux). The Ligand.Info Meta-Database can be used for virtual high-throughput screening of new potential drugs. Presented examples showed that using a known antiviral drug as query the system was able to find others antiviral drugs and inhibitors.

  13. [Functional selectivity of opioid receptors ligands].

    PubMed

    Audet, Nicolas; Archer-Lahlou, Elodie; Richard-Lalonde, Mélissa; Piñeyro-Filpo, Graciela

    2010-01-01

    Opiates are the most effective analgesics available for the treatment of severe pain. However, their clinical use is restricted by unwanted side effects such as tolerance, physical dependence and respiratory depression. The strategy to develop new opiates with reduced side effects has mainly focused on the study and production of ligands that specifically bind to different opiate receptors subtypes. However, this strategy has not allowed the production of novel therapeutic ligands with a better side effects profile. Thus, other research strategies need to be explored. One which is receiving increasing attention is the possibility of exploiting ligand ability to stabilize different receptor conformations with distinct signalling profiles. This newly described property, termed functional selectivity, provides a potential means of directing the stimulus generated by an activated receptor towards a specific cellular response. Here we summarize evidence supporting the existence of ligand-specific active conformations for two opioid receptors subtypes (delta and mu), and analyze how functional selectivity may contribute in the production of longer lasting, better tolerated opiate analgesics. double dagger.

  14. A new window towards multidimensional sensing of transition metal cations through dual mode sensing ability of N-benzyl-(3-hydoxy-2-naphthalene): emission enhancement coupled remarkable spectral shift.

    PubMed

    Paul, Bijan Kumar; Mahanta, Subrata; Singh, Rupashree Balia; Guchhait, Nikhil

    2011-06-01

    A structurally simple Schiff base N-benzyl-(3-hydroxy-2-naphthalene) (NBHN32) has been synthesized and characterized by (1)H NMR, (13)C NMR, and DEPT spectroscopy. The photophysical behaviour of NBHN32 in response to the presence of various transition metal cations has been explored by means of steady-state absorption, emission and time-resolved emission spectroscopy techniques. Efficient through space intramolecular photoinduced electron transfer (PET) between the naphthalene fluorophore and the imine group has been argued for extremely low fluorescence yield of NBHN32 compared to the parent molecule 3-hydroxy-2-naphthaldehyde (HN32) containing the same fluorophore but lacking the receptor moiety. Transition metal ion-induced emission enhancement is thus addressed on the lexicon of perturbation of the PET by the metal ions. Apart from fluorescence enhancement, transition metal ion imparts remarkable shift of the emission maxima of NBHN32, which is another unique aspect on the proposed ability of NBHN32 to function as a fluorescence chemosensor. Copyright © 2011 Elsevier B.V. All rights reserved.

  15. Rational Ligand Design for U(VI) and Pu(IV)

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

    Szigethy, Geza

    2009-08-12

    Nuclear power is an attractive alternative to hydrocarbon-based energy production at a time when moving away from carbon-producing processes is widely accepted as a significant developmental need. Hence, the radioactive actinide power sources for this industry are necessarily becoming more widespread, which is accompanied by the increased risk of exposure to both biological and environmental systems. This, in turn, requires the development of technology designed to remove such radioactive threats efficiently and selectively from contaminated material, whether that be contained nuclear waste streams or the human body. Raymond and coworkers (University of California, Berkeley) have for decades investigated the interactionmore » of biologically-inspired, hard Lewis-base ligands with high-valent, early-actinide cations. It has been established that such ligands bind strongly to the hard Lewis-acidic early actinides, and many poly-bidentate ligands have been developed and shown to be effective chelators of actinide contaminants in vivo. Work reported herein explores the effect of ligand geometry on the linear U(IV) dioxo dication (uranyl, UO 2 2+). The goal is to utilize rational ligand design to develop ligands that exhibit shape selectivity towards linear dioxo cations and provides thermodynamically favorable binding interactions. The uranyl complexes with a series of tetradentate 3-hydroxy-pyridin-2-one (3,2-HOPO) ligands were studied in both the crystalline state as well as in solution. Despite significant geometric differences, the uranyl affinities of these ligands vary only slightly but are better than DTPA, the only FDA-approved chelation therapy for actinide contamination. The terepthalamide (TAM) moiety was combined into tris-beidentate ligands with 1,2- and 3,2-HOPO moieties were combined into hexadentate ligands whose structural preferences and solution thermodynamics were measured with the uranyl cation. In addition to achieving coordinative saturation

  16. Ligand- and receptor-based docking with LiBELa

    NASA Astrophysics Data System (ADS)

    dos Santos Muniz, Heloisa; Nascimento, Alessandro S.

    2015-08-01

    Methodologies on molecular docking are constantly improving. The problem consists on finding an optimal interplay between the computational cost and a satisfactory physical description of ligand-receptor interaction. In pursuit of an advance in current methods we developed a mixed docking approach combining ligand- and receptor-based strategies in a docking engine, where tridimensional descriptors for shape and charge distribution of a reference ligand guide the initial placement of the docking molecule and an interaction energy-based global minimization follows. This hybrid docking was evaluated with soft-core and force field potentials taking into account ligand pose and scoring. Our approach was found to be competitive to a purely receptor-based dock resulting in improved logAUC values when evaluated with DUD and DUD-E. Furthermore, the smoothed potential as evaluated here, was not advantageous when ligand binding poses were compared to experimentally determined conformations. In conclusion we show that a combination of ligand- and receptor-based strategy docking with a force field energy model results in good reproduction of binding poses and enrichment of active molecules against decoys. This strategy is implemented in our tool, LiBELa, available to the scientific community.

  17. Mapping of ligand-binding cavities in proteins.

    PubMed

    Andersson, C David; Chen, Brian Y; Linusson, Anna

    2010-05-01

    The complex interactions between proteins and small organic molecules (ligands) are intensively studied because they play key roles in biological processes and drug activities. Here, we present a novel approach to characterize and map the ligand-binding cavities of proteins without direct geometric comparison of structures, based on Principal Component Analysis of cavity properties (related mainly to size, polarity, and charge). This approach can provide valuable information on the similarities and dissimilarities, of binding cavities due to mutations, between-species differences and flexibility upon ligand-binding. The presented results show that information on ligand-binding cavity variations can complement information on protein similarity obtained from sequence comparisons. The predictive aspect of the method is exemplified by successful predictions of serine proteases that were not included in the model construction. The presented strategy to compare ligand-binding cavities of related and unrelated proteins has many potential applications within protein and medicinal chemistry, for example in the characterization and mapping of "orphan structures", selection of protein structures for docking studies in structure-based design, and identification of proteins for selectivity screens in drug design programs. 2009 Wiley-Liss, Inc.

  18. Mapping of Ligand-Binding Cavities in Proteins

    PubMed Central

    Andersson, C. David; Chen, Brian Y.; Linusson, Anna

    2010-01-01

    The complex interactions between proteins and small organic molecules (ligands) are intensively studied because they play key roles in biological processes and drug activities. Here, we present a novel approach to characterise and map the ligand-binding cavities of proteins without direct geometric comparison of structures, based on Principal Component Analysis of cavity properties (related mainly to size, polarity and charge). This approach can provide valuable information on the similarities, and dissimilarities, of binding cavities due to mutations, between-species differences and flexibility upon ligand-binding. The presented results show that information on ligand-binding cavity variations can complement information on protein similarity obtained from sequence comparisons. The predictive aspect of the method is exemplified by successful predictions of serine proteases that were not included in the model construction. The presented strategy to compare ligand-binding cavities of related and unrelated proteins has many potential applications within protein and medicinal chemistry, for example in the characterisation and mapping of “orphan structures”, selection of protein structures for docking studies in structure-based design and identification of proteins for selectivity screens in drug design programs. PMID:20034113

  19. Visualizing ligand molecules in twilight electron density

    PubMed Central

    Weichenberger, Christian X.; Pozharski, Edwin; Rupp, Bernhard

    2013-01-01

    Three-dimensional models of protein structures determined by X-ray crystallo­graphy are based on the interpretation of experimentally derived electron-density maps. The real-space correlation coefficient (RSCC) provides an easily comprehensible, objective measure of the residue-based fit of atom coordinates to electron density. Among protein structure models, protein–ligand complexes are of special interest, given their contribution to understanding the molecular underpinnings of biological activity and to drug design. For consumers of such models, it is not trivial to determine the degree to which ligand-structure modelling is biased by subjective electron-density interpretation. A standalone script, Twilight, is presented for the analysis, visualization and annotation of a pre-filtered set of 2815 protein–ligand complexes deposited with the PDB as of 15 January 2012 with ligand RSCC values that are below a threshold of 0.6. It also provides simplified access to the visualization of any protein–ligand complex available from the PDB and annotated by the Uppsala Electron Density Server. The script runs on various platforms and is available for download at http://www.ruppweb.org/twilight/. PMID:23385767

  20. Modification of the 5' terminus of oligodeoxyribonucleotides for conjugation with ligands.

    PubMed

    Asseline, U; Thuong, N T

    2001-08-01

    Ligands can be introduced at the 5' terminus of an oligonucleotide by adding a linker to the ligand and modifying the 5' terminus of the oligonucleotide. These are then reacted to give the ligand-oligonucleotide conjugate. This unit describes the addition of carboxylated and aminoalkylated linkers, and phosphorothioate, phosphate, and masked thiol groups to the 5' terminus of an oligonucleotide. The addition of linkers to ligands and the final reaction that produces the ligand-conjugated oligonucleotide are described elsewhere in the series. This approach is particularly useful when there is a limited amount of ligand available, when the ligand is sensitive to chemical conditions required for oligonucleotide deprotection, or when the ligand is weakly soluble in solvents required for phosphoramidite- or H-phosphonate-mediated oligonucleotide synthesis.

  1. Water oxidation catalyzed by mononuclear ruthenium complexes with a 2,2'-bipyridine-6,6'-dicarboxylate (bda) ligand: how ligand environment influences the catalytic behavior.

    PubMed

    Staehle, Robert; Tong, Lianpeng; Wang, Lei; Duan, Lele; Fischer, Andreas; Ahlquist, Mårten S G; Sun, Licheng; Rau, Sven

    2014-02-03

    A new water oxidation catalyst [Ru(III)(bda)(mmi)(OH2)](CF3SO3) (2, H2bda = 2,2'-bipyridine-6,6'-dicarboxylic acid; mmi = 1,3-dimethylimidazolium-2-ylidene) containing an axial N-heterocyclic carbene ligand and one aqua ligand was synthesized and fully characterized. The kinetics of catalytic water oxidation by 2 were measured using stopped-flow technique, and key intermediates in the catalytic cycle were probed by density functional theory calculations. While analogous Ru-bda water oxidation catalysts [Ru(bda)L2] (L = pyridyl ligands) are supposed to catalyze water oxidation through a bimolecular coupling pathway, our study points out that 2, surprisingly, undergoes a single-site water nucleophilic attack (acid-base) pathway. The diversion of catalytic mechanisms is mainly ascribed to the different ligand environments, from nonaqua ligands to an aqua ligand. Findings in this work provide some critical proof for our previous hypothesis about how alternation of ancillary ligands of water oxidation catalysts influences their catalytic efficiency.

  2. Transient Ligand Docking Sites in Cerebratulus lacteus Mini-Hemoglobin

    PubMed Central

    Deng, Pengchi; Nienhaus, Karin; Palladino, Pasquale; Olson, John S.; Blouin, George; Moens, Luc; Dewilde, Sylvia; Geuens, Eva; Nienhaus, G. Ulrich

    2007-01-01

    The monomeric hemoglobin of the nemertean worm Cerebratulus lacteus functions as an oxygen storage protein to maintain neural activity under hypoxic conditions. It shares a large, apolar matrix tunnel with other small hemoglobins, which has been implicated as a potential ligand migration pathway. Here we explore ligand migration and binding within the distal heme pocket, to which the tunnel provides access to ligands from the outside. FTIR/TDS experiments performed at cryogenic temperatures reveal the presence of three transient ligand docking sites within the distal pocket, the primary docking site B on top of pyrrole C and secondary sites C and D. Site C is assigned to a cavity adjacent to the distal portion of the heme pocket, surrounded by the B and E helices. It has an opening to the apolar tunnel and is expected to be on the pathway for ligand entry and exit, whereas site D, circumscribed by TyrB10, GlnE7, and the CD corner, most likely is located on a side pathway of ligand migration. Flash photolysis experiments at ambient temperatures indicate that the rate-limiting step for ligand binding to CerHb is migration through the apolar channel to site C. Movement from C to B and iron-ligand bond formation involve low energy barriers and thus are very rapid processes in the wt protein. PMID:17531406

  3. Architecture effects on multivalent interactions by polypeptide-based multivalent ligands

    NASA Astrophysics Data System (ADS)

    Liu, Shuang

    Multivalent interactions are characterized by the simultaneous binding between multiple ligands and multiple binding sites, either in solutions or at interfaces. In biological systems, most multivalent interactions occur between protein receptors and carbohydrate ligands through hydrogen-bonding and hydrophobic interactions. Compared with weak affinity binding between one ligand and one binding site, i.e. monovalent interaction, multivalent interactioins provide greater avidity and specificity, and therefore play unique roles in a broad range of biological activities. Moreover, the studies of multivalent interactions are also essential for producing effective inhibitors and effectors of biological processes that could have important therapeutic applications. Synthetic multivalent ligands have been designed to mimic the biological functions of natural multivalent interactions, and various types of scaffolds have been used to display multiple ligands, including small molecules, linear polymers, dendrimers, nanoparticle surfaces, monolayer surfaces and liposomes. Studies have shown that multivalent interactions can be highly affected by various architectural parameters of these multivalent ligands, including ligand identities, valencies, spacing, ligand densities, nature of linker arms, scaffold length and scaffold conformation. Most of these multivalent ligands are chemically synthesized and have limitations of controlling over sequence and conformation, which is a barrier for mimicking ordered and controlled natural biological systems. Therefore, multivalent ligands with precisely controlled architecture are required for improved structure-function relationship studies. Protein engineering methods with subsequent chemical coupling of ligands provide significant advantages of controlling over backbone conformation and functional group placement, and therefore have been used to synthesize recombinant protein-based materials with desired properties similar to natural

  4. Ligand-Assisted Protein Structure (LAPS): An Experimental Paradigm for Characterizing Cannabinoid-Receptor Ligand-Binding Domains.

    PubMed

    Janero, David R; Korde, Anisha; Makriyannis, Alexandros

    2017-01-01

    Detailed characterization of the ligand-binding motifs and structure-function correlates of the principal GPCRs of the endocannabinoid-signaling system, the cannabinoid 1 (CB1R) and cannabinoid 2 (CB2R) receptors, is essential to inform the rational design of drugs that modulate CB1R- and CB2R-dependent biosignaling for therapeutic gain. We discuss herein an experimental paradigm termed "ligand-assisted protein structure" (LAPS) that affords a means of characterizing, at the amino acid level, CB1R and CB2R structural features key to ligand engagement and receptor-dependent information transmission. For this purpose, LAPS integrates three key disciplines and methodologies: (a) medicinal chemistry: design and synthesis of high-affinity, pharmacologically active probes as reporters capable of reacting irreversibly with particular amino acids at (or in the immediate vicinity of) the ligand-binding domain of the functionally active receptor; (b) molecular and cellular biology: introduction of discrete, conservative point mutations into the target GPCR and determination of their effect on probe binding and pharmacological activity; (c) analytical chemistry: identification of the site(s) of probe-GPCR interaction through focused, bottom-up, amino acid-level proteomic identification of the probe-receptor complex using liquid chromatography tandem mass spectrometry. Subsequent in silico methods including ligand docking and computational modeling provide supplementary data on the probe-receptor interaction as defined by LAPS. Examples of LAPS as applied to human CB2R orthosteric binding site characterization for a biarylpyrazole antagonist/inverse agonist and a classical cannabinoid agonist belonging to distinct chemical classes of cannabinergic compounds are given as paradigms for further application of this methodology to other therapeutic protein targets. LAPS is well positioned to complement other experimental and in silico methods in contemporary structural biology such

  5. Co-biodegradation of anthracene and naphthalene by the bacterium Acinetobacter johnsonii.

    PubMed

    Jiang, Yan; Qi, Hui; Zhang, Xian M

    2018-04-16

    NAP (Naphthalene) and ANT (anthracene) usually co-exist in environment and possessed interactional effects on their biodegradation in environment. Presently, a strain of Acinetobacter johnsonii was employed to degrade NAP and ANT in single- and dual-substrate systems. NAP was utilized as prefer substrate by cells to accelerate ANT biodegradation. As much as 200 mg L -1 ANT could be entirely degraded with 1,500 mg L -1 NAP, which was beyond bacterial potential in single substrate system. Especially, the shortest biodegradation period (103 h) for ANT was observed with the presence of 50 mg L -1 NAP. By contrast, ANT showed strong inhibition on NAP degradation, while the peak biodegradation of 1,950 mg L -1 NAP with 50 mg L -1 ANT could still proceed. By introducing an inhibition constant parameter to fit the inhibition on cells, modeling indicated the substrate inhibition for NAP and ANT over the concentrations of 174 and 49 mg L -1 , respectively. Furthermore, enzyme assay revealed the pathway of meta fission in NAP biodegradation due to the appearance of catechol 2,3-dioxygenase activity, and low-level lipase excretion was also found in both NAP and ANT biodegradation, but hardly affect NAP and ANT biodegradation in the present study. To research the interplay of NAP and ANT is conducive to targeted decontamination.

  6. Optical Absorbance Enhancement in PbS QD/Cinnamate Ligand Complexes.

    PubMed

    Kroupa, Daniel M; Vörös, Márton; Brawand, Nicholas P; Bronstein, Noah; McNichols, Brett W; Castaneda, Chloe V; Nozik, Arthur J; Sellinger, Alan; Galli, Giulia; Beard, Matthew C

    2018-06-08

    We studied the optical absorption enhancement in colloidal suspensions of PbS quantum dots (QD) upon ligand exchange from oleate to a series of cinnamate ligands. By combining experiments and ab initio simulations, we elucidate physical parameters that govern the optical absorption enhancement. We find that, within the cinnamate/PbS QD system, the optical absorption enhancement scales linearly with the electronic gap of the ligand, indicating that the ligand/QD coupling occurs equally efficient between the QD and ligand HOMO and their respective LUMO levels. Disruption of the conjugation that connects the aromatic ring and its substituents to the QD core causes a reduction of the electronic coupling. Our results further support the notion that the ligand/QD complex should be considered as a distinct chemical system with emergent behavior rather than a QD core with ligands whose sole purpose is to passivate surface dangling bonds and prevent agglomeration.

  7. New synthetic routes toward enantiopure nitrogen donor ligands.

    PubMed

    Sala, Xavier; Rodríguez, Anna M; Rodríguez, Montserrat; Romero, Isabel; Parella, Teodor; von Zelewsky, Alexander; Llobet, Antoni; Benet-Buchholz, Jordi

    2006-12-08

    New polypyridylic chiral ligands, having either C3 or lower symmetry, have been prepared via a de novo construction of the pyridine nucleus by means of Kröhnke methodology in the key step. The chiral moieties of these ligands originate from the monoterpen chiral pool, namely (-)-alpha-pinene ((-)-14, (-)-15) and (-)-myrtenal ((-)-9, (-)-10). Extension of the above-mentioned asymmetric synthesis procedure to the preparation of enantiopure derivatives of some commonly used polypyridylic ligands has been achieved through a new aldehyde building block ((-)-16). As an example, the synthesis of a chiral derivative of N,N-bis(2-pyridylmethyl)ethylamine (bpea) ligand, (-)-19, has been performed to illustrate the viability of the method. The coordinative ability of the ligands has been tested through the synthesis and characterization of complexes [Mn((-)-19)Br2], (-)-20, and [RuCl((-)-10)(bpy)](BF4), (-)-21. Some preliminary results related to the enantioselective catalytic epoxidation of styrene with the ruthenium complex are also presented.

  8. Thiophene-Core Estrogen Receptor Ligands Having Superagonist Activity

    PubMed Central

    Min, Jian; Wang, Pengcheng; Srinivasan, Sathish; Nwachukwu, Jerome C.; Guo, Pu; Huang, Minjian; Carlson, Kathryn E.; Katzenellenbogen, John A.; Nettles, Kendall W.; Zhou, Hai-Bing

    2013-01-01

    To probe the importance of the heterocyclic core of estrogen receptor (ER) ligands, we prepared a series of thiophene-core ligands by Suzuki cross-coupling of aryl boronic acids with bromo-thiophenes, and we assessed their receptor binding and cell biological activities. The disposition of the phenol substituents on the thiophene core, at alternate or adjacent sites, and the nature of substituents on these phenols all contribute to binding affinity and subtype selectivity. Most of the bis(hydroxyphenyl)-thiophenes were ERβ selective, whereas the tris(hydroxyphenyl)-thiophenes were ERα selective; analogous furan-core compounds generally have lower affinity and less selectivity. Some diarylthiophenes show distinct superagonist activity in reporter gene assays, giving maximal activities 2–3 times that of estradiol, and modeling suggests that these ligands have a different interaction with a hydrogen-bonding residue in helix-11. Ligand-core modification may be a new strategy for developing ER ligands whose selectivity is based on having transcriptional activity greater than that of estradiol. PMID:23586645

  9. Cloud computing for protein-ligand binding site comparison.

    PubMed

    Hung, Che-Lun; Hua, Guan-Jie

    2013-01-01

    The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery.

  10. Ligand binding by repeat proteins: natural and designed

    PubMed Central

    Grove, Tijana Z; Cortajarena, Aitziber L; Regan, Lynne

    2012-01-01

    Repeat proteins contain tandem arrays of small structural motifs. As a consequence of this architecture, they adopt non-globular, extended structures that present large, highly specific surfaces for ligand binding. Here we discuss recent advances toward understanding the functional role of this unique modular architecture. We showcase specific examples of natural repeat proteins interacting with diverse ligands and also present examples of designed repeat protein–ligand interactions. PMID:18602006

  11. How to Compute Labile Metal-Ligand Equilibria

    ERIC Educational Resources Information Center

    de Levie, Robert

    2007-01-01

    The different methods used for computing labile metal-ligand complexes, which are suitable for an iterative computer solution, are illustrated. The ligand function has allowed students to relegate otherwise tedious iterations to a computer, while retaining complete control over what is calculated.

  12. Angular-Shaped Naphthalene Bis(1,5-diamide-2,6-diylidene)malononitrile for High-Performance, Air-Stable N-Type Organic Field-Effect Transistors.

    PubMed

    Dhondge, Attrimuni P; Tsai, Pei-Chung; Nien, Chiao-Yun; Xu, Wei-Yu; Chen, Po-Ming; Hsu, Yu-Hung; Li, Kan-Wei; Yen, Feng-Ming; Tseng, Shin-Lun; Chang, Yu-Chang; Chen, Henry J H; Kuo, Ming-Yu

    2018-05-04

    The synthesis, characterization, and application of two angular-shaped naphthalene bis(1,5-diamide-2,6-diylidene)malononitriles (NBAMs) as high-performance air-stable n-type organic field effect transistor (OFET) materials are reported. NBAM derivatives exhibit deep lowest-unoccupied molecular orbital (LUMO) levels, suitable for air-stable n-type OFETs. The OFET device based on NBAM-EH fabricated by vapor deposition exhibits a maximum electron mobility of 0.63 cm 2 V -1 s -1 in air with an on/off current ratio ( I on / I off ) of 10 5 .

  13. Ligand binding was acquired during evolution of nuclear receptors

    PubMed Central

    Escriva, Hector; Safi, Rachid; Hänni, Catherine; Langlois, Marie-Claire; Saumitou-Laprade, Pierre; Stehelin, Dominique; Capron, André; Pierce, Raymond; Laudet, Vincent

    1997-01-01

    The nuclear receptor (NR) superfamily comprises, in addition to ligand-activated transcription factors, members for which no ligand has been identified to date. We demonstrate that orphan receptors are randomly distributed in the evolutionary tree and that there is no relationship between the position of a given liganded receptor in the tree and the chemical nature of its ligand. NRs are specific to metazoans, as revealed by a screen of NR-related sequences in early- and non-metazoan organisms. The analysis of the NR gene duplication pattern during the evolution of metazoans shows that the present NR diversity arose from two waves of gene duplications. Strikingly, our results suggest that the ancestral NR was an orphan receptor that acquired ligand-binding ability during subsequent evolution. PMID:9192646

  14. Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations

    PubMed Central

    Seeliger, Daniel; de Groot, Bert L.

    2010-01-01

    Biological function of proteins is frequently associated with the formation of complexes with small-molecule ligands. Experimental structure determination of such complexes at atomic resolution, however, can be time-consuming and costly. Computational methods for structure prediction of protein/ligand complexes, particularly docking, are as yet restricted by their limited consideration of receptor flexibility, rendering them not applicable for predicting protein/ligand complexes if large conformational changes of the receptor upon ligand binding are involved. Accurate receptor models in the ligand-bound state (holo structures), however, are a prerequisite for successful structure-based drug design. Hence, if only an unbound (apo) structure is available distinct from the ligand-bound conformation, structure-based drug design is severely limited. We present a method to predict the structure of protein/ligand complexes based solely on the apo structure, the ligand and the radius of gyration of the holo structure. The method is applied to ten cases in which proteins undergo structural rearrangements of up to 7.1 Å backbone RMSD upon ligand binding. In all cases, receptor models within 1.6 Å backbone RMSD to the target were predicted and close-to-native ligand binding poses were obtained for 8 of 10 cases in the top-ranked complex models. A protocol is presented that is expected to enable structure modeling of protein/ligand complexes and structure-based drug design for cases where crystal structures of ligand-bound conformations are not available. PMID:20066034

  15. Interaction between alkaline earth cations and oxo-ligands. DFT study of the affinity of the Ca2+ cation for carbonyl ligands.

    PubMed

    da Costa, Leonardo Moreira; Carneiro, José Walkimar de Mesquita; Romeiro, Gilberto Alves; Paes, Lilian Weitzel Coelho

    2011-02-01

    The affinity of the Ca(2+) ion for a set of substituted carbonyl ligands was analyzed with both the DFT (B3LYP/6-31+G(d)) and semi-empirical (PM6) methods. Two types of ligands were studied: a set of monosubstituted [O=CH(R)] and a set of disubstituted ligands [O=C(R)(2)] (R=H, F, Cl, Br, OH, OCH(3), CH(3), CN, NH(2) and NO(2)), with R either directly bound to the carbonyl carbon atom or to the para position of a phenyl ring. The interaction energy was calculated to quantify the affinity of the Ca(2+) cation for the ligands. Geometric and electronic parameters were correlated with the intensity of the metal-ligand interaction. The electronic nature of the substituent is the main parameter that determines the interaction energy. Donor groups make the interaction energy more negative (stabilizing the complex formed), while acceptor groups make the interaction energy less negative (destabilizing the complex formed).

  16. Proteome-wide covalent ligand discovery in native biological systems

    PubMed Central

    Backus, Keriann M.; Correia, Bruno E.; Lum, Kenneth M.; Forli, Stefano; Horning, Benjamin D.; González-Páez, Gonzalo E.; Chatterjee, Sandip; Lanning, Bryan R.; Teijaro, John R.; Olson, Arthur J.; Wolan, Dennis W.; Cravatt, Benjamin F.

    2016-01-01

    Small molecules are powerful tools for investigating protein function and can serve as leads for new therapeutics. Most human proteins, however, lack small-molecule ligands, and entire protein classes are considered “undruggable” 1,2. Fragment-based ligand discovery (FBLD) can identify small-molecule probes for proteins that have proven difficult to target using high-throughput screening of complex compound libraries 1,3. Although reversibly binding ligands are commonly pursued, covalent fragments provide an alternative route to small-molecule probes 4–10, including those that can access regions of proteins that are difficult to access through binding affinity alone 5,10,11. In this manuscript, we report a quantitative analysis of cysteine-reactive small-molecule fragments screened against thousands of proteins. Covalent ligands were identified for >700 cysteines found in both druggable proteins and proteins deficient in chemical probes, including transcription factors, adaptor/scaffolding proteins, and uncharacterized proteins. Among the atypical ligand-protein interactions discovered were compounds that react preferentially with pro- (inactive) caspases. We used these ligands to distinguish extrinsic apoptosis pathways in human cell lines versus primary human T-cells, showing that the former is largely mediated by caspase-8 while the latter depends on both caspase-8 and −10. Fragment-based covalent ligand discovery provides a greatly expanded portrait of the ligandable proteome and furnishes compounds that can illuminate protein functions in native biological systems. PMID:27309814

  17. Models of protein–ligand crystal structures: trust, but verify

    PubMed Central

    Deller, Marc C.

    2015-01-01

    X-ray crystallography provides the most accurate models of protein–ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein–ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein–ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein–ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein–ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein–ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein–ligand models for their computational and biological studies, and we provide an overview of how this can be achieved. PMID:25665575

  18. Models of protein-ligand crystal structures: trust, but verify.

    PubMed

    Deller, Marc C; Rupp, Bernhard

    2015-09-01

    X-ray crystallography provides the most accurate models of protein-ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein-ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein-ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein-ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein-ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein-ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein-ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.

  19. Quantitative analysis of protein-ligand interactions by NMR.

    PubMed

    Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

    2016-08-01

    Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used

  20. PLIP: fully automated protein-ligand interaction profiler.

    PubMed

    Salentin, Sebastian; Schreiber, Sven; Haupt, V Joachim; Adasme, Melissa F; Schroeder, Michael

    2015-07-01

    The characterization of interactions in protein-ligand complexes is essential for research in structural bioinformatics, drug discovery and biology. However, comprehensive tools are not freely available to the research community. Here, we present the protein-ligand interaction profiler (PLIP), a novel web service for fully automated detection and visualization of relevant non-covalent protein-ligand contacts in 3D structures, freely available at projects.biotec.tu-dresden.de/plip-web. The input is either a Protein Data Bank structure, a protein or ligand name, or a custom protein-ligand complex (e.g. from docking). In contrast to other tools, the rule-based PLIP algorithm does not require any structure preparation. It returns a list of detected interactions on single atom level, covering seven interaction types (hydrogen bonds, hydrophobic contacts, pi-stacking, pi-cation interactions, salt bridges, water bridges and halogen bonds). PLIP stands out by offering publication-ready images, PyMOL session files to generate custom images and parsable result files to facilitate successive data processing. The full python source code is available for download on the website. PLIP's command-line mode allows for high-throughput interaction profiling. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Ligand-based virtual screening under partial shape constraints.

    PubMed

    von Behren, Mathias M; Rarey, Matthias

    2017-04-01

    Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure. The new method is integrated into the LBVS tool mRAISE providing multiple options for such constraints. The applied constraints can either be derived automatically from a protein-ligand complex structure or by manual selection of ligand atoms. In this way, the descriptor directly encodes the fit of a ligand into the binding site. Furthermore, the conservation of close contacts between the binding site surface and the query ligand can be enforced. We validated our new method on the DUD and DUD-E datasets. Although the statistical performance remains on the same level, detailed analysis reveal that for certain and especially very flexible targets a significant improvement can be achieved. This is further highlighted looking at the quality of calculated molecular alignments using the recently introduced mRAISE dataset. The new partial shape constraints improved the overall quality of molecular alignments especially for difficult targets with highly flexible or different sized molecules. The software tool mRAISE is freely available on Linux operating systems for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise ).

  2. Ligand-based virtual screening under partial shape constraints

    NASA Astrophysics Data System (ADS)

    von Behren, Mathias M.; Rarey, Matthias

    2017-04-01

    Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure. The new method is integrated into the LBVS tool mRAISE providing multiple options for such constraints. The applied constraints can either be derived automatically from a protein-ligand complex structure or by manual selection of ligand atoms. In this way, the descriptor directly encodes the fit of a ligand into the binding site. Furthermore, the conservation of close contacts between the binding site surface and the query ligand can be enforced. We validated our new method on the DUD and DUD-E datasets. Although the statistical performance remains on the same level, detailed analysis reveal that for certain and especially very flexible targets a significant improvement can be achieved. This is further highlighted looking at the quality of calculated molecular alignments using the recently introduced mRAISE dataset. The new partial shape constraints improved the overall quality of molecular alignments especially for difficult targets with highly flexible or different sized molecules. The software tool mRAISE is freely available on Linux operating systems for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise).

  3. Selective hydrodesulfurization of 4,6-dimethyldibenzothiophene in the dominant presence of naphthalene over hybrid CoMo/A{sub 2}O{sub 3} and Ru/Al{sub 2}Al{sub 2}O{sub 3} catalyst

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

    Isoda, T.; Nagao, S.; Ma, X.

    1995-12-31

    Hydrodesulfurization of 4,6-dimethyldibenzothiophene (4,6-DMDBT) in decane containing significant amount of naphthalene was examined over a hybrid of CoMo/Al{sub 2}O{sub 3} and Ru/Al{sub 2}O{sub 3} to design the selective hydrogenation and successive desulfurization of 4,6-DMDBT in aromatic moiety, and its activity was compared to those of CoMo/Al{sub 2}O{sub 3}, NiMo/Al{sub 2}O{sub 3} and Ru/Al{sub 2}O{sub 3} in their single use. HDS activity of 4,6-DMDBT over NiMo/Al{sub 2}O{sub 3} was inferior to CoMo/Al{sub 2}O{sub 3}, although that of highest hydrogenation activity for naphthalene. The hybrid showed the highest activity for HDS of 4,6-DMDBT among these catalysts without excess hydrogenation of nahthalene.

  4. Ligand diffusion in proteins via enhanced sampling in molecular dynamics.

    PubMed

    Rydzewski, J; Nowak, W

    2017-12-01

    Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand-protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Lineage-specific co-evolution of the Egf receptor/ligand signaling system.

    PubMed

    Laisney, Juliette A G C; Braasch, Ingo; Walter, Ronald B; Meierjohann, Svenja; Schartl, Manfred

    2010-01-27

    The epidermal growth factor receptor (Egfr) with its numerous ligands has fundamental roles in development, cell differentiation and physiology. Dysfunction of the receptor-ligand system contributes to many human malignancies. Consistent with such various tasks, the Egfr gene family has expanded during vertebrate evolution as a consequence of several rounds of whole genome duplication. Of particular interest is the effect of the fish-specific whole genome duplication (FSGD) on the ligand-receptor system, as it has supplied this largest group of vertebrates with additional opportunities for sub- and/or neofunctionalization in this signaling system. We identified the predicted components of the Egf receptor-ligand signaling system in teleost fishes (medaka, platyfish, stickleback, pufferfishes and zebrafish). We found two duplicated egfr genes, egfra and egfrb, in all available teleost genomes. Surprisingly only one copy for each of the seven Egfr ligands could be identified in most fishes, with zebrafish hbegf being the only exception. Special focus was put on medaka, for which we more closely investigated all Egf receptors and Egfr ligands. The different expression patterns of egfra, egfrb and their ligands in medaka tissues and embryo stages suggest differences in role and function. Preferential co-expression of different subsets of Egfr ligands corroborates the possible subfunctionalization and specialization of the two receptors in adult tissues. Bioinformatic analyses of the ligand-receptor interface between Egfr and its ligands show a very weak evolutionary conservation within this region. Using in vitro analyses of medaka Egfra, we could show that this receptor is only activated by medaka ligands, but not by human EGF. Altogether, our data suggest a lineage-specific Egfr/Egfr ligand co-evolution. Our data indicate that medaka Egfr signaling occurs via its two copies, Egfra and Egfrb, each of them being preferentially coexpressed with different subsets of Egfr

  6. Lineage-specific co-evolution of the Egf receptor/ligand signaling system

    PubMed Central

    2010-01-01

    Background The epidermal growth factor receptor (Egfr) with its numerous ligands has fundamental roles in development, cell differentiation and physiology. Dysfunction of the receptor-ligand system contributes to many human malignancies. Consistent with such various tasks, the Egfr gene family has expanded during vertebrate evolution as a consequence of several rounds of whole genome duplication. Of particular interest is the effect of the fish-specific whole genome duplication (FSGD) on the ligand-receptor system, as it has supplied this largest group of vertebrates with additional opportunities for sub- and/or neofunctionalization in this signaling system. Results We identified the predicted components of the Egf receptor-ligand signaling system in teleost fishes (medaka, platyfish, stickleback, pufferfishes and zebrafish). We found two duplicated egfr genes, egfra and egfrb, in all available teleost genomes. Surprisingly only one copy for each of the seven Egfr ligands could be identified in most fishes, with zebrafish hbegf being the only exception. Special focus was put on medaka, for which we more closely investigated all Egf receptors and Egfr ligands. The different expression patterns of egfra, egfrb and their ligands in medaka tissues and embryo stages suggest differences in role and function. Preferential co-expression of different subsets of Egfr ligands corroborates the possible subfunctionalization and specialization of the two receptors in adult tissues. Bioinformatic analyses of the ligand-receptor interface between Egfr and its ligands show a very weak evolutionary conservation within this region. Using in vitro analyses of medaka Egfra, we could show that this receptor is only activated by medaka ligands, but not by human EGF. Altogether, our data suggest a lineage-specific Egfr/Egfr ligand co-evolution. Conclusions Our data indicate that medaka Egfr signaling occurs via its two copies, Egfra and Egfrb, each of them being preferentially coexpressed

  7. Translating in vitro ligand bias into in vivo efficacy.

    PubMed

    Luttrell, Louis M; Maudsley, Stuart; Gesty-Palmer, Diane

    2018-01-01

    It is increasingly apparent that ligand structure influences both the efficiency with which G protein-coupled receptors (GPCRs) engage their downstream effectors and the manner in which they are activated. Thus, 'biased' agonists, synthetic ligands whose intrinsic efficacy differs from the native ligand, afford a strategy for manipulating GPCR signaling in ways that promote beneficial signals while blocking potentially deleterious ones. Still, there are significant challenges in relating in vitro ligand efficacy, which is typically measured in heterologous expression systems, to the biological response in vivo, where the ligand is acting on natively expressed receptors and in the presence of the endogenous ligand. This is particularly true of arrestin pathway-selective 'biased' agonists. The type 1 parathyroid hormone receptor (PTH 1 R) is a case in point. Parathyroid hormone (PTH) is the principal physiological regulator of calcium homeostasis, and PTH 1 R expressed on cells of the osteoblast lineage are an established therapeutic target in osteoporosis. In vitro, PTH 1 R signaling is highly sensitive to ligand structure, and PTH analogs that affect the selectivity/kinetics of G protein coupling or that engage arrestin-dependent signaling mechanisms without activating heterotrimeric G proteins have been identified. In vivo, intermittent administration of conventional PTH analogs accelerates the rate of osteoblastic bone formation, largely through known cAMP-dependent mechanisms. Paradoxically, both intermittent and continuous administration of an arrestin pathway-selective PTH analog, which in vivo would be expected to antagonize endogenous PTH 1 R-cAMP signaling, also increases bone mass. Transcriptomic analysis of tissue from treated animals suggests that conventional and arrestin pathway-selective PTH1R ligands act in largely different ways, with the latter principally affecting pathways involved in the regulation of cell cycle, survival, and migration

  8. Balancing specificity, sensitivity, and speed of ligand discrimination by zero-order ultraspecificity

    NASA Astrophysics Data System (ADS)

    Kajita, Masashi K.; Aihara, Kazuyuki; Kobayashi, Tetsuya J.

    2017-07-01

    Specific interactions between receptors and their target ligands in the presence of nontarget ligands are crucial for biological processes such as T cell ligand discrimination. To discriminate between the target and nontarget ligands, cells have to increase specificity to the target ligands by amplifying the small differences in affinity among ligands. In addition, sensitivity to the ligand concentration and quick discrimination are also important to detect low amounts of target ligands and facilitate fast cellular decision making after ligand recognition. In this work we propose a mechanism for nonlinear specificity amplification (ultraspecificity) based on zero-order saturating reactions, which was originally proposed to explain nonlinear sensitivity amplification (ultrasensitivity) to the ligand concentration. In contrast to the previously proposed proofreading mechanisms that amplify the specificity by a multistep reaction, our model can produce an optimal balance of specificity, sensitivity, and quick discrimination. Furthermore, we show that a model for insensitivity to a large number of nontarget ligands can be naturally derived from a model with the zero-order ultraspecificity. The zero-order ultraspecificity, therefore, may provide an alternative way to understand ligand discrimination from the viewpoint of nonlinear properties in biochemical reactions.

  9. Work function and temperature dependence of electron tunneling through an N-type perylene diimide molecular junction with isocyanide surface linkers.

    PubMed

    Smith, Christopher E; Xie, Zuoti; Bâldea, Ioan; Frisbie, C Daniel

    2018-01-18

    Conducting probe atomic force microscopy (CP-AFM) was employed to examine electron tunneling in self-assembled monolayer (SAM) junctions. A 2.3 nm long perylene tetracarboxylic acid diimide (PDI) acceptor molecule equipped with isocyanide linker groups was synthesized, adsorbed onto Ag, Au and Pt substrates, and the current-voltage (I-V) properties were measured by CP-AFM. The dependence of the low-bias resistance (R) on contact work function indicates that transport is LUMO-assisted ('n-type behavior'). A single-level tunneling model combined with transition voltage spectroscopy (TVS) was employed to analyze the experimental I-V curves and to extract the effective LUMO position ε l = E LUMO - E F and the effective electronic coupling (Γ) between the PDI redox core and the contacts. This analysis revealed a strong Fermi level (E F ) pinning effect in all the junctions, likely due to interface dipoles that significantly increased with increasing contact work function, as revealed by scanning Kelvin probe microscopy (SKPM). Furthermore, the temperature (T) dependence of R was found to be substantial. For Pt/Pt junctions, R varied more than two orders of magnitude in the range 248 K < T < 338 K. Importantly, the R(T) data are consistent with a single step electron tunneling mechanism and allow independent determination of ε l , giving values compatible with estimates of ε l based on analysis of the full I-V data. Theoretical analysis revealed a general criterion to unambiguously rule out a two-step transport mechanism: namely, if measured resistance data exhibit a pronounced Arrhenius-type temperature dependence, a two-step electron transfer scenario should be excluded in cases where the activation energy depends on contact metallurgy. Overall, our results indicate (1) the generality of the Fermi level pinning phenomenon in molecular junctions, (2) the utility of employing the single level tunneling model for determining essential electronic structure parameters

  10. Preconcentration and Spectrophotometric Determination of a Naphthalene Analog of Medetomidine Using Modified Maghemite Nanoparticles

    NASA Astrophysics Data System (ADS)

    Maddah, B.; Hosseini, F.; Ahmadi, M.; Rajabi, A. Asghar; Beik-Mohammadlood, Z.

    2016-05-01

    A novel and sensitive extraction procedure using sodium dodecyl sulfate (SDS) modified maghemite nanoparticles (MNPs) as an efficient solid phase has been developed for removal, preconcentration, and spectrophotometric determination of trace amounts of a naphthalene analog of dexmedetomidine (4-(1-(na phthalene-1-yl)ethyl)-1Himidazole, NMED). The MNPs were obtained by a coprecipitation method, and their surfaces were furthermore modified by SDS. The size and morphological properties of the synthesized MNPs were determined by X-ray diffraction analysis, FT-IR, vibrating sample magnetometry, and scanning electron microscopy. NMED was adsorbed at pH 3.0. The adsorbed drug was then desorbed and determined by spectrophotometry at 280 nm. The calibration graph was linear in the range 1 × 10-6-1 × 10-4 mol/L of NMED with a correlation coefficient of 0.989. The detection limit of the method for NMED determination was 3.7 × 10-7 mol/L. The method was successfully applied to the determination of NMED in human urine samples.

  11. The Retinoid X Receptors and Their Ligands

    PubMed Central

    Dawson, Marcia I.; Xia, Zebin

    2014-01-01

    This chapter presents an overview of the current status of studies on the structural and molecular biology of the retinoid X receptor subtypes α, β, and γ (RXRs, NR2B1–3), their nuclear and cytoplasmic functions, post-transcriptional processing, and recently reported ligands. Points of interest are the different changes in the ligand-binding pocket induced by variously shaped agonists, the communication of the ligand–bound pocket with the coactivator binding surface and the heterodimerization interface, and recently identified ligands that are natural products, those that function as environmental toxins or drugs that had been originally designed to interact with other targets, as well as those that were deliberately designed as RXR-selective transcriptional agonists, synergists, or antagonists. Of these synthetic ligands, the general trend in design appears to be away from fully aromatic rigid structures to those containing partial elements of the flexible tetraene side chain of 9-cis-retinoic acid. PMID:22020178

  12. Control of Energy Flow Dynamics between Tetracene Ligands and PbS Quantum Dots by Size Tuning and Ligand Coverage

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

    Kroupa, Daniel M.; Arias, Dylan H.; Blackburn, Jeffrey L.

    We have prepared a series of samples with the ligand 6,13-bistri(iso-propyl)silylethynyl tetracene 2-carboxylic acid (TIPS-Tc-COOH) attached to PbS quantum dot (QD) samples of three different sizes in order to monitor and control the extent and time scales of energy flow after photoexcitation. Fast energy transfer (~1 ps) to the PbS QD occurs upon direct excitation of the ligand for all samples. The largest size QD maintains the microsecond exciton lifetime characteristic of the as-prepared oleate terminated PbS QDs. However, two smaller QD sizes with lowest exciton energies similar to or larger than the TIPS-Tc-COO- triplet energy undergo energy transfer betweenmore » QD core and ligand triplet on nanosecond to microsecond timescales. For the intermediate size QDs in particular, energy can be recycled many times between ligand and core, but the triplet remains the dominant excited species at long times, living for ~3 us for fully exchanged QDs and up to 30 us for partial ligand exchange, which is revealed as a method for controlling the triplet lifetime. A unique upconverted luminescence spectrum is observed that results from annihilation of triplets after exclusive excitation of the QD core.« less

  13. Control of Energy Flow Dynamics between Tetracene Ligands and PbS Quantum Dots by Size Tuning and Ligand Coverage

    DOE PAGES

    Kroupa, Daniel M.; Arias, Dylan H.; Blackburn, Jeffrey L.; ...

    2018-01-24

    We have prepared a series of samples with the ligand 6,13-bistri(iso-propyl)silylethynyl tetracene 2-carboxylic acid (TIPS-Tc-COOH) attached to PbS quantum dot (QD) samples of three different sizes in order to monitor and control the extent and time scales of energy flow after photoexcitation. Fast energy transfer (~1 ps) to the PbS QD occurs upon direct excitation of the ligand for all samples. The largest size QD maintains the microsecond exciton lifetime characteristic of the as-prepared oleate terminated PbS QDs. However, two smaller QD sizes with lowest exciton energies similar to or larger than the TIPS-Tc-COO- triplet energy undergo energy transfer betweenmore » QD core and ligand triplet on nanosecond to microsecond timescales. For the intermediate size QDs in particular, energy can be recycled many times between ligand and core, but the triplet remains the dominant excited species at long times, living for ~3 us for fully exchanged QDs and up to 30 us for partial ligand exchange, which is revealed as a method for controlling the triplet lifetime. A unique upconverted luminescence spectrum is observed that results from annihilation of triplets after exclusive excitation of the QD core.« less

  14. Ligand-independent Dimer Formation of Epidermal Growth Factor Receptor (EGFR) Is a Step Separable from Ligand-induced EGFR Signaling

    PubMed Central

    Yu, Xiaochun; Sharma, Kailash D.; Takahashi, Tsuyoshi; Iwamoto, Ryo; Mekada, Eisuke

    2002-01-01

    Dimerization and phosphorylation of the epidermal growth factor (EGF) receptor (EGFR) are the initial and essential events of EGF-induced signal transduction. However, the mechanism by which EGFR ligands induce dimerization and phosphorylation is not fully understood. Here, we demonstrate that EGFRs can form dimers on the cell surface independent of ligand binding. However, a chimeric receptor, comprising the extracellular and transmembrane domains of EGFR and the cytoplasmic domain of the erythropoietin receptor (EpoR), did not form a dimer in the absence of ligands, suggesting that the cytoplasmic domain of EGFR is important for predimer formation. Analysis of deletion mutants of EGFR showed that the region between 835Ala and 918Asp of the EGFR cytoplasmic domain is required for EGFR predimer formation. In contrast to wild-type EGFR ligands, a mutant form of heparin-binding EGF-like growth factor (HB2) did not induce dimerization of the EGFR-EpoR chimeric receptor and therefore failed to activate the chimeric receptor. However, when the dimerization was induced by a monoclonal antibody to EGFR, HB2 could activate the chimeric receptor. These results indicate that EGFR can form a ligand-independent inactive dimer and that receptor dimerization and activation are mechanistically distinct and separable events. PMID:12134089

  15. Differential hydrogen/deuterium exchange mass spectrometry analysis of protein–ligand interactions

    PubMed Central

    Chalmers, Michael J; Busby, Scott A; Pascal, Bruce D; West, Graham M; Griffin, Patrick R

    2011-01-01

    Functional regulation of ligand-activated receptors is driven by alterations in the conformational dynamics of the protein upon ligand binding. Differential hydrogen/deuterium exchange (HDX) coupled with mass spectrometry has emerged as a rapid and sensitive approach for characterization of perturbations in conformational dynamics of proteins following ligand binding. While this technique is sensitive to detecting ligand interactions and alterations in receptor dynamics, it also can provide important mechanistic insights into ligand regulation. For example, HDX has been used to determine a novel mechanism of ligand activation of the nuclear receptor peroxisome proliferator activated receptor-γ, perform detailed analyses of binding modes of ligands within the ligand-binding pocket of two estrogen receptor isoforms, providing insight into selectivity, and helped classify different types of estrogen receptor-α ligands by correlating their pharmacology with the way they interact with the receptor based solely on hierarchical clustering of receptor HDX signatures. Beyond small-molecule–receptor interactions, this technique has also been applied to study protein–protein complexes, such as mapping antibody–antigen interactions. In this article, we summarize the current state of the differential HDX approaches and the future outlook. We summarize how HDX analysis of protein–ligand interactions has had an impact on biology and drug discovery. PMID:21329427

  16. A grand unified model for liganded gold clusters

    NASA Astrophysics Data System (ADS)

    Xu, Wen Wu; Zhu, Beien; Zeng, Xiao Cheng; Gao, Yi

    2016-12-01

    A grand unified model (GUM) is developed to achieve fundamental understanding of rich structures of all 71 liganded gold clusters reported to date. Inspired by the quark model by which composite particles (for example, protons and neutrons) are formed by combining three quarks (or flavours), here gold atoms are assigned three `flavours' (namely, bottom, middle and top) to represent three possible valence states. The `composite particles' in GUM are categorized into two groups: variants of triangular elementary block Au3(2e) and tetrahedral elementary block Au4(2e), all satisfying the duet rule (2e) of the valence shell, akin to the octet rule in general chemistry. The elementary blocks, when packed together, form the cores of liganded gold clusters. With the GUM, structures of 71 liganded gold clusters and their growth mechanism can be deciphered altogether. Although GUM is a predictive heuristic and may not be necessarily reflective of the actual electronic structure, several highly stable liganded gold clusters are predicted, thereby offering GUM-guided synthesis of liganded gold clusters by design.

  17. Cloud Computing for Protein-Ligand Binding Site Comparison

    PubMed Central

    2013-01-01

    The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity. The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome. SMAP can also predict drug side effects and reassign existing drugs to new indications. However, the computing scale of SMAP is limited. We have developed a high availability, high performance system that expands the comparison scale of SMAP. This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform. To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool. Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery. PMID:23762824

  18. A grand unified model for liganded gold clusters

    PubMed Central

    Xu, Wen Wu; Zhu, Beien; Zeng, Xiao Cheng; Gao, Yi

    2016-01-01

    A grand unified model (GUM) is developed to achieve fundamental understanding of rich structures of all 71 liganded gold clusters reported to date. Inspired by the quark model by which composite particles (for example, protons and neutrons) are formed by combining three quarks (or flavours), here gold atoms are assigned three ‘flavours' (namely, bottom, middle and top) to represent three possible valence states. The ‘composite particles' in GUM are categorized into two groups: variants of triangular elementary block Au3(2e) and tetrahedral elementary block Au4(2e), all satisfying the duet rule (2e) of the valence shell, akin to the octet rule in general chemistry. The elementary blocks, when packed together, form the cores of liganded gold clusters. With the GUM, structures of 71 liganded gold clusters and their growth mechanism can be deciphered altogether. Although GUM is a predictive heuristic and may not be necessarily reflective of the actual electronic structure, several highly stable liganded gold clusters are predicted, thereby offering GUM-guided synthesis of liganded gold clusters by design. PMID:27910848

  19. Dual genetically encoded phage-displayed ligands.

    PubMed

    Mohan, Kritika; Weiss, Gregory A

    2014-05-15

    M13 bacteriophage display presents polypeptides as fusions to phage coat proteins. Such phage-displayed ligands offer useful reagents for biosensors. Here, we report a modified phage propagation protocol for the consistent and robust display of two different genetically encoded ligands on the major coat protein, P8. The results demonstrate that the phage surface reaches a saturation point for maximum peptide display. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. High-performance peroxidase mimics for rapid colorimetric detection of H2O2 and glucose derived from perylene diimides functionalized Co3O4 nanoparticles.

    PubMed

    Ding, Yanan; Chen, Miaomiao; Wu, Kaili; Chen, Mingxing; Sun, Lifang; Liu, Zhenxue; Shi, Zhiqiang; Liu, Qingyun

    2017-11-01

    N,N'-di-caboxy methyl perylene diimides (PDI), as one of the most promising functional materials in optional chemosensing, was first used to combine with Co 3 O 4 nanoparticles through a facile two-step hydrothermal method and obtain the PDI functionalized Co 3 O 4 nanocomposites (PDI-Co 3 O 4 NCs). PDI-Co 3 O 4 NCs were characterized by a series of technical analysis including transmission electron microscope (TEM), X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FT-IR), respectively. The experimental results indicated that the as-prepared PDI-Co 3 O 4 NCs possessed the higher peroxidase-like activity than that of Co 3 O 4 nanoparticles without PDI, and could rapidly catalyze oxidation reaction of the chromogenic substrate TMB in the presence of H 2 O 2 to a blue product (oxTMB) observed by the naked eye. The improved catalytic activity of PDI-Co 3 O 4 NCs for colorimetric reactions could be attributed to the synergistic effects of PDI and Co 3 O 4 nanoparticles. On the basis of these experimental results, a convenient colorimetric system based on PDI-Co 3 O 4 as enzyme mimic that is highly sensitive and selective was developed for glucose detection. Meanwhile, the electron transfer between H 2 O 2 and TMB was responsible for the oxidation of TMB. The present work demonstrates a general strategy for the design of organic molecules functionalized oxide for different applications, such as nanocatalysts, biosensors and nanomedicine. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Spatiotemporal Targeting of a Dual-Ligand Nanoparticle to Cancer Metastasis.

    PubMed

    Doolittle, Elizabeth; Peiris, Pubudu M; Doron, Gilad; Goldberg, Amy; Tucci, Samantha; Rao, Swetha; Shah, Shruti; Sylvestre, Meilyn; Govender, Priya; Turan, Oguz; Lee, Zhenghong; Schiemann, William P; Karathanasis, Efstathios

    2015-08-25

    Various targeting strategies and ligands have been employed to direct nanoparticles to tumors that upregulate specific cell-surface molecules. However, tumors display a dynamic, heterogeneous microenvironment, which undergoes spatiotemporal changes including the expression of targetable cell-surface biomarkers. Here, we investigated a dual-ligand nanoparticle to effectively target two receptors overexpressed in aggressive tumors. By using two different chemical specificities, the dual-ligand strategy considered the spatiotemporal alterations in the expression patterns of the receptors in cancer sites. As a case study, we used two mouse models of metastasis of triple-negative breast cancer using the MDA-MB-231 and 4T1 cells. The dual-ligand system utilized two peptides targeting P-selectin and αvβ3 integrin, which are functionally linked to different stages of the development of metastatic disease at a distal site. Using in vivo multimodal imaging and post mortem histological analyses, this study shows that the dual-ligand nanoparticle effectively targeted metastatic disease that was otherwise missed by single-ligand strategies. The dual-ligand nanoparticle was capable of capturing different metastatic sites within the same animal that overexpressed either receptor or both of them. Furthermore, the highly efficient targeting resulted in 22% of the injected dual-ligand nanoparticles being deposited in early-stage metastases within 2 h after injection.

  2. The role of ligands in coinage-metal nanoparticles for electronics

    PubMed Central

    Kanelidis, Ioannis

    2017-01-01

    Coinage-metal nanoparticles are key components of many printable electronic inks. They can be combined with polymers to form conductive composites and have been used as the basis of molecular electronic devices. This review summarizes the multidimensional role of surface ligands that cover their metal cores. Ligands not only passivate crystal facets and determine growth rates and shapes; they also affect size and colloidal stability. Particle shapes can be tuned via the ligand choice while ligand length, size, ω-functionalities, and chemical nature influence shelf-life and stability of nanoparticles in dispersions. When particles are deposited, ligands affect the electrical properties of the resulting film, the morphology of particle films, and the nature of the interfaces. The effects of the ligands on sintering, cross-linking, and self-assembly of particles in electronic materials are discussed. PMID:29259877

  3. Polymerization catalysts containing electron-withdrawing amide ligands

    DOEpatents

    Watkin, John G.; Click, Damon R.

    2002-01-01

    The present invention describes methods of making a series of amine-containing organic compounds which are used as ligands for group 3-10 and lanthanide metal compounds. The ligands have electron-withdrawing groups bonded to them. The metal compounds, when combined with a cocatalyst, are catalysts for the polymerization of olefins.

  4. Selectivity in ligand recognition of G-quadruplex loops.

    PubMed

    Campbell, Nancy H; Patel, Manisha; Tofa, Amina B; Ghosh, Ragina; Parkinson, Gary N; Neidle, Stephen

    2009-03-03

    A series of disubstituted acridine ligands have been cocrystallized with a bimolecular DNA G-quadruplex. The ligands have a range of cyclic amino end groups of varying size. The crystal structures show that the diagonal loop in this quadruplex results in a large cavity for these groups, in contrast to the steric constraints imposed by propeller loops in human telomeric quadruplexes. We conclude that the nature of the loop has a significant influence on ligand selectivity for particular quadruplex folds.

  5. Sigma Receptor (σR) Ligands with Antiproliferative and Anticancer Activity.

    PubMed

    Georgiadis, Markos-Orestis; Karoutzou, Olga; Foscolos, Angeliki-Sofia; Papanastasiou, Ioannis

    2017-08-25

    Sigma receptor (σR) ligands have proven to be useful as cancer diagnostics and anticancer therapeutics and their ligands have been developed as molecular probes in oncology. Moreover, various σR ligands generate cancer cell death in vitro and in vivo. These σR ligands have exhibited promising results against numerous human and rodent cancers and are investigated under preclinical and clinical study trials, indicating a new category of drugs in cancer therapy.

  6. Ligand Entry and Exit Pathways in the β2-adrenergic Receptor

    PubMed Central

    Wang, Ting; Duan, Yong

    2009-01-01

    The recently determined crystal structure of the human β2-adrenergic (β2AR) G-protein coupled receptor provides an excellent structural basis for exploring β2AR -ligand binding and dissociation process. Based on this crystal structure, we simulated ligand exit from the β2AR receptor by applying the random acceleration molecular dynamics (RAMD) simulation method. The simulation results showed that the extracellular opening on the receptor surface was the most frequently observed egress point (referred to as pathway A) and a few other pathways through inter-helical clefts were also observed with significantly lower frequencies. In the egress trajectories along pathway A, the D192-K305 salt bridge between the extracellular loop 2 (ECL2) and the apex of the transmembrane helix 7 (TM7) was exclusively broken. The spatial occupancy maps of the ligand computed from the 100 RAMD simulation trajectories indicated that the receptor-ligand interactions that restrained the ligand in the binding pocket were the major resistance encountered by the ligand during exit and no second barrier was notable. We next performed RAMD simulations by using a putative ligand-free conformation of the receptor as input structure. This conformation was obtained in a standard MD simulation in the absence of the ligand and it differed from the ligand-bound conformation in a hydrophobic patch bridging ECL2 and TM7 due to the rotation of F193 of ECL2. Results from the RAMD simulations with this putative ligand-free conformation suggest that the cleft formed by the hydrophobic bridge, TM2, TM3 and TM7 on the extracellular surface likely serves as a more specific ligand-entry site and the ECL2-TM7 hydrophobic junction can be partially interrupted upon the entry of ligand that pushes F193 to rotate, resulting in a conformation as observed in the ligand-bound crystal structure. These results may help design β2AR-targeting drugs with improved efficacy as well as understand the receptor subtype

  7. New ligands for melanocortin receptors.

    PubMed

    Kaelin, C B; Candille, S I; Yu, B; Jackson, P; Thompson, D A; Nix, M A; Binkley, J; Millhauser, G L; Barsh, G S

    2008-12-01

    Named originally for their effects on peripheral end organs, the melanocortin system controls a diverse set of physiological processes through a series of five G-protein-coupled receptors and several sets of small peptide ligands. The central melanocortin system plays an essential role in homeostatic regulation of body weight, in which two alternative ligands, alpha-melanocyte-stimulating hormone and agouti-related protein, stimulate and inhibit receptor signaling in several key brain regions that ultimately affect food intake and energy expenditure. Much of what we know about the relationship between central melanocortin signaling and body weight regulation stems from genetic studies. Comparative genomic studies indicate that melanocortin receptors used for controlling pigmentation and body weight regulation existed more than 500 million years ago in primitive vertebrates, but that fine-grained control of melanocortin receptors through neuropeptides and endogenous antagonists developed more recently. Recent studies based on dog coat-color genetics revealed a new class of melanocortin ligands, the beta-defensins, which reveal the potential for cross talk between the melanocortin and the immune systems.

  8. H-Bonding Assisted Self-Assembly of Anionic and Neutral Ligand on Metal: A Comprehensive Strategy To Mimic Ditopic Ligands in Olefin Polymerization.

    PubMed

    Mote, Nilesh R; Patel, Ketan; Shinde, Dinesh R; Gaikwad, Shahaji R; Koshti, Vijay S; Gonnade, Rajesh G; Chikkali, Samir H

    2017-10-16

    Self-assembly of two neutral ligands on a metal to mimic bidentate ligand coordination has been frequently encountered in the recent past, but self-assembly of an anionic ligand on a metal template alongside a neutral ligand remains an elusive target. Such a self-assembly is hampered by additional complexity, wherein a highly negatively charged anion can form intermolecular hydrogen bonding with the supramolecular motif, leaving no scope for self-assembly with neutral ligand. Presented here is the self-association of anionic ligand 3-ureidobenzoic acid (2a) and neutral ligand 1-(3-(diphenylphosphanyl)phenyl)urea (1a) on a metal template to yield metal complex [{COOC 6 H 4 NH(CO)NH 2 }{Ph 2 PC 6 H 4 NH(CO)NH 2 }PdMeDMSO] (4a). The identity of 4a was established by NMR and mass spectroscopy. Along the same lines, 3-(3-phenylureido)benzoic acid (2b) and 1-(3-(diphenylphosphanyl)phenyl)-3-phenylurea (1b) self-assemble on a metal template to produce palladium complex [{COOC 6 H 4 NH(CO)NHPh}{Ph 2 PC 6 H 4 NH(CO)NHPh}PdMePy] (5c). The existence of 5c was confirmed by Job plot, 1-2D NMR spectroscopy, deuterium labeling, IR spectroscopy, UV-vis spectroscopy, model complex synthesis, and DFT calculations. These solution and gas phase investigations authenticated the presence of intramolecular hydrogen bonding between hydrogen's of 1b and carbonyl oxygen of 2b. The generality of the supramolecular approach has been validated by preparing six complexes from four monodentate ligands, and their synthetic utility was demonstrated in ethylene polymerization. Complex 4a was found to be the most active, leading to the production of highly branched polyethylene with a molecular weight of 55700 g/mol and melting temperature of 112 °C.

  9. Free-energy relationships in ion channels activated by voltage and ligand

    PubMed Central

    Chowdhury, Sandipan

    2013-01-01

    Many ion channels are modulated by multiple stimuli, which allow them to integrate a variety of cellular signals and precisely respond to physiological needs. Understanding how these different signaling pathways interact has been a challenge in part because of the complexity of underlying models. In this study, we analyzed the energetic relationships in polymodal ion channels using linkage principles. We first show that in proteins dually modulated by voltage and ligand, the net free-energy change can be obtained by measuring the charge-voltage (Q-V) relationship in zero ligand condition and the ligand binding curve at highly depolarizing membrane voltages. Next, we show that the voltage-dependent changes in ligand occupancy of the protein can be directly obtained by measuring the Q-V curves at multiple ligand concentrations. When a single reference ligand binding curve is available, this relationship allows us to reconstruct ligand binding curves at different voltages. More significantly, we establish that the shift of the Q-V curve between zero and saturating ligand concentration is a direct estimate of the interaction energy between the ligand- and voltage-dependent pathway. These free-energy relationships were tested by numerical simulations of a detailed gating model of the BK channel. Furthermore, as a proof of principle, we estimate the interaction energy between the ligand binding and voltage-dependent pathways for HCN2 channels whose ligand binding curves at various voltages are available. These emerging principles will be useful for high-throughput mutagenesis studies aimed at identifying interaction pathways between various regulatory domains in a polymodal ion channel. PMID:23250866

  10. Identification and characterization of PPARα ligands in the hippocampus

    PubMed Central

    Roy, Avik; Kundu, Madhuchhanda; Jana, Malabendu; Mishra, Rama K.; Yung, Yeni; Luan, Chi-Hao; Gonzalez, Frank J.; Pahan, Kalipada

    2016-01-01

    Peroxisome proliferator-activated receptor alpha (PPARα) regulates hepatic fatty acid catabolism and mediates the metabolic response to starvation. Recently, we have found that PPARα is constitutively activated in nuclei of hippocampal neurons and controls plasticity via direct transcriptional activation of CREB. Here, three endogenous ligands of PPARα, 3-hydroxy-(2,2)-dimethyl butyrate, hexadecanamide, and 9-octadecenamide were discovered in mouse brain hippocampus. Mass spectrometric detection of these compounds in mouse hippocampal nuclear extracts, in silico interaction studies, time-resolved FRET analyses, and thermal shift assay clearly indicated that these three compounds served as ligands of PPARα. Site-directed mutagenesis studies further revealed that PPARα Tyr 464 and Tyr 314 were involved in binding these hippocampal ligands. Moreover, these ligands activated PPARα and upregulated synaptic function of hippocampal neurons. These results highlight the discovery of hippocampal ligands of PPARα capable of modulating synaptic functions. PMID:27748752

  11. Identification and characterization of PPARα ligands in the hippocampus.

    PubMed

    Roy, Avik; Kundu, Madhuchhanda; Jana, Malabendu; Mishra, Rama K; Yung, Yeni; Luan, Chi-Hao; Gonzalez, Frank J; Pahan, Kalipada

    2016-12-01

    Peroxisome proliferator-activated receptor-α (PPARα) regulates hepatic fatty acid catabolism and mediates the metabolic response to starvation. Recently we found that PPARα is constitutively activated in nuclei of hippocampal neurons and controls plasticity via direct transcriptional activation of CREB. Here we report the discovery of three endogenous PPARα ligands-3-hydroxy-(2,2)-dimethyl butyrate, hexadecanamide, and 9-octadecenamide-in mouse brain hippocampus. Mass spectrometric detection of these compounds in mouse hippocampal nuclear extracts, in silico interaction studies, time-resolved FRET analyses, and thermal shift assay results clearly indicated that these three compounds served as ligands of PPARα. Site-directed mutagenesis studies further revealed that PPARα Y464 and Y314 are involved in binding these hippocampal ligands. Moreover, these ligands activated PPARα and upregulated the synaptic function of hippocampal neurons. These results highlight the discovery of hippocampal ligands of PPARα capable of modulating synaptic functions.

  12. Ligand-protein docking using a quantum stochastic tunneling optimization method.

    PubMed

    Mancera, Ricardo L; Källblad, Per; Todorov, Nikolay P

    2004-04-30

    A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened. Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 858-864, 2004

  13. Spatiotemporal Targeting of a Dual-Ligand Nanoparticle to Cancer Metastasis

    PubMed Central

    Doolittle, Elizabeth; Peiris, Pubudu M.; Doron, Gilad; Goldberg, Amy; Tucci, Samantha; Rao, Swetha; Shah, Shruti; Sylvestre, Meilyn; Govender, Priya; Turan, Oguz; Lee, Zhenghong; Schiemann, William P.; Karathanasis, Efstathios

    2015-01-01

    Various targeting strategies and ligands have been employed to direct nanoparticles to tumors that upregulate specific cell-surface molecules. However, tumors display a dynamic, heterogeneous microenvironment, which undergoes spatiotemporal changes including the expression of targetable cell-surface biomarkers. Here, we investigated a dual-ligand nanoparticle to effectively target two receptors overexpressed in aggressive tumors. By using two different chemical specificities, the dual-ligand strategy considered the spatiotemporal alterations in the expression patterns of the receptors in cancer sites. As a case study, we used two mouse models of metastasis of triple-negative breast cancer using the MDA-MB-231 and 4T1 cells. The dual-ligand system utilized two peptides targeting P-selectin and αvβ3 integrin, which are functionally linked to different stages of the development of metastatic disease at a distal site. Using in vivo multimodal imaging and post mortem histological analyses, this study shows that the dual-ligand nanoparticle effectively targeted metastatic disease that was otherwise missed by single-ligand strategies. The dual-ligand nanoparticle was capable of capturing different metastatic sites within the same animal that overexpressed either receptor or both of them. Furthermore, the highly efficient targeting resulted in 22% of the injected dual-ligand nanoparticles being deposited in early-stage metastases within 2 h after injection. PMID:26203676

  14. Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

    DOE PAGES

    Janowski, Pawel A.; Moriarty, Nigel W.; Kelley, Brian P.; ...

    2016-08-31

    Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows.PHENIX–AFITTrefinement uses a full molecular-mechanics force field for user-selected small-molecule ligands during refinement, eliminating the potentiallymore » difficult problem of finding or generating high-quality geometry restraints. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, making it ideal for high-throughput workflows.PHENIX–AFITTrefinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combiningAFITTand thePHENIXsoftware suite on a data set of 189 protein–ligand PDB structures are presented. Refinements usingPHENIX–AFITTsignificantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. Finally, for the data presented,PHENIX–AFITTrefinements result in more chemically accurate models for small-molecule ligands.« less

  15. Liquid crystalline perylene diimide outperforming nonliquid crystalline counterpart: higher power conversion efficiencies (PCEs) in bulk heterojunction (BHJ) cells and higher electron mobility in space charge limited current (SCLC) devices.

    PubMed

    Zhang, Youdi; Wang, Helin; Xiao, Yi; Wang, Ligang; Shi, Dequan; Cheng, Chuanhui

    2013-11-13

    In this work, we propose the application of liquid crystalline acceptors as a potential means to improve the performances of bulk heterojunction (BHJ) organic solar cells. LC-1, a structurally-simple perylene diimide (PDI), has been adopted as a model for thorough investigation. It exhibits a broad temperature range of liquid crystalline (LC) phase from 41 °C to 158 °C, and its LC properties have been characterized by differental scanning calorimetry (DSC), polarization optical microscopy (POM), and X-ray diffraction (XRD). The BHJ devices, using P3HT:LC-1 (1:2) as an organic photovoltaic active layer undergoing thermal annealing at 120 °C, shows an optimized efficiency of 0.94 %. By contrast, the devices based on PDI-1, a nonliquid crystalline PDI counterpart, only obtain a much lower efficiency of 0.22%. Atomic force microscopy (AFM) images confirm that the active layers composed of P3HT:LC-1 have smooth and ordered morphology. In space charge limited current (SCLC) devices fabricated via a spin-coating technique, LC-1 shows the intrinsic electron mobility of 2.85 × 10(-4) cm(2)/(V s) (at 0.3 MV/cm) which is almost 5 times that of PDI-1 (5.83 × 10(-5) cm(2)/(V s)) under the same conditions for thermal annealing at 120 °C.

  16. Aza-macrocyclic Triphenylamine Ligands for G-Quadruplex Recognition.

    PubMed

    García-España, Enrique Victor; Pont, Isabel; González-García, Jorge; Inclán, Mario; Reynolds, Matthew; Delgado-Pinar, Estefanía; Albelda, M Teresa; Vilar, Ramon

    2018-05-16

    A new series of triphenylamine-based ligands with one (TPA1PY), two (TPA2PY) or three pending aza-macrocycle(s) (TPA3PY) have been synthesised and studied by means of pH-metric titrations, UV/Vis spectroscopy and fluorescence experiments. The affinity of these ligands for G-quadruplex (G4) DNA and its selectivity over duplex DNA were investigated by FRET melting assays, fluorimetric titrations and circular dichroism (CD) spectroscopy. Interestingly, the interaction of the bi- and specially the tri-branched ligand with G4 leads to a very intense red-shifted fluorescence emission band which may be associated with intermolecular aggregation between the molecule and the DNA. This light-up effect allows the application of the ligands as fluorescence probes to selectivity detect G4. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Ligand migration in the truncated hemoglobin of Mycobacterium tuberculosis.

    PubMed

    Heroux, Maxime S; Mohan, Anne D; Olsen, Kenneth W

    2011-03-01

    The truncated hemoglobin of Mycobacterium tuberculosis (Mt-trHbO) is a small heme protein belonging to the hemoglobin superfamily. Truncated hemoglobins (trHbs) are believed to have functional roles such as terminal oxidases and oxygen sensors involved in the response to oxidative and nitrosative stress, nitric oxide (NO) detoxification, O₂/NO chemistry, O₂ delivery under hypoxic conditions, and long-term ligand storage. Based on sequence similarities, they are classified into three groups. Experimental studies revealed that all trHbs display a 2-on-2 α-helical sandwich fold rather than the 3-on-3 α-helical sandwich fold of the classical hemoglobin fold. Using locally enhanced sampling (LESMD) molecular dynamics, the ligand-binding escape pathways from the distal heme binding cavity of Mt-trHbO were determined to better understand how this protein functions. The importance of specific residues, such as the group II and III invariant W(G8) residue, can be seen in terms of ligand diffusion pathways and ligand dynamics. LESMD simulations show that the wild-type Mt-trHbO has three diffusion pathways while the W(G8)F Mt-trHbO mutant has only two. The W(G8) residue plays a critical role in ligand binding and stabilization and helps regulate the rate of ligand escape from the distal heme pocket. Thus, this invariant residue is important in creating ligand diffusion pathways and possibly in the enzymatic functions of this protein. Copyright © 2011 Wiley Periodicals, Inc.

  18. In vitro evaluation of biodegradable microspheres with surface-bound ligands.

    PubMed

    Keegan, Mark E; Royce, Sara M; Fahmy, Tarek; Saltzman, W Mark

    2006-02-21

    Protein ligands were conjugated to the surface of biodegradable microspheres. These microsphere-ligand conjugates were then used in two in vitro model systems to evaluate the effect of conjugated ligands on microsphere behavior. Microsphere retention in agarose columns was increased by ligands on the microsphere surface specific for receptors on the agarose matrix. In another experiment, conjugating the lectin Ulex europaeus agglutinin 1 to the microsphere surface increased microsphere adhesion to Caco-2 monolayers compared to control microspheres. This increase in microsphere adhesion was negated by co-administration of l-fucose, indicating that the increase in adhesion is due to specific interaction of the ligand with carbohydrate receptors on the cell surface. These results demonstrate that the ligands conjugated to the microspheres maintain their receptor binding activity and are present on the microsphere surface at a density sufficient to target the microspheres to both monolayers and three-dimensional matrices bearing complementary receptors.

  19. Distinct Iron-binding Ligands in the Upper Water Column at Station ALOHA

    NASA Astrophysics Data System (ADS)

    Bundy, R.; Boiteau, R.; Repeta, D.

    2016-02-01

    The distribution and chemical properties of iron-binding organic ligands at station ALOHA were examined using a combination of solid phase extraction (SPE) followed by high pressure liquid chromatography-inductively coupled plasma mass spectrometry (HPLC-ICPMS). HPLC-ICPMS ligand measurements were complemented by competitive ligand exchange adsorptive cathodic stripping voltammetry (CLE-ACSV) analysis using salicylaldoxime as the added ligand. By HPLC-ICPMS, we find enhanced concentrations of distinct naturally-occurring polar iron-binding ligands present at the surface and in the chlorophyll maximum. Lower concentrations were found in the subsurface, where a suite of non-polar ligands was detected. Siderophores were present at the deepest depths sampled at station ALOHA, down to 400m. Incubation studies provided evidence for the production of iron-binding ligands associated with nutrient amended phytoplankton growth in surface waters, and as a result of microbial particle remineralization in the subsurface water column. Ligands classes identified via SPE were then compared to CLE-ACSV ligand measurements, as well as the conditional stability constants measured from model polar and non-polar siderophores, yielding insight to the sources of iron-binding ligands throughout the water column at station ALOHA.

  20. New Stable Cu(I) Catalyst Supported on Weakly Acidic Polyacrylate Resin for Green C-N Coupling: Synthesis of N-(Pyridin-4-yl)benzene Amines and N,N-Bis(pyridine-4-yl)benzene Amines.

    PubMed

    Kore, Nitin; Pazdera, Pavel

    2016-12-22

    A method for preparation of a new stable Cu(I) catalyst supported on weakly acidic polyacrylate resin without additional stabilizing ligands is described. A simple and efficient methodology for Ullmann Cu(I) catalyzed C-N cross coupling reactions using this original catalyst is reported. Coupling reactions of 4-chloropyridinium chloride with anilines containing electron donating (EDG) or electron withdrawing (EWG) groups, naphthalen-2-amine and piperazine, respectively, are successfully demonstrated.