WorldWideScience

Sample records for methyl side chain

  1. Prediction of methyl-side Chain Dynamics in Proteins

    International Nuclear Information System (INIS)

    Ming Dengming; Brueschweiler, Rafael

    2004-01-01

    A simple analytical model is presented for the prediction of methyl-side chain dynamics in comparison with S 2 order parameters obtained by NMR relaxation spectroscopy. The model, which is an extension of the local contact model for backbone order parameter prediction, uses a static 3D protein structure as input. It expresses the methyl-group S 2 order parameters as a function of local contacts of the methyl carbon with respect to the neighboring atoms in combination with the number of consecutive mobile dihedral angles between the methyl group and the protein backbone. For six out of seven proteins the prediction results are good when compared with experimentally determined methyl-group S 2 values with an average correlation coefficient r-bar=0.65±0.14. For the unusually rigid cytochrome c 2 no significant correlation between prediction and experiment is found. The presented model provides independent support for the reliability of current side-chain relaxation methods along with their interpretation by the model-free formalism

  2. Carbon-14 methylation of the 2-methylbutyryl side chain of mevinolin and its analogs

    International Nuclear Information System (INIS)

    Prakash, S.R.; Ellsworth, R.L.

    1988-01-01

    A one step procedure for the preparation of three labeled mevinolin analogs possessing the 2,2-dimethylbutyryloxy side chain is described. Three lactones were converted into potassium salts of their corresponding di or trihydroxy carboxylic acids from which anionic ester enolates were generated and alkylated with [ 14 ]methyl iodide. Workup and purification by reverse phase HPLC provided the three radiochemically pure mevinolin analogs. The labeled lactones were converted into ammonium salts of their corresponding di or trihydroxy acids. (author)

  3. Accessing ns-μs side chain dynamics in ubiquitin with methyl RDCs

    International Nuclear Information System (INIS)

    Fares, Christophe; Lakomek, Nils-Alexander; Walter, Korvin F. A.; Frank, Benedikt T. C.; Meiler, Jens; Becker, Stefan; Griesinger, Christian

    2009-01-01

    This study presents the first application of the model-free analysis (MFA) (Meiler in J Am Chem Soc 123:6098-6107, 2001; Lakomek in J Biomol NMR 34:101-115, 2006) to methyl group RDCs measured in 13 different alignment media in order to describe their supra-τ c dynamics in ubiquitin. Our results indicate that methyl groups vary from rigid to very mobile with good correlation to residue type, distance to backbone and solvent exposure, and that considerable additional dynamics are effective at rates slower than the correlation time τ c . In fact, the average amplitude of motion expressed in terms of order parameters S 2 associated with the supra-τ c window brings evidence to the existence of fluctuations contributing as much additional mobility as those already present in the faster ps-ns time scale measured from relaxation data. Comparison to previous results on ubiquitin demonstrates that the RDC-derived order parameters are dominated both by rotameric interconversions and faster libration-type motions around equilibrium positions. They match best with those derived from a combined J-coupling and residual dipolar coupling approach (Chou in J Am Chem Soc 125:8959-8966, 2003) taking backbone motion into account. In order to appreciate the dynamic scale of side chains over the entire protein, the methyl group order parameters are compared to existing dynamic ensembles of ubiquitin. Of those recently published, the broadest one, namely the EROS ensemble (Lange in Science 320:1471-1475, 2008), fits the collection of methyl group order parameters presented here best. Last, we used the MFA-derived averaged spherical harmonics to perform highly-parameterized rotameric searches of the side chains conformation and find expanded rotamer distributions with excellent fit to our data. These rotamer distributions suggest the presence of concerted motions along the side chains

  4. Effect of methylation on the side-chain pKa value of arginine.

    Science.gov (United States)

    Evich, Marina; Stroeva, Ekaterina; Zheng, Yujun George; Germann, Markus W

    2016-02-01

    Arginine methylation is important in biological systems. Recent studies link the deregulation of protein arginine methyltransferases with certain cancers. To assess the impact of methylation on interaction with other biomolecules, the pKa values of methylated arginine variants were determined using NMR data. The pKa values of monomethylated, symmetrically dimethylated, and asymmetrically dimethylated arginine are similar to the unmodified arginine (14.2 ± 0.4). Although the pKa value has not been significantly affected by methylation, consequences of methylation include changes in charge distribution and steric effects, suggesting alternative mechanisms for recognition. © 2015 The Protein Society.

  5. Backbone and stereospecific (13)C methyl Ile (δ1), Leu and Val side-chain chemical shift assignments of Crc.

    Science.gov (United States)

    Sharma, Rakhi; Sahu, Bhubanananda; Ray, Malay K; Deshmukh, Mandar V

    2015-04-01

    Carbon catabolite repression (CCR) allows bacteria to selectively assimilate a preferred compound among a mixture of several potential carbon sources, thus boosting growth and economizing the cost of adaptability to variable nutrients in the environment. The RNA-binding catabolite repression control (Crc) protein acts as a global post-transcriptional regulator of CCR in Pseudomonas species. Crc triggers repression by inhibiting the expression of genes involved in transport and catabolism of non-preferred substrates, thus indirectly favoring assimilation of preferred one. We report here a nearly complete backbone and stereospecific (13)C methyl side-chain chemical shift assignments of Ile (δ1), Leu and Val of Crc (~ 31 kDa) from Pseudomonas syringae Lz4W.

  6. Influence of α-methyl group on molecular aggregation structure and surface physicochemical properties of fluoroalkyl side chain polymers

    International Nuclear Information System (INIS)

    Honda, K; Yamaguchi, H; Takahara, A; Sakata, O; Sasaki, S; Takata, M; Morita, M

    2009-01-01

    Influence of α-methyl group on molecular aggregation states and surface physicochemical properties of poly(fluoroalkyl acrylate)s [PFA-C y , where y is fluoromethylene number in R f group] and poly(fluoroalkykl methacrylate)s [PFMA-C y ] thin films were systematically investigated. Spin-coated PFA-C y and PFMA-C y thin films were characterized by dynamic contact angle measurements and grazing-incidence wide-angle X-ray diffraction (GIWAXD) measurements. GIWAXD data revealed that fluoroalkyl side chains of PFA-C y and PFMA-C y with y≥8 formed regular structures in the surface region as well as bulk one. However, the degree of orientation and ordering of the R f groups of PFMA-C 8 thin films was low. Also, the receding contact angle (θ r ) of PFMA-C 8 thin films was lower than that of PFA-C 8 ones. By annealing treatment, the θ r of PFMA-C 8 was increased. These results suggest that the R f groups of PFMA-C 8 were disordered due to presence of the α-methyl group. The R f groups became ordered to pack closely each other by annealing treatment, so that the water repellency was increased.

  7. Estimating side-chain order in methyl-protonated, perdeuterated proteins via multiple-quantum relaxation violated coherence transfer NMR spectroscopy

    International Nuclear Information System (INIS)

    Sun Hechao; Godoy-Ruiz, Raquel; Tugarinov, Vitali

    2012-01-01

    Relaxation violated coherence transfer NMR spectroscopy (Tugarinov et al. in J Am Chem Soc 129:1743–1750, 2007) is an established experimental tool for quantitative estimation of the amplitudes of side-chain motions in methyl-protonated, highly deuterated proteins. Relaxation violated coherence transfer experiments monitor the build-up of methyl proton multiple-quantum coherences that can be created in magnetically equivalent spin-systems as long as their transverse magnetization components relax with substantially different rates. The rate of this build-up is a reporter of the methyl-bearing side-chain mobility. Although the build-up of multiple-quantum 1 H coherences is monitored in these experiments, the decay of the methyl signal during relaxation delays occurs when methyl proton magnetization is in a single-quantum state. We describe a relaxation violated coherence transfer approach where the relaxation of multiple-quantum 1 H– 13 C methyl coherences during the relaxation delay period is quantified. The NMR experiment and the associated fitting procedure that models the time-dependence of the signal build-up, are applicable to the characterization of side-chain order in [ 13 CH 3 ]-methyl-labeled, highly deuterated protein systems up to ∼100 kDa in molecular weight. The feasibility of extracting reliable measures of side-chain order is experimentally verified on methyl-protonated, perdeuterated samples of an 8.5-kDa ubiquitin at 10°C and an 82-kDa Malate Synthase G at 37°C.

  8. The interplay between transient a-helix formation and side chain rotamer distributions in disordered proteins probed by methyl chemical shifts

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Iesmantavicius, Vytautas; Poulsen, Flemming M

    2011-01-01

    and retinoid receptors (ACTR). We find that small differences in the methyl carbon chemical shifts due to the ¿-gauche effect may provide information about the side chain rotamer distributions. However, the effects of neighboring residues on the methyl group chemical shifts obscure the direct observation...... of ¿-gauche effect. To overcome this, we reference the chemical shifts to those in a more disordered state resulting in residue specific random coil chemical shifts. The (13)C secondary chemical shifts of the methyl groups of valine, leucine, and isoleucine show sequence specific effects, which allow...

  9. Observation of the side chain O-methylation of glutamic acid or aspartic acid containing model peptides by electrospray ionization-mass spectrometry.

    Science.gov (United States)

    Atik, A Emin; Guray, Melda Z; Yalcin, Talat

    2017-03-15

    O-methylation of the side chains of glutamic acid (E) and aspartic acid (D) residues is generally observed modification when an acidified methanol/water (MeOH/dH 2 O) mixture is used as a solvent system during sample preparation for proteomic research. This chemical modification may result misidentification with endogenous protein methylation; therefore, a special care should be taken during sample handling prior to mass spectrometric analysis. In the current study, we systematically examined the extent of E/D methylation and C-terminus carboxyl group of synthetic model peptides in terms of different incubation temperatures, storage times, and added acid types as well as its percentages. To monitor these effects, C-terminus amidated and free acid forms of synthetic model peptides comprised of E or D residue(s) have been analyzed by electrospray ionization-mass spectrometry (ESI-MS). Additionally, LC-MS/MS experiments were performed to confirm the formation of methylated peptide product. The results showed that the rate of methylation was increased as the temperature increases along with prolong incubation times. Moreover, the extent of methylation was remarkably high when formic acid (FA) used as a protonation agent instead of acetic acid (AA). In addition, it was found that the degree of methylation was significantly decreased by lowering acid percentages in ESI solution. More than one acidic residue containing model peptides have been also used to explore the extent of multiple methylation reaction. Lastly, the ethanol (EtOH) and isopropanol (iPrOH) have been substituted separately with MeOH in sample preparation step to investigate the extent of esterification reaction under the same experimental conditions. However, in the positive perspective of view, this method can be used as a simple, rapid and cheap method for methylation of acidic residues under normal laboratory conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Synthesis and anti-HIV activity of novel N-1 side chain-modified analogs of 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT).

    Science.gov (United States)

    Pontikis, R; Benhida, R; Aubertin, A M; Grierson, D S; Monneret, C

    1997-06-06

    A series of 33 N-1 side chain-modified analogs of 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (1, HEPT) were synthesized and evaluated for their anti-HIV-1 activity. In particular, the influence of substitution of the terminal hydroxy group of the acyclic structure of HEPT and the structural rigidity of this side chain were investigated. Halo (7, 8), azido (9), and amino (10-15) derivatives were synthesized from HEPT via the p-tosylate derivative 6. Acylation of the primary amine 15 afforded the amido analogs 16-20. The diaryl derivatives 26-29 were prepared by reaction of HEPT, or of the 6-(2-pyridylthio) analog 23, with diaryl disulfides in the presence of tri-n-butylphosphine. Compounds 39-41, in which the N-1 side chain is rigidified by incorporation of an E-configured double bond, were obtained by palladium(0)-catalyzed coupling of several different 6-(arylthio)uracil derivatives (37, 38) with allyl acetates 33. Compounds 13, 40a,c,d,f, and 41, incorporating an aromatic ring at the end of the acyclic side chain, were found to be more potent than the known diphenyl-substituted HEPT analog BPT (2), two of them, 40c,d, being 10-fold more active.

  11. Side chain effect on electronic structure of spin-coated films of [6,6]-phenyl-C61-butyric acid methyl ester and its bis-adduct

    International Nuclear Information System (INIS)

    Akaike, Kouki; Kanai, Kaname; Ouchi, Yukio; Seki, Kazuhiko

    2013-01-01

    Highlights: ► Electronic structure of spin-coated films of PCBM and bis-PCBM was investigated. ► Ionization energy and electron affinity of bis-PCBM are smaller than those of PCBM. ► Electron donation from the side chain to C 60 -backbone raises the HOMO and LUMO. ► Open circuit voltages of PCBM-based solar cells relates to electron affinities. - Abstract: We investigated the electronic structure of spin-coated films of two soluble fullerenes; [6,6]-phenyl-C 61 -butyric acid methyl ester (PCBM) and its bis-adduct (bis-PCBM) using ultraviolet photoelectron spectroscopy, inverse photoemission spectroscopy and molecular orbital calculations. The ionization energy and electron affinity of spin-coated films of bis-PCBM were determined to be 6.01 eV and 3.4 eV, respectively. Analysis of electron density suggested the stronger electron donation from the two side chains to fullerene-backbone in a bis-PCBM molecule, compared with PCBM. The electron donation raises the energies of the frontier orbitals of bis-PCBM, which mainly consist of π-orbitals of fullerene-backbone. As a result, the ionization energy and electron affinity of bis-PCBM are smaller than those of PCBM. Moreover, we also concluded that the larger open circuit voltage observed for bis-PCBM based organic photovoltaics was explained by the higher-lying unoccupied molecular orbital of bis-PCBM

  12. Accurate Determination of Leucine and Valine Side-chain Conformations using U-[15N/13C/2H]/[1H-(methine/methyl)-Leu/Val] Isotope Labeling, NOE Pattern Recognition, and Methine Cγ-Hγ/Cβ-Hβ Residual Dipolar Couplings

    International Nuclear Information System (INIS)

    Tang, Chun; Iwahara, Junji; Clore, G. Marius

    2005-01-01

    An isotope labeling scheme is described in which specific protonation of methine and methyl protons of leucine and valine is obtained on a 15 N/ 13 C labeled background with uniform deuteration of all other non-exchangeable protons. The presence of a protonated methine group has little effect on the favorable relaxation properties of the methyl protons of Leu and Val. This labeling scheme permits the rotameric state of leucine side-chains to be readily determined by simple inspection of the pattern of Hγ(i)-H N (i) and Hγ(i)-H N (i+1) NOEs in a 3D 15 N-separated NOE spectrum free of complications arising from spectral overlap and spin-diffusion. In addition, one-bond residual dipolar couplings for the methine 13 C- 1 H bond vectors of Leu and Val can be accurately determined from an intensity J-modulated constant-time HCCH-COSY experiment and used to accurately orient the side-chains of Leu and Val. Incorporation of these data into structure refinement improves the accuracy with which the conformations of Leu and Val side-chains can be established. This is important to ensure optimal packing both within the protein core and at intermolecular interfaces. The impact of the method on protein structure determination is illustrated by application to enzyme IIA Chitobiose , a 34 kDa homotrimeric phosphotransferase protein

  13. Tuning Surface Properties of Poly(methyl methacrylate) Film Using Poly(perfluoromethyl methacrylate)s with Short Perfluorinated Side Chains.

    Science.gov (United States)

    Sohn, Eun-Ho; Ha, Jong-Wook; Lee, Soo-Bok; Park, In Jun

    2016-09-27

    To control the surface properties of a commonly used polymer, poly(methyl methacrylate) (PMMA), poly(perfluoromethyl methacrylate)s (PFMMAs) with short perfluorinated side groups (i.e., -CF3, -CF2CF3, -(CF3)2, -CF2CF2CF3) were used as blend components because of their good solubility in organic solvents, low surface energies, and high optical transmittance. The surface energies of the blend films of PFMMA with the -CF3 group and PMMA increased continuously with increasing PMMA contents from 17.6 to 26.0 mN/m, whereas those of the other polymer blend films remained at very low levels (10.2-12.6 mN/m), similar to those of pure PFMMAs, even when the blends contained 90 wt %PMMA. Surface morphology and composition measurements revealed that this result originated from the different blend structures, such as lateral and vertical phase separations. We expect that these PFMMAs will be useful in widening the applicable window of PMMA.

  14. Side chain effect on electronic structure of spin-coated films of [6,6]-phenyl-C{sub 61}-butyric acid methyl ester and its bis-adduct

    Energy Technology Data Exchange (ETDEWEB)

    Akaike, Kouki, E-mail: akaike@riken.jp [Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan); Kanai, Kaname [Department of Physics, Faculty of Science and Technology, Tokyo University of Science, Yamazaki 2641, Noda 278-8510 (Japan); Ouchi, Yukio; Seki, Kazuhiko [Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan)

    2013-03-29

    Highlights: ► Electronic structure of spin-coated films of PCBM and bis-PCBM was investigated. ► Ionization energy and electron affinity of bis-PCBM are smaller than those of PCBM. ► Electron donation from the side chain to C{sub 60}-backbone raises the HOMO and LUMO. ► Open circuit voltages of PCBM-based solar cells relates to electron affinities. - Abstract: We investigated the electronic structure of spin-coated films of two soluble fullerenes; [6,6]-phenyl-C{sub 61}-butyric acid methyl ester (PCBM) and its bis-adduct (bis-PCBM) using ultraviolet photoelectron spectroscopy, inverse photoemission spectroscopy and molecular orbital calculations. The ionization energy and electron affinity of spin-coated films of bis-PCBM were determined to be 6.01 eV and 3.4 eV, respectively. Analysis of electron density suggested the stronger electron donation from the two side chains to fullerene-backbone in a bis-PCBM molecule, compared with PCBM. The electron donation raises the energies of the frontier orbitals of bis-PCBM, which mainly consist of π-orbitals of fullerene-backbone. As a result, the ionization energy and electron affinity of bis-PCBM are smaller than those of PCBM. Moreover, we also concluded that the larger open circuit voltage observed for bis-PCBM based organic photovoltaics was explained by the higher-lying unoccupied molecular orbital of bis-PCBM.

  15. Side Chain Engineering in Solution-Processable Conjugated Polymers

    KAUST Repository

    Mei, Jianguo; Bao, Zhenan

    2014-01-01

    Side chains in conjugated polymers have been primarily utilized as solubilizing groups. However, these side chains have roles that are far beyond. We advocate using side chain engineering to tune a polymer's physical properties, including absorption

  16. Side chain polysiloxanes with phthalocyanine moieties

    Directory of Open Access Journals (Sweden)

    T. Ganicz

    2012-05-01

    Full Text Available Side chain polysiloxane with 5-(pentyloxy-3-methyloxy-9,10,16,17,23,24-hexakis(octenyloxyphthalocyanine moieties is synthesized by hydrosilylation reaction. The phase behavior and thermooptical properties of the polysiloxane and starting 2-(pent-4-enyloxy-3-methyloxy-9,10,16,17,23,24-hexakis(octenyloxyphthalocyanine is examined by POM (Polarizing optical microscopy, TOA (thermooptical analysis, DSC (differential scanning calorimetry, AFM (atomic force microscopy and SAXS (small angle X-ray scattering studies. The effect of the attachment of phthalocyanine to polysiloxane chains over phase transitions and phase morphology is discussed in details.

  17. Side Chain Cyclized Aromatic Amino Acids

    DEFF Research Database (Denmark)

    Van der Poorten, Olivier; Knuhtsen, Astrid; Sejer Pedersen, Daniel

    2016-01-01

    Constraining the conformation of flexible peptides is a proven strategy to increase potency, selectivity, and metabolic stability. The focus has mostly been on constraining the backbone dihedral angles; however, the correct orientation of the amino acid side chains (χ-space) that constitute...... the peptide pharmacophore is equally important. Control of χ-space utilizes conformationally constrained amino acids that favor, disfavor, or exclude the gauche (-), the gauche (+), or the trans conformation. In this review we focus on cyclic aromatic amino acids in which the side chain is connected...... to the peptide backbone to provide control of χ(1)- and χ(2)-space. The manifold applications for cyclized analogues of the aromatic amino acids Phe, Tyr, Trp, and His within peptide medicinal chemistry are showcased herein with examples of enzyme inhibitors and ligands for G protein-coupled receptors....

  18. Side Chain Engineering in Solution-Processable Conjugated Polymers

    KAUST Repository

    Mei, Jianguo

    2014-01-14

    Side chains in conjugated polymers have been primarily utilized as solubilizing groups. However, these side chains have roles that are far beyond. We advocate using side chain engineering to tune a polymer\\'s physical properties, including absorption, emission, energy level, molecular packing, and charge transport. To date, numerous flexible substituents suitable for constructing side chains have been reported. In this Perspective article, we advocate that the side chain engineering approach can advance better designs for next-generation conjugated polymers. © 2013 American Chemical Society.

  19. SCit: web tools for protein side chain conformation analysis.

    Science.gov (United States)

    Gautier, R; Camproux, A-C; Tufféry, P

    2004-07-01

    SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit.

  20. Rational Design of Coordination Polymers with Flexible Oxyethylene Side Chains

    International Nuclear Information System (INIS)

    Choi, Eun Young; Gao, Chunji; Lee, Suck Hyun; Kwon, O Pil

    2012-01-01

    We rationally designed and synthesized metallopolymers with organic 1,4-benzenedicarboxylic acid (BDC) linkers with different lengths of oxyethylene side chains in order to examine the influence of side chains on the coordination characteristics. While in a previous report the BDC linkers with alkyl side chains were found to form three-dimensional (3D) isoreticular metal-organic framework (IRMOF) structures or one-dimensional (1D) coordination polymeric structures with short -O(CH 2 ) 6 CH 3 or long -O(CH 2 ) 9 CH 3 side chains, respectively, new BDC linkers with oxyethylene side chains of the same lengths, -(OCH 2 CH 2 ) 2 CH 3 and -(OCH 2 CH 2 ) 3 CH 3 , form only 3D IRMOF structures. This result is attributed to the higher flexibility and smaller volume of oxyethylene side chains compared to alkyl side chains

  1. Modelling antibody side chain conformations using heuristic database search.

    Science.gov (United States)

    Ritchie, D W; Kemp, G J

    1997-01-01

    We have developed a knowledge-based system which models the side chain conformations of residues in the variable domains of antibody Fv fragments. The system is written in Prolog and uses an object-oriented database of aligned antibody structures in conjunction with a side chain rotamer library. The antibody database provides 3-dimensional clusters of side chain conformations which can be copied en masse into the model structure. The object-oriented database architecture facilitates a navigational style of database access, necessary to assemble side chains clusters. Around 60% of the model is built using side chain clusters and this eliminates much of the combinatorial complexity associated with many other side chain placement algorithms. Construction and placement of side chain clusters is guided by a heuristic cost function based on a simple model of side chain packing interactions. Even with a simple model, we find that a large proportion of side chain conformations are modelled accurately. We expect our approach could be used with other homologous protein families, in addition to antibodies, both to improve the quality of model structures and to give a "smart start" to the side chain placement problem.

  2. Accurate Determination of Leucine and Valine Side-chain Conformations using U-[{sup 15}N/{sup 13}C/{sup 2}H]/[{sup 1}H-(methine/methyl)-Leu/Val] Isotope Labeling, NOE Pattern Recognition, and Methine C{gamma}-H{gamma}/C{beta}-H{beta} Residual Dipolar Couplings

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Chun; Iwahara, Junji; Clore, G. Marius [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Laboratory of Chemical Physics (United States)], E-mail: mariusc@intra.niddk.nih.gov

    2005-10-15

    An isotope labeling scheme is described in which specific protonation of methine and methyl protons of leucine and valine is obtained on a {sup 15}N/{sup 13}C labeled background with uniform deuteration of all other non-exchangeable protons. The presence of a protonated methine group has little effect on the favorable relaxation properties of the methyl protons of Leu and Val. This labeling scheme permits the rotameric state of leucine side-chains to be readily determined by simple inspection of the pattern of H{gamma}(i)-H{sub N}(i) and H{gamma}(i)-H{sub N}(i+1) NOEs in a 3D {sup 15}N-separated NOE spectrum free of complications arising from spectral overlap and spin-diffusion. In addition, one-bond residual dipolar couplings for the methine {sup 13}C-{sup 1}H bond vectors of Leu and Val can be accurately determined from an intensity J-modulated constant-time HCCH-COSY experiment and used to accurately orient the side-chains of Leu and Val. Incorporation of these data into structure refinement improves the accuracy with which the conformations of Leu and Val side-chains can be established. This is important to ensure optimal packing both within the protein core and at intermolecular interfaces. The impact of the method on protein structure determination is illustrated by application to enzyme IIA{sup Chitobiose}, a 34 kDa homotrimeric phosphotransferase protein.

  3. SCit: web tools for protein side chain conformation analysis

    OpenAIRE

    Gautier, R.; Camproux, A.-C.; Tufféry, P.

    2004-01-01

    SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each...

  4. Integrated planning in supply chains with buy-side and sell-side

    Indian Academy of Sciences (India)

    Supply chain management; dynamic pricing; partner selection; supply chain planning; electronic marketplaces. Abstract. In this paper we develop a quadratic programming model for partner selection and planning in integrated supply chain networks embedded with both sell-side and buy-side electronic marketplaces.

  5. Simultaneous in vivo truncation of pectic side chains

    DEFF Research Database (Denmark)

    Øbro, Jens; Borkhardt, Bernhard; Harholt, Jesper

    2009-01-01

    . These modifications often prevent gelation, which has been a major functional requirement of commercial pectins until recently. We have previously shown that modification of pectin is possible through heterologous expression of pectin degrading enzymes in planta. To test the effect of simultaneous modification......Despite the wide occurrence of pectin in nature only a few source materials have been used to produce commercial pectins. One of the reasons for this is that many plant species contain pectins with high levels of neutral sugar side chains or that are highly substituted with acetyl or other groups...... of the two main neutral pectic side chains in pectic rhamnogalacturonan I (RGI), we constitutively expressed two different enzymes in Arabidopsis thaliana that would either modify the galactan or the arabinan side chains, or both side chains simultaneously. Our analysis showed that the simultaneous...

  6. A protein-dependent side-chain rotamer library.

    KAUST Repository

    Bhuyan, M.S.

    2011-12-14

    Protein side-chain packing problem has remained one of the key open problems in bioinformatics. The three main components of protein side-chain prediction methods are a rotamer library, an energy function and a search algorithm. Rotamer libraries summarize the existing knowledge of the experimentally determined structures quantitatively. Depending on how much contextual information is encoded, there are backbone-independent rotamer libraries and backbone-dependent rotamer libraries. Backbone-independent libraries only encode sequential information, whereas backbone-dependent libraries encode both sequential and locally structural information. However, side-chain conformations are determined by spatially local information, rather than sequentially local information. Since in the side-chain prediction problem, the backbone structure is given, spatially local information should ideally be encoded into the rotamer libraries. In this paper, we propose a new type of backbone-dependent rotamer library, which encodes structural information of all the spatially neighboring residues. We call it protein-dependent rotamer libraries. Given any rotamer library and a protein backbone structure, we first model the protein structure as a Markov random field. Then the marginal distributions are estimated by the inference algorithms, without doing global optimization or search. The rotamers from the given library are then re-ranked and associated with the updated probabilities. Experimental results demonstrate that the proposed protein-dependent libraries significantly outperform the widely used backbone-dependent libraries in terms of the side-chain prediction accuracy and the rotamer ranking ability. Furthermore, without global optimization/search, the side-chain prediction power of the protein-dependent library is still comparable to the global-search-based side-chain prediction methods.

  7. A protein-dependent side-chain rotamer library.

    KAUST Repository

    Bhuyan, M.S.; Gao, Xin

    2011-01-01

    Protein side-chain packing problem has remained one of the key open problems in bioinformatics. The three main components of protein side-chain prediction methods are a rotamer library, an energy function and a search algorithm. Rotamer libraries summarize the existing knowledge of the experimentally determined structures quantitatively. Depending on how much contextual information is encoded, there are backbone-independent rotamer libraries and backbone-dependent rotamer libraries. Backbone-independent libraries only encode sequential information, whereas backbone-dependent libraries encode both sequential and locally structural information. However, side-chain conformations are determined by spatially local information, rather than sequentially local information. Since in the side-chain prediction problem, the backbone structure is given, spatially local information should ideally be encoded into the rotamer libraries. In this paper, we propose a new type of backbone-dependent rotamer library, which encodes structural information of all the spatially neighboring residues. We call it protein-dependent rotamer libraries. Given any rotamer library and a protein backbone structure, we first model the protein structure as a Markov random field. Then the marginal distributions are estimated by the inference algorithms, without doing global optimization or search. The rotamers from the given library are then re-ranked and associated with the updated probabilities. Experimental results demonstrate that the proposed protein-dependent libraries significantly outperform the widely used backbone-dependent libraries in terms of the side-chain prediction accuracy and the rotamer ranking ability. Furthermore, without global optimization/search, the side-chain prediction power of the protein-dependent library is still comparable to the global-search-based side-chain prediction methods.

  8. Liquid crystal polymers: evidence of hairpin defects in nematic main chains, comparison with side chain polymers

    Science.gov (United States)

    Li, M. H.; Brûlet, A.; Keller, P.; Cotton, J. P.

    1996-09-01

    This article describes the conformation of two species of liquid crystalline polymers as revealed by small angle neutron scattering. The results obtained with side chain polymers are recalled. The procedure used to analyze the scattering data of main chains in the nematic phase is reported in this paper. It permits a demonstration of the existence of hairpins. Comparison of both polymer species shows that in the isotropic phase, the two polymers adopt a random coil conformation. In the nematic phase, the conformations are very different; the side chains behave as a melt of penetrable random coils whereas the main chains behave as a nematic phase of non penetrable cylinders.

  9. Photoinduced Circular Anisotropy in Side-Chain Azobenzene Polyesters

    DEFF Research Database (Denmark)

    Nikolova, L.; Todorov, T.; Ivanov, M.

    1997-01-01

    We report for the first time the inducing of large circular anisotropy in previously unoriented films of side-chain azobenzene polyesters on illumination with circularly polarized light at a wavelength of 488 nm. The circular dichroism and optical activity are measured simultaneously in real time...

  10. Access to Functionalized Steroid Side Chains via Modified Julia Olefination

    Science.gov (United States)

    Izgu, Enver Cagri; Burns, Aaron C.; Hoye, Thomas R.

    2011-01-01

    Various functionalized steroidal side chains were conveniently accessed by a modified Julia olefination strategy using a common sulfone donor and an appropriate α-branched aldehyde acceptor. For the coupling of these hindered classes of reaction partners (and in contrast to typically observed trends), the benzothiazolyl(BT)-sulfone anion gave superior outcomes compared to the phenyltetrazolyl(PT)-sulfone anion. PMID:21244047

  11. The influence of chirality in the amide side chain on the carbonyl orientation in rotational isomers of 3-carbamoylpyridinium halides

    NARCIS (Netherlands)

    Bastiaansen, L.A.M.; Vermeulen, T.J.M.; Buck, H.M.; Smeets, W.J.J.; Kanters, J.A.

    1988-01-01

    The direction of the carbonyl orientation in solid amide rotamers of 3-(N-methyl-N-a-methylbenzylcarbamoyl)-1,2,4-trimethylpyridinium iodide is governed by the (R)- or (S)-chirality in the amide side chain; X-ray structures and c.d. spectra are correlated.

  12. Interplay Between Side Chain Pattern, Polymer Aggregation, and Charge Carrier Dynamics in PBDTTPD:PCBM Bulk-Heterojunction Solar Cells

    KAUST Repository

    Dyer-Smith, Clare; Howard, Ian A.; Cabanetos, Clement; El Labban, Abdulrahman; Beaujuge, Pierre; Laquai, Fré dé ric

    2015-01-01

    Poly(benzo[1,2-b:4,5-b′]dithiophene–alt–thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymer donors with linear side-chains yield bulk-heterojunction (BHJ) solar cell power conversion efficiencies (PCEs) of about 4% with phenyl-C71-butyric acid methyl

  13. TROSY of side-chain amides in large proteins

    Science.gov (United States)

    Liu, Aizhuo; Yao, Lishan; Li, Yue; Yan, Honggao

    2012-01-01

    By using the mixed solvent of 50% H2O/50% D2O and employing deuterium decoupling, TROSY experiments exclusively detect NMR signals from semideuterated isotopomers of carboxamide groups with high sensitivities for proteins with molecular weights up to 80 kDa. This isotopomer-selective strategy extends TROSY experiments from exclusively detecting backbone to both backbone and side-chain amides, particularly in large proteins. Because of differences in both TROSY effect and dynamics between 15N–HE{DZ} and 15N–HZ{DE} isotopomers of the same carboxamide, the 15N transverse magnetization of the latter relaxes significantly faster than that of the former, which provides a direct and reliable stereospecific distinction between the two configurations. The TROSY effects on the 15N–HE{DZ} isotopomers of side-chain amides are as significant as on backbone amides. PMID:17347000

  14. Side-chain liquid crystalline polyesters for optical information storage

    DEFF Research Database (Denmark)

    Ramanujam, P.S.; Holme, Christian; Hvilsted, Søren

    1996-01-01

    and holographic storage in one particular polyester are described in detail and polarized Fourier transform infrared spectroscopic data complementing the optical data are presented. Optical and atomic force microscope investigations point to a laser-induced aggregation as responsible for permanent optical storage.......Azobenzene side-chain liquid crystalline polyester structures suitable for permanent optical storage are described. The synthesis and characterization of the polyesters together with differential scanning calorimetry and X-ray investigations are discussed. Optical anisotropic investigations...

  15. Highly conductive side chain block copolymer anion exchange membranes.

    Science.gov (United States)

    Wang, Lizhu; Hickner, Michael A

    2016-06-28

    Block copolymers based on poly(styrene) having pendent trimethyl styrenylbutyl ammonium (with four carbon ring-ionic group alkyl linkers) or benzyltrimethyl ammonium groups with a methylene bridge between the ring and ionic group were synthesized by reversible addition-fragmentation radical (RAFT) polymerization as anion exchange membranes (AEMs). The C4 side chain polymer showed a 17% increase in Cl(-) conductivity of 33.7 mS cm(-1) compared to the benzyltrimethyl ammonium sample (28.9 mS cm(-1)) under the same conditions (IEC = 3.20 meq. g(-1), hydration number, λ = ∼7.0, cast from DMF/1-propanol (v/v = 3 : 1), relative humidity = 95%). As confirmed by small angle X-ray scattering (SAXS), the side chain block copolymers with tethered ammonium cations showed well-defined lamellar morphologies and a significant reduction in interdomain spacing compared to benzyltrimethyl ammonium containing block copolymers. The chemical stabilities of the block copolymers were evaluated under severe, accelerated conditions, and degradation was observed by (1)H NMR. The block copolymer with C4 side chain trimethyl styrenylbutyl ammonium motifs displayed slightly improved stability compared to that of a benzyltrimethyl ammonium-based AEM at 80 °C in 1 M NaOD aqueous solution for 30 days.

  16. Investigating side chain mediated electroluminescence from carbazole-modified polyfluorene.

    Science.gov (United States)

    Liao, Jin-Long; Chen, Xiwen; Liu, Ching-Yang; Chen, Show-An; Su, Chiu-Huen; Su, An-Chung

    2007-09-06

    In molecular design of electroluminescent (EL) conjugated polymers, introducing a charge transport moiety on a side chain is found to be a promising method for balancing electron and hole fluxes in EL devices without changing the emitting color if there is no interaction between moiety and main chain. In the case of grafting a carbazole (Cz) moiety (hole transporting) on blue emitting polyfluorene, a green emission appears with intensity comparable to the blue emission, which was attributed to a possible interaction between main chain and Cz as previously reported by us. Here, a detailed study of its EL mechanism was carried out by means of time-resolved EL with the assistance of molecular simulation and thermally stimulated current measurements; exploration of how main chain segments interact with the transport moiety was performed. We found the Cz groups in Cz100PF play multiple roles: they act as (1) hole transporter to improve hole injection, (2) hole trapping site for efficient electron-hole recombination to yield blue-emitting excitons, and (3) source of green emission from electroplex formed via electric field-mediated interaction of the Cz/Cz radical cation with an electron in the nearby PF backbone. In combination, these observations suggest that integrated consideration for both intramolecular and intermolecular interactions provides a new route of molecular design of efficient EL polymers.

  17. Beta-scission of side-chain alkoxyl radicals on peptides and proteins results in the loss of side-chains as aldehydes and ketones

    DEFF Research Database (Denmark)

    Headlam, Henrietta A; Davies, Michael Jonathan

    2002-01-01

    Exposure of proteins to radicals in the presence of O(2) results in side-chain oxidation and backbone fragmentation; the interrelationship between these processes is not fully understood. Recently, initial attack on Ala side-chains was shown to give alpha-carbon radicals (and hence backbone cleav...

  18. Light scattering of thin azobenzene side-chain polyester layers

    DEFF Research Database (Denmark)

    Kerekes, Á.; Lörincz, E.; Ramanujam, P.S.

    2002-01-01

    Light scattering properties of liquid crystalline and amorphous azobenzene side-chain polyester layers used for optical data storage were examined by means of transmissive scatterometry. Comparative experiments show that the amorphous polyester has significantly lower light scattering...... characteristics than the liquid crystalline polyester. The amorphous samples have negligible polarization part orthogonal to the incident beam. the liquid crystalline samples have relative high orthogonal polarization part in light scattering, The light scattering results can be used to give a lower limit...... for the domain size in thin liquid crystalline polyester layers being responsible for the dominant light scattering. The characteristic domain Sizes obtained from the Fourier transformation of polarization microscopic Pictures confirm these values....

  19. The C8 side chain is one of the key functional group of Garcinol for its anti-cancer effects.

    Science.gov (United States)

    Zhou, Xin-Ying; Cao, Jing; Han, Chao-Ming; Li, Shu-Wen; Zhang, Chen; Du, Yin-Duan; Zhou, Qian-Qian; Zhang, Xin-Yan; Chen, Xin

    2017-04-01

    Garcinol from the fruit rind of Garcinia indica shows anti-carcinogenic and anti-inflammatory properties, but its mechanism and key functional groups were still need to be identified. Our previous computer modeling suggested that the C8 side chain of Garcinol is so large that it may influence the bioactivity of the compound. 8-Me Garcinol, a derivative of Garcinol in which the bulky side chain at the C8 position of Garcinol is replaced with a much smaller methyl group, was synthesized through a 12-step procedure starting from 1,3-cyclohexanedione. The antitumor activity of Garcinol and 8-Me Garcinol was evaluated in vitro by MTT, cell cycle and cell apoptosis assays. The results showed that 8-Me Garcinol had weaker inhibitory activity on cells proliferation, and little effects on cell cycle and apoptosis in oral cancer cell line SCC15 cells when compared with Garcinol. All of the results indicated 8-Me Garcinol exerts weaker antitumor activity than Garcinol, and the C8 side chain might be an important active site in Garcinol. Changing the C8 side chain will affect the inhibitory effect of Garcinol. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Solvent Exchange Rates of Side-chain Amide Protons in Proteins

    International Nuclear Information System (INIS)

    Rajagopal, Ponni; Jones, Bryan E.; Klevit, Rachel E.

    1998-01-01

    Solvent exchange rates and temperature coefficients for Asn/Gln side-chain amide protons have been measured in Escherichia coli HPr. The protons of the eight side-chain amide groups (two Asn and six Gln) exhibit varying exchange rates which are slower than some of the fast exchanging backbone amide protons. Differences in exchange rates of the E and Z protons of the same side-chain amide group are obtained by measuring exchange rates at pH values > 8. An NOE between a side-chain amide proton and a bound water molecule was also observed

  1. Impact of the Nature of the Side-Chains on the Polymer-Fullerene Packing in the Mixed Regions of Bulk Heterojunction Solar Cells

    KAUST Repository

    Wang, Tonghui; Ravva, Mahesh Kumar; Bredas, Jean-Luc

    2016-01-01

    Polymer-fullerene packing in mixed regions of a bulk heterojunction solar cell is expected to play a major role in exciton-dissociation, charge-separation, and charge-recombination processes. Here, molecular dynamics simulations are combined with density functional theory calculations to examine the impact of nature and location of polymer side-chains on the polymer-fullerene packing in mixed regions. The focus is on poly-benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-c]pyrrole-4,6-dione (PBDTTPD) as electron-donating material and [6,6]-phenyl-C61-butyric acid methyl ester (PC61BM) as electron-accepting material. Three polymer side-chain patterns are considered: i) linear side-chains on both benzodithiophene (BDT) and thienopyrroledione (TPD) moieties; ii) two linear side-chains on BDT and a branched side-chain on TPD; and iii) two branched side-chains on BDT and a linear side-chain on TPD. Increasing the number of branched side-chains is found to decrease the polymer packing density and thereby to enhance PBDTTPD–PC61 BM mixing. The nature and location of side-chains are found to play a determining role in the probability of finding PC61BM molecules close to either BDT or TPD. The electronic couplings relevant for the exciton-dissociation and charge-recombination processes are also evaluated. Overall, the findings are consistent with the experimental evolution of the PBDTTPD–PC61BM solar-cell performance as a function of side-chain patterns. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

  2. Impact of the Nature of the Side-Chains on the Polymer-Fullerene Packing in the Mixed Regions of Bulk Heterojunction Solar Cells

    KAUST Repository

    Wang, Tonghui

    2016-06-20

    Polymer-fullerene packing in mixed regions of a bulk heterojunction solar cell is expected to play a major role in exciton-dissociation, charge-separation, and charge-recombination processes. Here, molecular dynamics simulations are combined with density functional theory calculations to examine the impact of nature and location of polymer side-chains on the polymer-fullerene packing in mixed regions. The focus is on poly-benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-c]pyrrole-4,6-dione (PBDTTPD) as electron-donating material and [6,6]-phenyl-C61-butyric acid methyl ester (PC61BM) as electron-accepting material. Three polymer side-chain patterns are considered: i) linear side-chains on both benzodithiophene (BDT) and thienopyrroledione (TPD) moieties; ii) two linear side-chains on BDT and a branched side-chain on TPD; and iii) two branched side-chains on BDT and a linear side-chain on TPD. Increasing the number of branched side-chains is found to decrease the polymer packing density and thereby to enhance PBDTTPD–PC61 BM mixing. The nature and location of side-chains are found to play a determining role in the probability of finding PC61BM molecules close to either BDT or TPD. The electronic couplings relevant for the exciton-dissociation and charge-recombination processes are also evaluated. Overall, the findings are consistent with the experimental evolution of the PBDTTPD–PC61BM solar-cell performance as a function of side-chain patterns. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

  3. Synthesis and characterization of novel side-chain liquid crystalline polycarbonates, 4 - Synthesis of side-chain liquid crystalline polycarbonates with mesogenic groups having tails of different lengths

    NARCIS (Netherlands)

    Jansen, J.C.; Addink, R.; Nijenhuis, K.T.; Mijs, W.J.

    1999-01-01

    Side-chain liquid crystalline polycarbonates with alkoxyphenylbenzoate side groups, having a short spacer and tails ranging from 1 to 8 C-atoms, were synthesized. The polymers were prepared by an organo-zinc catalysed copolymerization of carbon dioxide and mesogenic 4-alkoxyphenyl

  4. Synthesis and characterization of novel side-chain liquid crystalline polycarbonates, 5 - Mesophase characterization of side-chain liquid crystalline polycarbonates with tails of different lengths

    NARCIS (Netherlands)

    Jansen, J.C.; Addink, R.; Nijenhuis, K.T.; Mijs, W.J.

    1999-01-01

    The mesomorphic properties and thermal stability of side-chain LC polycarbonates with alkoxyphenyl benzoate side groups having a short spacer and alkoxy tails ranging from 1 to 8 carbon atoms were studied by DSC, X-ray diffraction and polarized light optical microscopy. All polymers have a smectic A

  5. THE DEAD-END ELIMINATION THEOREM AND ITS USE IN PROTEIN SIDE-CHAIN POSITIONING

    NARCIS (Netherlands)

    DESMET, J; DEMAEYER, M; HAZES, B; LASTERS, [No Value

    1992-01-01

    THE prediction of a protein's tertiary structure is still a considerable problem because the huge amount of possible conformational space' makes it computationally difficult. With regard to side-chain modelling, a solution has been attempted by the grouping of side-chain conformations into

  6. The influence of aliphatic side chain of anacardic acid on molecular ...

    African Journals Online (AJOL)

    Interestingly, the presence of the aliphatic side chain in AnMcr resulted in more uniform imprinted beads as compared to particle agglomerates obtained from SaMcr in the presence of propranolol template. Therefore, the aliphatic side chain of anacardic acid improves both molecular recognition of imprinted polymers as ...

  7. Microphase Separation within a Comb Copolymer with Attractive Side Chains : A Computer Simulation Study

    NARCIS (Netherlands)

    Vasilevskaya, V.V.; Klochkov, A.A.; Khalatur, P.G.; Khokhlov, A.R.; Brinke, G. ten

    2001-01-01

    Computer simulation modelling of a flexible comb copolymer with attractive interactions between the monomer units of the side chains is performed. The conditions for the coil-globule transition, induced by the increase of attractive interaction, ε, between side chain monomer units, are analysed for

  8. Automated side-chain model building and sequence assignment by template matching

    International Nuclear Information System (INIS)

    Terwilliger, Thomas C.

    2002-01-01

    A method for automated macromolecular side-chain model building and for aligning the sequence to the map is described. An algorithm is described for automated building of side chains in an electron-density map once a main-chain model is built and for alignment of the protein sequence to the map. The procedure is based on a comparison of electron density at the expected side-chain positions with electron-density templates. The templates are constructed from average amino-acid side-chain densities in 574 refined protein structures. For each contiguous segment of main chain, a matrix with entries corresponding to an estimate of the probability that each of the 20 amino acids is located at each position of the main-chain model is obtained. The probability that this segment corresponds to each possible alignment with the sequence of the protein is estimated using a Bayesian approach and high-confidence matches are kept. Once side-chain identities are determined, the most probable rotamer for each side chain is built into the model. The automated procedure has been implemented in the RESOLVE software. Combined with automated main-chain model building, the procedure produces a preliminary model suitable for refinement and extension by an experienced crystallographer

  9. Effect of side chain position on solar cell performance in cyclopentadithiophene-based copolymers

    International Nuclear Information System (INIS)

    Lee, Sang Kyu; Seo, Jung Hwa; Cho, Nam Sung; Cho, Shinuk

    2012-01-01

    The photovoltaic properties of a series of low band-gap conjugated copolymers, in which alkyl side chains were substituted at various positions, were investigated using donor–acceptor (D–A) conjugated copolymers consisting of a cyclopentadithiophene derivative and dithienyl-benzothiadiazole. The base polymer, which has no alkyl side chains, yielded promising power conversion efficiency of 3.8%. Polymers with alkyl side chains, however, exhibited significantly decreased performance. In addition, the effects of processing additive became negligible. The results indicate that substituted side chains, which were introduced to improve solubility, critically affected the optical and electronic properties of D–A conjugated copolymers. Furthermore, the position of the side chain was also very important for controlling the morphological properties of the D–A conjugated copolymers. - Highlights: ► Effect of side chain position on solar cell performance was investigated. ► Polymer without alkyl chains yielded promising power conversion efficiency of 3.8%. ► Position of side chains critically affected the optical and electronic properties.

  10. Different DNA methylation patterns detected by the Amplified Methylation Polymorphism Polymerase Chain Reaction (AMP PCR) technique among various cell types of bulls

    OpenAIRE

    Phutikanit, Nawapen; Suwimonteerabutr, Junpen; Harrison, Dion; D'Occhio, Michael; Carroll, Bernie; Techakumphu, Mongkol

    2010-01-01

    Abstract Background The purpose of this study was to apply an arbitrarily primed methylation sensitive polymerase chain reaction (PCR) assay called Amplified Methylation Polymorphism Polymerase Chain Reaction (AMP PCR) to investigate the methylation profiles of somatic and germ cells obtained from Holstein bulls. Methods Genomic DNA was extracted from sperm, leukocytes and fibroblasts obtained from three bulls and digested with a methylation sensitive endonuclease (HpaII). The native genomic ...

  11. Charge photogeneration and transport in side-chain carbazole polymers and co-polymers

    KAUST Repository

    Li, Huawei; Termine, Roberto; Godbert, Nicolas; Angiolini, Luigi; Giorgini, Loris; Golemme, Attilio

    2011-01-01

    The photoconductivity, hole mobility and charge photogeneration efficiency of a series of side-chain carbazole homopolymers and copolymers (with azo side-chains) have been investigated. Cyclic voltammetry measurement of frontier orbitals energies show that the HOMO energy is determined by the nature and the position of attachment of the linker between the main chain and the carbazole, the azo-moiety being not relevant in this respect. Hole mobility is not influenced by the HOMO energy but seems to depend on the degree of conformational mobility of the side-chains, reaching values of the order of 10-3cm2V-1s-1 in the best cases. The HOMO energy is instead extremely important when considering photogeneration efficiency, that can change by 10 orders of magnitude depending on the density of the carbazole side-chains in co-polymers and on the linker nature and attachment position. © 2011 Elsevier B.V. All rights reserved.

  12. Charge photogeneration and transport in side-chain carbazole polymers and co-polymers

    KAUST Repository

    Li, Huawei

    2011-07-01

    The photoconductivity, hole mobility and charge photogeneration efficiency of a series of side-chain carbazole homopolymers and copolymers (with azo side-chains) have been investigated. Cyclic voltammetry measurement of frontier orbitals energies show that the HOMO energy is determined by the nature and the position of attachment of the linker between the main chain and the carbazole, the azo-moiety being not relevant in this respect. Hole mobility is not influenced by the HOMO energy but seems to depend on the degree of conformational mobility of the side-chains, reaching values of the order of 10-3cm2V-1s-1 in the best cases. The HOMO energy is instead extremely important when considering photogeneration efficiency, that can change by 10 orders of magnitude depending on the density of the carbazole side-chains in co-polymers and on the linker nature and attachment position. © 2011 Elsevier B.V. All rights reserved.

  13. Residue-Specific Side-Chain Polymorphisms via Particle Belief Propagation.

    Science.gov (United States)

    Ghoraie, Laleh Soltan; Burkowski, Forbes; Li, Shuai Cheng; Zhu, Mu

    2014-01-01

    Protein side chains populate diverse conformational ensembles in crystals. Despite much evidence that there is widespread conformational polymorphism in protein side chains, most of the X-ray crystallography data are modeled by single conformations in the Protein Data Bank. The ability to extract or to predict these conformational polymorphisms is of crucial importance, as it facilitates deeper understanding of protein dynamics and functionality. In this paper, we describe a computational strategy capable of predicting side-chain polymorphisms. Our approach extends a particular class of algorithms for side-chain prediction by modeling the side-chain dihedral angles more appropriately as continuous rather than discrete variables. Employing a new inferential technique known as particle belief propagation, we predict residue-specific distributions that encode information about side-chain polymorphisms. Our predicted polymorphisms are in relatively close agreement with results from a state-of-the-art approach based on X-ray crystallography data, which characterizes the conformational polymorphisms of side chains using electron density information, and has successfully discovered previously unmodeled conformations.

  14. Automated side-chain model building and sequence assignment by template matching.

    Science.gov (United States)

    Terwilliger, Thomas C

    2003-01-01

    An algorithm is described for automated building of side chains in an electron-density map once a main-chain model is built and for alignment of the protein sequence to the map. The procedure is based on a comparison of electron density at the expected side-chain positions with electron-density templates. The templates are constructed from average amino-acid side-chain densities in 574 refined protein structures. For each contiguous segment of main chain, a matrix with entries corresponding to an estimate of the probability that each of the 20 amino acids is located at each position of the main-chain model is obtained. The probability that this segment corresponds to each possible alignment with the sequence of the protein is estimated using a Bayesian approach and high-confidence matches are kept. Once side-chain identities are determined, the most probable rotamer for each side chain is built into the model. The automated procedure has been implemented in the RESOLVE software. Combined with automated main-chain model building, the procedure produces a preliminary model suitable for refinement and extension by an experienced crystallographer.

  15. Interplay Between Side Chain Pattern, Polymer Aggregation, and Charge Carrier Dynamics in PBDTTPD:PCBM Bulk-Heterojunction Solar Cells

    KAUST Repository

    Dyer-Smith, Clare

    2015-05-01

    Poly(benzo[1,2-b:4,5-b′]dithiophene–alt–thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymer donors with linear side-chains yield bulk-heterojunction (BHJ) solar cell power conversion efficiencies (PCEs) of about 4% with phenyl-C71-butyric acid methyl ester (PC71BM) as the acceptor, while a PBDTTPD polymer with a combination of branched and linear substituents yields a doubling of the PCE to 8%. Using transient optical spectroscopy it is shown that while the exciton dissociation and ultrafast charge generation steps are not strongly affected by the side chain modifications, the polymer with branched side chains exhibits a decreased rate of nongeminate recombination and a lower fraction of sub-nanosecond geminate recombination. In turn the yield of long-lived charge carriers increases, resulting in a 33% increase in short circuit current (J sc). In parallel, the two polymers show distinct grazing incidence X-ray scattering spectra indicative of the presence of stacks with different orientation patterns in optimized thin-film BHJ devices. Independent of the packing pattern the spectroscopic data also reveals the existence of polymer aggregates in the pristine polymer films as well as in both blends which trap excitons and hinder their dissociation.

  16. Side chain variations radically alter the diffusion of poly(2-alkyl-2-oxazoline) functionalised nanoparticles through a mucosal barrier.

    Science.gov (United States)

    Mansfield, Edward D H; de la Rosa, Victor R; Kowalczyk, Radoslaw M; Grillo, Isabelle; Hoogenboom, Richard; Sillence, Katy; Hole, Patrick; Williams, Adrian C; Khutoryanskiy, Vitaliy V

    2016-08-16

    Functionalised nanomaterials are gaining popularity for use as drug delivery vehicles and, in particular, mucus penetrating nanoparticles may improve drug bioavailability via the oral route. To date, few polymers have been investigated for their muco-penetration, and the effects of systematic structural changes to polymer architectures on the penetration and diffusion of functionalised nanomaterials through mucosal tissue have not been reported. We investigated the influence of poly(2-oxazoline) alkyl side chain length on nanoparticle diffusion; poly(2-methyl-2-oxazoline), poly(2-ethyl-2-oxazoline), and poly(2-n-propyl-2-oxazoline) were grafted onto the surface of thiolated silica nanoparticles and characterised by FT-IR, Raman and NMR spectroscopy, thermogravimetric analysis, and small angle neutron scattering. Diffusion coefficients were determined in water and in a mucin dispersion (using Nanoparticle Tracking Analysis), and penetration through a mucosal barrier was assessed using an ex vivo fluorescence technique. The addition of a single methylene group in the side chain significantly altered the penetration and diffusion of the materials in both mucin dispersions and mucosal tissue. Nanoparticles functionalised with poly(2-methyl-2-oxazoline) were significantly more diffusive than particles with poly(2-ethyl-2-oxazoline) while particles with poly(2-n-propyl-2-oxazoline) showed no significant increase compared to the unfunctionalised particles. These data show that variations in the polymer structure can radically alter their diffusive properties with clear implications for the future design of mucus penetrating systems.

  17. Theoretical predictions for side-chain liquid-crystal polymers and comparison to experiment

    International Nuclear Information System (INIS)

    Dowell, F.

    1988-01-01

    This paper presents results from a new unique microscopic molecular theory for side-chain liquid-crystalline polymers (LCPs) in the nematic (N) and multiple smectic-A (SA) LC phases and the isotropic (I) liquid phase. There are no ad hoc or arbitrarily adjustable parameters in this theory. The agreement between the theoretical and experimental values for various properties (including transition temperatures and quadratic characteristic radii) is very good (relative deviations between 0% and less than 6.2%). The theoretical results also show--for the first time--that the N and I phases for these LCPs involve the packing of plate-like sections of backbones and side chains and that the local bilayer SA phase involves packing of side-chains within a plate-like section. This type of packing is predicted to be typical for side-chain LCPs. This theory can predict--for the first time--whether the side chains of a molecule pack on the same or alternating opposite sides of the backbone and whether side chains on different molecules interdigitate (overlap) with each other. 13 refs., 1 fig., 4 tabs

  18. Studies on the Model Synthesis of the Brassinolide and Dolicholide Side Chains

    Institute of Scientific and Technical Information of China (English)

    Li Zeng PENG; Feng Zhi ZHANG; Tian Sheng MEI; Yu Lin LI

    2003-01-01

    A stereoselective synthesis of brassinolide and dolicholide, which involves constructionof the side chain enantiomers by a highly stereoselective aldol reaction of aldehyde 5 with theanion of α-silyloxy ketone 6 is described.

  19. Effect of side chain length on the stability and structural properties of 3

    African Journals Online (AJOL)

    thiophene (DOOPT) and their dimers studied by Hartree-Fock (HF) and Density Functional Theory (DFT) methods. The DFT calculations suggest that dimers of the dialkoxyphenylthiophenes with longer side chains are thermodynamically more ...

  20. Cylindrical polymer brushes with dendritic side chains by iterative anionic reactions

    KAUST Repository

    Zhang, Hefeng; Qu, Chengke; He, Junpo

    2015-01-01

    We report in this paper an easy method for the synthesis of cylindrical polymer brushes with dendritic side chains through anionic reaction. The synthesis is accomplished by iteratively grafting a living block copolymer, polyisoprene-. b

  1. From Labdanes to Drimanes. Degradation of the Side Chain of Dihydrozamoranic Acid.

    Directory of Open Access Journals (Sweden)

    Pedro M. Rocha

    2004-04-01

    Full Text Available A new route for the degradation of the saturated side chain of dihydrozamoranic acid has been devised, giving an advanced intermediate, compound 14, useful for the synthesis of insect antifeedants such as warburganal and polygodial.

  2. From labdanes to drimanes. Degradation of the side chain of dihydrozamoranic acid.

    Science.gov (United States)

    Rodilla, Jesús M L; Díez, D; Urones, J G; Rocha, Pedro M

    2004-04-30

    A new route for the degradation of the saturated side chain of dihydrozamoranic acid has been devised, giving an advanced intermediate, compound 14, useful for the synthesis of insect antifeedants such as warburganal and polygodial.

  3. Synthesis and solution self-assembly of side-chain cobaltocenium-containing block copolymers.

    Science.gov (United States)

    Ren, Lixia; Hardy, Christopher G; Tang, Chuanbing

    2010-07-07

    The synthesis of side-chain cobaltocenium-containing block copolymers and their self-assembly in solution was studied. Highly pure monocarboxycobaltocenium was prepared and subsequently attached to side chains of poly(tert-butyl acrylate)-block-poly(2-hydroxyethyl acrylate), yielding poly(tert-butyl acrylate)-block-poly(2-acryloyloxyethyl cobaltoceniumcarboxylate). The cobaltocenium block copolymers exhibited vesicle morphology in the mixture of acetone and water, while micelles of nanotubes were formed in the mixture of acetone and chloroform.

  4. Synthesis and antimalarial activity of new chloroquine analogues carrying a multifunctional linear side chain

    OpenAIRE

    Iwaniuk, Daniel P.; Whetmore, Eric D.; Rosa, Nicholas; Ekoue-Kovi, Kekeli; Alumasa, John; de Dios, Angel C.; Roepe, Paul D.; Wolf, Christian

    2009-01-01

    We report the synthesis and in vitro antimalarial activity of several new 4-amino-and 4-alkoxy-7-chloroquinolines carrying a linear dibasic side chain. Many of these chloroquine analogues have submicromolar antimalarial activity versus HB3 (chloroquine sensitive) and Dd2 (chloroquine resistant strain of P. falciparum) and low resistance indices were obtained in most cases. Importantly, compounds 11–15 and 24 proved to be more potent against Dd2 than chloroquine. Branching of the side chain st...

  5. Off-resonance rotating-frame relaxation dispersion experiment for 13C in aromatic side chains using L-optimized TROSY-selection

    DEFF Research Database (Denmark)

    Weininger, Ulrich; Brath, Ulrika; Modig, Kristofer

    2014-01-01

    Protein dynamics on the microsecond-millisecond time scales often play a critical role in biological function. NMR relaxation dispersion experiments are powerful approaches for investigating biologically relevant dynamics with site-specific resolution, as shown by a growing number of publications...... on enzyme catalysis, protein folding, ligand binding, and allostery. To date, the majority of studies has probed the backbone amides or side-chain methyl groups, while experiments targeting other sites have been used more sparingly. Aromatic side chains are useful probes of protein dynamics, because...... they are over-represented in protein binding interfaces, have important catalytic roles in enzymes, and form a sizable part of the protein interior. Here we present an off-resonance R 1ρ experiment for measuring microsecond to millisecond conformational exchange of aromatic side chains in selectively (13)C...

  6. Methanol to olefin Conversion on HSAPO-34 zeolite from periodic density functional theory calculations: a complete cycle of side chain hydrocarbon pool mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Wang, C.M.; Wang, Y.D.; Xie, Z.K.; Liu, Z.P. [SINOPEC, Shanghai (China)

    2009-03-15

    For its unique position in the coal chemical industry, the methanol to olefin (MTO) reaction has been a hot topic in zeolite catalysis. Due to the complexities of catalyst structure and reaction networks, many questions such as how the olefin chain is built from methanol remain elusive. On the basis of periodic density functional theory calculations, this work establishes the first complete catalytic cycle for MTO reaction via hexamethylbenzene (HMB) trapped in HSAPO-34 zeolite based on the so-called side chain hydrocarbon pool mechanism. The cycle starts from the methylation of HMB that leads to heptamethylbenzenium ion (heptaMB{sup +}) intermediate. This is then followed by the growth of side chain via repeated deprotonation of benzenium ions and methylation of the exocyclic double bond. Ethene and propene can finally be released from the side ethyl and isopropyl groups of benzenium ions by deprotonation and subsequent protonation steps. We demonstrate that (i) HMB/HSAPO-34 only yields propene as the primary product based on the side chain hydrocarbon pool mechanism and (ii) an indirect proton-shift step mediated by water that is always available in the system is energetically more favorable than the traditionally regarded internal hydrogen-shift step. Finally, the implications of our results toward understanding the effect of acidity of zeolite on MTO activity are also discussed.

  7. Structural characterization of saturated branched chain fatty acid methyl esters by collisional dissociation of molecular ions generated by electron ionization.

    Science.gov (United States)

    Ran-Ressler, Rinat R; Lawrence, Peter; Brenna, J Thomas

    2012-01-01

    Saturated branched chain fatty acids (BCFA) are present as complex mixtures in numerous biological samples. The traditional method for structure elucidation, electron ionization (EI) mass spectrometry, sometimes does not unambiguously enable assignment of branching in isomeric BCFA. Zirrolli and Murphy (Zirrolli , J. A. , and R. A. Murphy. 1993. Low-energy tandem mass spectrometry of the molecular ion derived from fatty acid methyl esters: a novel method for analysis of branched-chain fatty acids. J. Am. Soc. Mass Spectrom. 4: 223-229.) showed that the molecular ions of four BCFA methyl ester (BCFAME) yield highly characteristic fragments upon collisional dissociation using a triple quadrupole instrument. Here, we confirm and extend these results by analysis using a tabletop 3-D ion trap for activated molecular ion EI-MS/MS to 30 BCFAME. iso-BCFAME produces a prominent ion (30-100% of base peak) for [M-43] (M-C₃H₇), corresponding to the terminal isopropyl moiety in the original iso-BCFAME. Anteiso-FAME yield prominent ions (20-100% of base peak) corresponding to losses on both side of the methyl branch, [M-29] and [M-57], and tend to produce more prominent m/z 115 peaks corresponding to a cyclization product around the ester. Dimethyl and tetramethyl FAME, with branches separated by at least one methylene group, yield fragment on both sides of the sites of methyl branches that are more than 6 C away from the carboxyl carbon. EI-MS/MS yields uniquely specific ions that enable highly confident structural identification and quantification of BCFAME.

  8. Linear rheology and structure of molecular bottlebrushes with short side chains

    International Nuclear Information System (INIS)

    López-Barrón, Carlos R.; Brant, Patrick; Crowther, Donna J.; Eberle, Aaron P. R.

    2015-01-01

    We investigate the microstructure and linear viscoelasticity of model molecular bottlebrushes (BBs) using rheological and small-angle X-ray and neutron scattering measurements. Our polymers have short atactic polypropylene (aPP) side chains of molecular weight ranging from 119 g/mol to 259 g/mol and narrow molecular weight distribution (M w /M n 1.02–1.05). The side chain molecular weights are a small fraction of the entanglement molecular weight of the corresponding linear polymer (M e,aPP = 7.05 kg/mol), and as such, they are unentangled. The morphology of the aPP BBs is characterized as semiflexible thick chains with small side chain interdigitation. Their dynamic master curves, obtained by time-temperature superposition, reveal two sequential relaxation processes corresponding to the segmental relaxation and the relaxation of the BB backbone. Due to the short length of the side chains, their fast relaxation could not be distinguished from the glassy relaxation. The fractional free volume is an increasing function of the side chain length (N SC ). Therefore, the glassy behavior of these polymers as well as their molecular friction and dynamic properties are influenced by their N SC values. The apparent flow activation energies are a decreasing function of N SC , and their values explain the differences in zero-shear viscosity measured at different temperatures

  9. Exploring the impact of the side-chain length on peptide/RNA binding events.

    Science.gov (United States)

    Sbicca, Lola; González, Alejandro López; Gresika, Alexandra; Di Giorgio, Audrey; Closa, Jordi Teixido; Tejedor, Roger Estrada; Andréola, Marie-Line; Azoulay, Stéphane; Patino, Nadia

    2017-07-19

    The impact of the amino-acid side-chain length on peptide-RNA binding events has been investigated using HIV-1 Tat derived peptides as ligands and the HIV-1 TAR RNA element as an RNA model. Our studies demonstrate that increasing the length of all peptide side-chains improves unexpectedly the binding affinity (K D ) but reduces the degree of compactness of the peptide-RNA complex. Overall, the side-chain length appears to modulate in an unpredictable way the ability of the peptide to compete with the cognate TAR RNA partner. Beyond the establishment of non-intuitive fundamental relationships, our results open up new perspectives in the design of effective RNA ligand competitors, since a large number of them have already been identified but few studies report on the modulation of the biological activity by modifying in the same way the length of all chains connecting RNA recognition motives to the central scaffold of a ligand.

  10. Conformational exchange of aromatic side chains characterized by L-optimized TROSY-selected ¹³C CPMG relaxation dispersion.

    Science.gov (United States)

    Weininger, Ulrich; Respondek, Michal; Akke, Mikael

    2012-09-01

    Protein dynamics on the millisecond time scale commonly reflect conformational transitions between distinct functional states. NMR relaxation dispersion experiments have provided important insights into biologically relevant dynamics with site-specific resolution, primarily targeting the protein backbone and methyl-bearing side chains. Aromatic side chains represent attractive probes of protein dynamics because they are over-represented in protein binding interfaces, play critical roles in enzyme catalysis, and form an important part of the core. Here we introduce a method to characterize millisecond conformational exchange of aromatic side chains in selectively (13)C labeled proteins by means of longitudinal- and transverse-relaxation optimized CPMG relaxation dispersion. By monitoring (13)C relaxation in a spin-state selective manner, significant sensitivity enhancement can be achieved in terms of both signal intensity and the relative exchange contribution to transverse relaxation. Further signal enhancement results from optimizing the longitudinal relaxation recovery of the covalently attached (1)H spins. We validated the L-TROSY-CPMG experiment by measuring fast folding-unfolding kinetics of the small protein CspB under native conditions. The determined unfolding rate matches perfectly with previous results from stopped-flow kinetics. The CPMG-derived chemical shift differences between the folded and unfolded states are in excellent agreement with those obtained by urea-dependent chemical shift analysis. The present method enables characterization of conformational exchange involving aromatic side chains and should serve as a valuable complement to methods developed for other types of protein side chains.

  11. Sparse networks of directly coupled, polymorphic, and functional side chains in allosteric proteins.

    Science.gov (United States)

    Soltan Ghoraie, Laleh; Burkowski, Forbes; Zhu, Mu

    2015-03-01

    Recent studies have highlighted the role of coupled side-chain fluctuations alone in the allosteric behavior of proteins. Moreover, examination of X-ray crystallography data has recently revealed new information about the prevalence of alternate side-chain conformations (conformational polymorphism), and attempts have been made to uncover the hidden alternate conformations from X-ray data. Hence, new computational approaches are required that consider the polymorphic nature of the side chains, and incorporate the effects of this phenomenon in the study of information transmission and functional interactions of residues in a molecule. These studies can provide a more accurate understanding of the allosteric behavior. In this article, we first present a novel approach to generate an ensemble of conformations and an efficient computational method to extract direct couplings of side chains in allosteric proteins, and provide sparse network representations of the couplings. We take the side-chain conformational polymorphism into account, and show that by studying the intrinsic dynamics of an inactive structure, we are able to construct a network of functionally crucial residues. Second, we show that the proposed method is capable of providing a magnified view of the coupled and conformationally polymorphic residues. This model reveals couplings between the alternate conformations of a coupled residue pair. To the best of our knowledge, this is the first computational method for extracting networks of side chains' alternate conformations. Such networks help in providing a detailed image of side-chain dynamics in functionally important and conformationally polymorphic sites, such as binding and/or allosteric sites. © 2014 Wiley Periodicals, Inc.

  12. PMMA-g-OEtOx Graft Copolymers: Influence of Grafting Degree and Side Chain Length on the Conformation in Aqueous Solution

    Directory of Open Access Journals (Sweden)

    Irina Muljajew

    2018-03-01

    Full Text Available Depending on the degree of grafting (DG and the side chain degree of polymerization (DP, graft copolymers may feature properties similar to statistical copolymers or to block copolymers. This issue is approached by studying aqueous solutions of PMMA-g-OEtOx graft copolymers comprising a hydrophobic poly(methyl methacrylate (PMMA backbone and hydrophilic oligo(2-ethyl-2-oxazoline (OEtOx side chains. The graft copolymers were synthesized via reversible addition-fragmentation chain transfer (RAFT copolymerization of methyl methacrylate (MMA and OEtOx-methacrylate macromonomers of varying DP. All aqueous solutions of PMMA-g-OEtOx (9% ≤ DG ≤ 34%; 5 ≤ side chain DP ≤ 24 revealed lower critical solution temperature behavior. The graft copolymer architecture significantly influenced the aggregation behavior, the conformation in aqueous solution and the coil to globule transition, as verified by means of turbidimetry, dynamic light scattering, nuclear magnetic resonance spectroscopy, and analytical ultracentrifugation. The aggregation behavior of graft copolymers with a side chain DP of 5 was significantly affected by small variations of the DG, occasionally forming mesoglobules above the cloud point temperature (Tcp, which was around human body temperature. On the other hand, PMMA-g-OEtOx with elongated side chains assembled into well-defined structures below the Tcp (apparent aggregation number (Nagg = 10 that were able to solubilize Disperse Orange 3. The thermoresponsive behavior of aqueous solutions thus resembled that of micelles comprising a poly(2-ethyl-2-oxazoline (PEtOx shell (Tcp > 60 °C.

  13. An in-situ FTIR study of the side-chain alkylation of toluene with methanol

    International Nuclear Information System (INIS)

    King, S.T.; Garces, J.

    1985-01-01

    The side-chain alkylation of toluene with methanol to styrene and ethylbenzene can be an economically attractive industrial process if it has high enough conversion and selectivity. This process has been investigated by many others using zeolites or metal oxides as the catalyst. It has been generally accepted that high basicity in certain size pores in the catalyst is required for such side-chain alkylation. However, the actual reaction mechanism is still not understood. In this paper the results of an in-situ FT-IR study of the side-chain alkylation in Li, Na, K, Rb and Cs exchanged X zeolites is discussed. It was found that the KX, RbX and CsX zeolites, which are capable of side-chain alkylation, also form surface formate and a surface precursor of formate from methanol decomposition. While the surface formate itself is not the alkylation agent, the observed formate precursor may be the intermediate for side-chain alkylation

  14. Can understanding the packing of side chains improve the design of protein-protein interactions?

    Science.gov (United States)

    Zhou, Alice; O'Hern, Corey; Regan, Lynne

    2011-03-01

    With the long-term goal to improve the design of protein-protein interactions, we have begun extensive computational studies to understand how side-chains of key residues of binding partners geometrically fit together at protein-peptide interfaces, e.g. the tetratrico-peptide repeat protein and its cognate peptide). We describe simple atomic-scale models of hydrophobic dipeptides, which include hard-core repulsion, bond length and angle constraints, and Van der Waals attraction. By completely enumerating all minimal energy structures in these systems, we are able to reproduce important features of the probability distributions of side chain dihedral angles of hydrophic residues in the protein data bank. These results are the crucial first step in developing computational models that can predict the side chain conformations of residues at protein-peptide interfaces. CSO acknowledges support from NSF grant no. CMMT-1006527.

  15. Record high hole mobility in polymer semiconductors via side-chain engineering.

    Science.gov (United States)

    Kang, Il; Yun, Hui-Jun; Chung, Dae Sung; Kwon, Soon-Ki; Kim, Yun-Hi

    2013-10-09

    Charge carrier mobility is still the most challenging issue that should be overcome to realize everyday organic electronics in the near future. In this Communication, we show that introducing smart side-chain engineering to polymer semiconductors can facilitate intermolecular electronic communication. Two new polymers, P-29-DPPDBTE and P-29-DPPDTSE, which consist of a highly conductive diketopyrrolopyrrole backbone and an extended branching-position-adjusted side chain, showed unprecedented record high hole mobility of 12 cm(2)/(V·s). From photophysical and structural studies, we found that moving the branching position of the side chain away from the backbone of these polymers resulted in increased intermolecular interactions with extremely short π-π stacking distances, without compromising solubility of the polymers. As a result, high hole mobility could be achieved even in devices fabricated using the polymers at room temperature.

  16. Asymmetric functional contributions of acidic and aromatic side chains in sodium channel voltage-sensor domains

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Elstone, Fisal D; Niciforovic, Ana P

    2014-01-01

    largely enigmatic. To this end, natural and unnatural side chain substitutions were made in the S2 hydrophobic core (HC), the extracellular negative charge cluster (ENC), and the intracellular negative charge cluster (INC) of the four VSDs of the skeletal muscle sodium channel isoform (NaV1......Voltage-gated sodium (NaV) channels mediate electrical excitability in animals. Despite strong sequence conservation among the voltage-sensor domains (VSDs) of closely related voltage-gated potassium (KV) and NaV channels, the functional contributions of individual side chains in Nav VSDs remain.......4). The results show that the highly conserved aromatic side chain constituting the S2 HC makes distinct functional contributions in each of the four NaV domains. No obvious cation-pi interaction exists with nearby S4 charges in any domain, and natural and unnatural mutations at these aromatic sites produce...

  17. Incorporation of basic side chains into cryptolepine scaffold: structure-antimalarial activity relationships and mechanistic studies.

    Science.gov (United States)

    Lavrado, João; Cabal, Ghislain G; Prudêncio, Miguel; Mota, Maria M; Gut, Jiri; Rosenthal, Philip J; Díaz, Cecília; Guedes, Rita C; dos Santos, Daniel J V A; Bichenkova, Elena; Douglas, Kenneth T; Moreira, Rui; Paulo, Alexandra

    2011-02-10

    The synthesis of cryptolepine derivatives containing basic side-chains at the C-11 position and their evaluations for antiplasmodial and cytotoxicity properties are reported. Propyl, butyl, and cycloalkyl diamine side chains significantly increased activity against chloroquine-resistant Plasmodium falciparum strains while reducing cytotoxicity when compared with the parent compound. Localization studies inside parasite blood stages by fluorescence microscopy showed that these derivatives accumulate inside the nucleus, indicating that the incorporation of a basic side chain is not sufficient enough to promote selective accumulation in the acidic digestive vacuole of the parasite. Most of the compounds within this series showed the ability to bind to a double-stranded DNA duplex as well to monomeric hematin, suggesting that these are possible targets associated with the observed antimalarial activity. Overall, these novel cryptolepine analogues with substantially improved antiplasmodial activity and selectivity index provide a promising starting point for development of potent and highly selective agents against drug-resistant malaria parasites.

  18. Bis(thienothiophenyl) diketopyrrolopyrrole-based conjugated polymers with various branched alkyl side chains and their applications in thin-film transistors and polymer solar cells.

    Science.gov (United States)

    Shin, Jicheol; Park, Gi Eun; Lee, Dae Hee; Um, Hyun Ah; Lee, Tae Wan; Cho, Min Ju; Choi, Dong Hoon

    2015-02-11

    New thienothiophene-flanked diketopyrrolopyrrole and thiophene-containing π-extended conjugated polymers with various branched alkyl side-chains were successfully synthesized. 2-Octyldodecyl, 2-decyltetradecyl, 2-tetradecylhexadecyl, 2-hexadecyloctadecyl, and 2-octadecyldocosyl groups were selected as the side-chain moieties and were anchored to the N-positions of the thienothiophene-flanked diketopyrrolopyrrole unit. All five polymers were found to be soluble owing to the bulkiness of the side chains. The thin-film transistor based on the 2-tetradecylhexadecyl-substituted polymer showed the highest hole mobility of 1.92 cm2 V(-1) s(-1) due to it having the smallest π-π stacking distance between the polymer chains, which was determined by grazing incidence X-ray diffraction. Bulk heterojunction polymer solar cells incorporating [6,6]-phenyl-C71-butyric acid methyl ester as the n-type molecule and the additive 1,8-diiodooctane (1 vol %) were also constructed from the synthesized polymers without thermal annealing; the device containing the 2-octyldodecyl-substituted polymer exhibited the highest power conversion efficiency of 5.8%. Although all the polymers showed similar physical properties, their device performance was clearly influenced by the sizes of the branched alkyl side-chain groups.

  19. Histidine side-chain dynamics and protonation monitored by C-13 CPMG NMR relaxation dispersion

    DEFF Research Database (Denmark)

    Hass, M. A. S.; Yilmaz, A.; Christensen, Hans Erik Mølager

    2009-01-01

    the chemical shift titration experiments, and the CPMG derived exchange rates agree with those obtained previously from N-15 backbone relaxation measurements. Compared to measurements of backbone nuclei, C-13(epsilon 1) dispersion provides a more direct method to monitor interchanging protonation states...... or other kinds of conformational changes of histidine side chains or their environment. Advantages and shortcomings of using the C-13(epsilon 1) dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains...

  20. Synthesis and antimalarial activity of new chloroquine analogues carrying a multifunctional linear side chain.

    Science.gov (United States)

    Iwaniuk, Daniel P; Whetmore, Eric D; Rosa, Nicholas; Ekoue-Kovi, Kekeli; Alumasa, John; de Dios, Angel C; Roepe, Paul D; Wolf, Christian

    2009-09-15

    We report the synthesis and in vitro antimalarial activity of several new 4-amino- and 4-alkoxy-7-chloroquinolines carrying a linear dibasic side chain. Many of these chloroquine analogues have submicromolar antimalarial activity versus HB3 (chloroquine sensitive) and Dd2 (chloroquine resistant strain of Plasmodium falciparum) and low resistance indices were obtained in most cases. Importantly, compounds 11-15 and 24 proved to be more potent against Dd2 than chloroquine. Branching of the side chain structure proved detrimental to the activity against the CQR strain.

  1. Exploring backbone-cation alkyl spacers for multi-cation side chain anion exchange membranes

    Science.gov (United States)

    Zhu, Liang; Yu, Xuedi; Hickner, Michael A.

    2018-01-01

    In order to systematically study how the arrangement of cations on the side chain and length of alkyl spacers between cations impact the performance of multi-cation AEMs for alkaline fuel cells, a series of polyphenylene oxide (PPO)-based AEMs with different cationic side chains were synthesized. This work resulted in samples with two or three cations in a side chain pendant to the PPO backbone. More importantly, the length of the spacer between cations varied from 3 methylene (-CH2-) (C3) groups to 8 methylene (C8) groups. The highest conductivity, up to 99 mS/cm in liquid water at room temperature, was observed for the triple-cation side chain AEM with pentyl (C5) or hexyl (C6) spacers. The multi-cation AEMs were found to have decreased water uptake and ionic conductivity when the spacer chains between cations were lengthened from pentyl (C5) or hexyl (C6) to octyl (C8) linking groups. The triple-cation membranes with pentyl (C5) or hexyl (C6) groups between cations showed greatest stability after immersion in 1 M NaOH at 80 °C for 500 h.

  2. Synthesis of porphyryl boronates with (un)saturated side-chains

    OpenAIRE

    SENGE, MATHIAS; SERGEEVA, NATALIA

    2008-01-01

    PUBLISHED Porphyrins with (un)saturated side?chains containing boron residues were developed as synthons for porphyrin functionalization. Porphyrins with mono and bis-substituted unsaturated boronyl residues were prepared in good yields (52?66 %) using a cross?metathesis approach in the presence of Grubbs I-generation catalysts. In all cases complete E?stereoselectivity (100 %) was observed. Furthermore, formal cross?metathesis products with ?,??unsaturated chains smoothly underwent additi...

  3. Pressure dependence of side chain 13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

    Science.gov (United States)

    Beck Erlach, Markus; Koehler, Joerg; Crusca, Edson; Munte, Claudia E; Kainosho, Masatsune; Kremer, Werner; Kalbitzer, Hans Robert

    2017-10-01

    For evaluating the pressure responses of folded as well as intrinsically unfolded proteins detectable by NMR spectroscopy the availability of data from well-defined model systems is indispensable. In this work we report the pressure dependence of 13 C chemical shifts of the side chain atoms in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH 2 (Xxx, one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of a number of nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The size of the polynomial pressure coefficients B 1 and B 2 is dependent on the type of atom and amino acid studied. For H N , N and C α the first order pressure coefficient B 1 is also correlated to the chemical shift at atmospheric pressure. The first and second order pressure coefficients of a given type of carbon atom show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure also are weakly correlated. The downfield shifts of the methyl resonances suggest that gauche conformers of the side chains are not preferred with pressure. The valine and leucine methyl groups in the model peptides were assigned using stereospecifically 13 C enriched amino acids with the pro-R carbons downfield shifted relative to the pro-S carbons.

  4. side chains

    African Journals Online (AJOL)

    USER

    The effect of ionic exchange degree of aluminated mesoporous materials H(X)- ... zeolites catalysts in cumene conversion and observed distinct differences in the ... with HCl acid solution with varied concentration going from 0.01 N to 0.5 N by .... 14. 16. 18. 20. Number of pulse. Cu m en e co n v ersio n. (%. ) 673. 673. 623.

  5. side chains

    African Journals Online (AJOL)

    USER

    Metropolis Monte Carlo (MC) simulations using only ion-water pair ... the subjects of numerous experimental [42] and theoretical investigations. .... The probability of finding the O-Fe(III)-O angle (θ) in the first hydration shell, the first-shell.

  6. Simulation study of the initial crystallization processes of poly(3-hexylthiophene) in solution: ordering dynamics of main chains and side chains.

    Science.gov (United States)

    Takizawa, Yuumi; Shimomura, Takeshi; Miura, Toshiaki

    2013-05-23

    We study the initial nucleation dynamics of poly(3-hexylthiophene) (P3HT) in solution, focusing on the relationship between the ordering process of main chains and that of side chains. We carried out Langevin dynamics simulation and found that the initial nucleation processes consist of three steps: the ordering of ring orientation, the ordering of main-chain vectors, and the ordering of side chains. At the start, the normal vectors of thiophene rings aligned in a very short time, followed by alignment of main-chain end-to-end vectors. The flexible side-chain ordering took almost 5 times longer than the rigid-main-chain ordering. The simulation results indicated that the ordering of side chains was induced after the formation of the regular stack structure of main chains. This slow ordering dynamics of flexible side chains is one of the factors that cause anisotropic nuclei growth, which would be closely related to the formation of nanofiber structures without external flow field. Our simulation results revealed how the combined structure of the planar and rigid-main-chain backbones and the sparse flexible side chains lead to specific ordering behaviors that are not observed in ordinary linear polymer crystallization processes.

  7. Arabidopsis GUX Proteins Are Glucuronyltransferases Responsible for the Addition of Glucuronic Acid Side Chains onto Xylan

    Science.gov (United States)

    Xylan, the second most abundant cell wall polysaccharide, is composed of a linear backbone of β-(1,4)-linked xylosyl residues that are often substituted with sugar side chains, such as glucuronic acid (GlcA) and methylglucuronic acid (MeGlcA). It has recently been shown that muta...

  8. Synthesis of β-1,4-Linked Galactan Side-Chains of Rhamnogalacturonan I

    DEFF Research Database (Denmark)

    Andersen, Mathias Christian Franch; Kracun, Stjepan; Rydahl, Maja

    2016-01-01

    The synthesis of linear- and (1→6)-branched-β-(1→4)-D-galactans, side chains of the pectic polysaccharide rhamnogalacturonan I is described. The strategy relies on iterative couplings of n-pentenyl disaccharides followed by a late stage glycosylation of a common hexasaccharide core. Reaction...

  9. Side-chain degradation of ultrapure π-conjugated oligomers: implications for organic electronics

    NARCIS (Netherlands)

    Abbel, R.J.; Wolffs, M.; Bovee, R.A.A.; Dongen, van J.L.J.; Lou, X.W.; Henze, O.; Feast, W.J.; Meijer, E.W.; Schenning, A.P.H.J.

    2009-01-01

    The degrdn. of two defect-free pi-conjugated oligomers and the participation of their solubilizing side chains in the process are studied in unprecedented detail. The detected intermediate products reveal a mechanism of successive shortening of alkyl and oligo(ethylene glycol) substituents.

  10. Novel biphotonic holographic storage in a side-chain liquid crystalline polyester

    DEFF Research Database (Denmark)

    Ramanujam, P.S.; Hvilsted, S.; Andruzzi, F.

    1993-01-01

    We report novel biphotonic holographic storage of text and gratings on unoriented films of a side-chain liquid crystalline polyester capable of high density storage and complete erasure. The holograms have a typical size of 1 mm. The recording utilizes unusual photochemistry involving azo dye...

  11. Light-induced circular birefringence in cyanoazobenzene side-chain liquid-crystalline polyester films

    DEFF Research Database (Denmark)

    Naydenova, I; Nikolova, L; Ramanujam, P.S.

    1999-01-01

    We report the inducement of large circular birefringence (optical activity) in films of a cyanoazobenzene side-chain liquid-crystalline polyester on illumination with circularly polarized light. The polyester has no chiral groups and is initially isotropic. The induced optical rotation is up to 5...

  12. Liquid-crystalline side chain block copolymers - synthesis, morphology and LC behavior

    NARCIS (Netherlands)

    Arnold, M.; Poser, S.; Fischer, H.R.; Frank, W.; Utschick, H.

    1994-01-01

    Side-chain liq.-cryst. 2-hydroxyethyl methacrylate-styrene diblock copolymer (I) was prepd. by polymn. of 2-(trimethylsiloxy)ethyl methacrylate with styrene with further treatment with cholesteryl chloroformate. Morphol. and phase behavior of I were investigated. [on SciFinder (R)

  13. Influence of structures of polymer backbones on cooperative photoreorientation behavior of p-cyanoazobenzene side chains

    DEFF Research Database (Denmark)

    Han, Mina; Kidowaki, Masatoshi; Ichimura, Kunihiro

    2001-01-01

    Photoinduced orientational behavior of a polymethacrylate (CN6) and a polyester (p6a12) with p-cyanoazobenzene side chains was studied to reveal the structural effect of the liquid crystalline polymer backbones. Irradiation with linearly polarized W light resulted in the reorientation of the azob...

  14. New approaches towards the synthesis of the side-chain of mycolactones A and B

    NARCIS (Netherlands)

    van Summeren, RP; Feringa, BL; Minnaard, AJ; Summeren, Ruben P. van

    2005-01-01

    New approaches towards the synthesis of the C1' - C16' side-chain of mycolactones A and B from Mycobacterium ulcerans are reported. Chiral building block 4 ( Fig. 2) with the correct stereochemistry was obtained starting from naturally occurring monosaccharides, i.e. D-glucose or L-rhamnose. The

  15. Dependence of crystallite formation and preferential backbone orientations on the side chain pattern in PBDTTPD polymers

    KAUST Repository

    El Labban, Abdulrahman; Warnan, Julien; Cabanetos, Clement; Ratel, Olivier; Tassone, Christopher J.; Toney, Michael F.; Beaujuge, Pierre

    2014-01-01

    -effect transistors (FETs) and bulk-heterojunction (BHJ) solar cells. Beyond film-forming properties, recent work has emphasized the determining role that side-chain substituents play on polymer self-assembly and thin-film nanostructural order, and, in turn, on device

  16. Conjugation of diisocyanate side chains to dimethacrylate reduces polymerization shrinkage and increases the hardness of composite resins

    Directory of Open Access Journals (Sweden)

    Yih-Dean Jan

    2014-04-01

    Conclusion: Conjugation of diisocyanate side chains to dimethacrylate represents an effective means of reducing polymerization shrinkage and increasing the surface hardness of dental composite resins.

  17. Arginine side chain interactions and the role of arginine as a gating charge carrier in voltage sensitive ion channels

    Science.gov (United States)

    Armstrong, Craig T.; Mason, Philip E.; Anderson, J. L. Ross; Dempsey, Christopher E.

    2016-02-01

    Gating charges in voltage-sensing domains (VSD) of voltage-sensitive ion channels and enzymes are carried on arginine side chains rather than lysine. This arginine preference may result from the unique hydration properties of the side chain guanidinium group which facilitates its movement through a hydrophobic plug that seals the center of the VSD, as suggested by molecular dynamics simulations. To test for side chain interactions implicit in this model we inspected interactions of the side chains of arginine and lysine with each of the 19 non-glycine amino acids in proteins in the protein data bank. The arginine guanidinium interacts with non-polar aromatic and aliphatic side chains above and below the guanidinium plane while hydrogen bonding with polar side chains is restricted to in-plane positions. In contrast, non-polar side chains interact largely with the aliphatic part of the lysine side chain. The hydration properties of arginine and lysine are strongly reflected in their respective interactions with non-polar and polar side chains as observed in protein structures and in molecular dynamics simulations, and likely underlie the preference for arginine as a mobile charge carrier in VSD.

  18. The Role of the Side Chain on the Performance of N-type Conjugated Polymers in Aqueous Electrolytes

    KAUST Repository

    Giovannitti, Alexander

    2018-04-24

    We report a design strategy that allows the preparation of solution processable n-type materials from low boiling point solvents for organic electrochemical transistors (OECTs). The polymer backbone is based on NDI-T2 copolymers where a branched alkyl side chain is gradually exchanged for a linear ethylene glycol-based side chain. A series of random copolymers was prepared with glycol side chain percentages of 0, 10, 25, 50, 75, 90, and 100 with respect to the alkyl side chains. These were characterized to study the influence of the polar side chains on interaction with aqueous electrolytes, their electrochemical redox reactions, and performance in OECTs when operated in aqueous electrolytes. We observed that glycol side chain percentages of >50% are required to achieve volumetric charging, while lower glycol chain percentages show a mixed operation with high required voltages to allow for bulk charging of the organic semiconductor. A strong dependence of the electron mobility on the fraction of glycol chains was found for copolymers based on NDI-T2, with a significant drop as alkyl side chains are replaced by glycol side chains.

  19. The Role of the Side Chain on the Performance of N-type Conjugated Polymers in Aqueous Electrolytes

    KAUST Repository

    Giovannitti, Alexander; Maria, Iuliana P.; Hanifi, David; Donahue, Mary J.; Bryant, Daniel; Barth, Katrina J.; Makdah, Beatrice E.; Savva, Achilleas; Moia, Davide; Zetek, Matyá š; Barnes, Piers R.F.; Reid, Obadiah G.; Inal, Sahika; Rumbles, Garry; Malliaras, George G.; Nelson, Jenny; Rivnay, Jonathan; McCulloch, Iain

    2018-01-01

    We report a design strategy that allows the preparation of solution processable n-type materials from low boiling point solvents for organic electrochemical transistors (OECTs). The polymer backbone is based on NDI-T2 copolymers where a branched alkyl side chain is gradually exchanged for a linear ethylene glycol-based side chain. A series of random copolymers was prepared with glycol side chain percentages of 0, 10, 25, 50, 75, 90, and 100 with respect to the alkyl side chains. These were characterized to study the influence of the polar side chains on interaction with aqueous electrolytes, their electrochemical redox reactions, and performance in OECTs when operated in aqueous electrolytes. We observed that glycol side chain percentages of >50% are required to achieve volumetric charging, while lower glycol chain percentages show a mixed operation with high required voltages to allow for bulk charging of the organic semiconductor. A strong dependence of the electron mobility on the fraction of glycol chains was found for copolymers based on NDI-T2, with a significant drop as alkyl side chains are replaced by glycol side chains.

  20. Nanophase separation in side chain polymers: new evidence from structure and dynamics

    International Nuclear Information System (INIS)

    Hiller, S; Pascui, O; Budde, H; Kabisch, O; Reichert, D; Beiner, M

    2004-01-01

    New evidence for a nanophase separation of incompatible main and side chain parts in amorphous poly(n-alkyl methacrylates) with long alkyl groups are presented. Independent indications for the existence of alkyl nanodomains with a typical dimension in the 1 nm range from studies on dynamics and structure are reported. Results from nuclear magnetic resonance (NMR) experiments are compared with data from different relaxation spectroscopy methods on poly(n-decyl methacrylate). The NMR results in combination with relaxation spectroscopy data support the existence of an independent polyethylene-like glass transition, α PE , within the alkyl nanodomains in addition to the conventional glass transition a at higher temperatures. X-ray scattering data show that the situation in homopolymers is similar to that for random poly(n-alkyl methacrylate) copolymers with the same average length of the alkyl group in the side chains. Scattering data for a series of n-butyl methacrylate samples with polymerization degrees reaching from P=1 to 405 indicate that nanophase separation is chain-length independent above P=25, while the nanophase separation tends to disappear below P=6. Insensitivity of structural aspects in nanophase-separated poly(n-alkyl methacrylates) to changes in the molecular microstructure and consistency of NMR results with independent conclusions from relaxation spectroscopy underline the general importance of nanophase separation effects in a broad class of side chain polymers

  1. Direct observation of backbone planarization via side-chain alignment in single bulky-substituted polythiophenes

    Science.gov (United States)

    Raithel, Dominic; Simine, Lena; Pickel, Sebastian; Schötz, Konstantin; Panzer, Fabian; Baderschneider, Sebastian; Schiefer, Daniel; Lohwasser, Ruth; Köhler, Jürgen; Thelakkat, Mukundan; Sommer, Michael; Köhler, Anna; Rossky, Peter J.; Hildner, Richard

    2018-03-01

    The backbone conformation of conjugated polymers affects, to a large extent, their optical and electronic properties. The usually flexible substituents provide solubility and influence the packing behavior of conjugated polymers in films or in bad solvents. However, the role of the side chains in determining and potentially controlling the backbone conformation, and thus the optical and electronic properties on the single polymer level, is currently under debate. Here, we investigate directly the impact of the side chains by studying the bulky-substituted poly(3-(2,5-dioctylphenyl)thiophene) (PDOPT) and the common poly(3-hexylthiophene) (P3HT), both with a defined molecular weight and high regioregularity, using low-temperature single-chain photoluminescence (PL) spectroscopy and quantum-classical simulations. Surprisingly, the optical transition energy of PDOPT is significantly (˜2,000 cm‑1 or 0.25 eV) red-shifted relative to P3HT despite a higher static and dynamic disorder in the former. We ascribe this red shift to a side-chain induced backbone planarization in PDOPT, supported by temperature-dependent ensemble PL spectroscopy. Our atomistic simulations reveal that the bulkier 2,5-dioctylphenyl side chains of PDOPT adopt a clear secondary helical structural motif and thus protect conjugation, i.e., enforce backbone planarity, whereas, for P3HT, this is not the case. These different degrees of planarity in both thiophenes do not result in different conjugation lengths, which we found to be similar. It is rather the stronger electronic coupling between the repeating units in the more planar PDOPT which gives rise to the observed spectral red shift as well as to a reduced calculated electron‑hole polarization.

  2. Abnormal viscoelastic behavior of side-chain liquid-crystal polymers

    Science.gov (United States)

    Gallani, J. L.; Hilliou, L.; Martinoty, P.; Keller, P.

    1994-03-01

    We show that, contrary to what is commonly believed, the isotropic phase of side-chain liquid-crystal polymers has viscoelastic properties which are totally different from those of ordinary flexible melt polymers. The results can be explained by the existence of a transient network created by the dynamic association of mesogenic groups belonging to different chains. The extremely high sensitivity of the compound to the state of the surfaces with which it is in contact offers us an unexpected method of studying surface states.

  3. Effect of side chain length on charge transport, morphology, and photovoltaic performance of conjugated polymers in bulk heterojunction solar cells

    NARCIS (Netherlands)

    Duan, C.; Willems, R.E.M.; van Franeker, J.J.; Bruijnaers, B.J.; Wienk, M.M.; Janssen, R.A.J.

    2016-01-01

    The effect of side chain length on the photovoltaic properties of conjugated polymers is systematically investigated with two sets of polymers that bear different alkyl side chain lengths based on benzodithiophene and benzo[2,1,3]thiadiazole or 5,6-difluorobenzo[2,1,3]thiadiazole. Characterization

  4. The Influence of Side-Chain Position on the Optoelectronic Properties of a Red-Emitting Conjugated Polymer

    NARCIS (Netherlands)

    Lu, Li Ping; Finlayson, Chris E.; Kabra, Dinesh; Albert-Seifried, Sebastian; Song, Myoung Hoon; Havenith, Remco W. A.; Tu, Guoli; Huck, Wilhelm T. S.; Friend, Richard H.

    2013-01-01

    A study of the organic semiconductor F8TBT is presented, directly comparing a conventional form (F8TBT-out) with a form with varied alkyl side-chain position (F8TBT-in), in terms of optical properties and device performance in light-emitting-diodes (LEDs). Computational simulations of the side-chain

  5. Molecular origin of urea driven hydrophobic polymer collapse and unfolding depending on side chain chemistry.

    Science.gov (United States)

    Nayar, Divya; Folberth, Angelina; van der Vegt, Nico F A

    2017-07-19

    Osmolytes affect hydrophobic collapse and protein folding equilibria. The underlying mechanisms are, however, not well understood. We report large-scale conformational sampling of two hydrophobic polymers with secondary and tertiary amide side chains using extensive molecular dynamics simulations. The calculated free energy of unfolding increases with urea for the secondary amide, yet decreases for the tertiary amide, in agreement with experiment. The underlying mechanism is rooted in opposing entropic driving forces: while urea screens the hydrophobic macromolecular interface and drives unfolding of the tertiary amide, urea's concomitant loss in configurational entropy drives collapse of the secondary amide. Only at sufficiently high urea concentrations bivalent urea hydrogen bonding interactions with the secondary amide lead to further stabilisation of its collapsed state. The observations provide a new angle on the interplay between side chain chemistry, urea hydrogen bonding, and the role of urea in attenuating or strengthening the hydrophobic effect.

  6. Correlation between protein secondary structure, backbone bond angles, and side-chain orientations

    Science.gov (United States)

    Lundgren, Martin; Niemi, Antti J.

    2012-08-01

    We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central Cα carbon of a protein backbone, and for this we develop new visualization techniques to analyze high-resolution x-ray structures in the Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse-grained energy function to describe the ensuing side-chain geometry in terms of the Cβ carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the Cα-Cβ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 Å in root-mean-square distance from the experimental x-ray structure.

  7. MgO encapsulated mesoporous zeolite for the side chain alkylation of toluene with methanol.

    Science.gov (United States)

    Jiang, Nanzhe; Jin, Hailian; Jeong, Eun-Young; Park, Sang-Eon

    2010-01-01

    Side chain alkylation of toluene with methanol was studied over mesoporous zeolite supported MgO catalysts. MgO were supported onto the carbon templated mesoporous silicalite-1 by direct synthesis route under microwave conditions. This direct synthesis route yields the majority of MgO highly dispersed into the mesopores of the silicalite-1 crystals. The vapor phase alkylation of toluene with methanol was performed over these catalysts under vapor phase conditions at atmospheric pressure. Mesoporous silicalite-1 supported MgO catalysts gave improved yields towards side chain alkylated products compared to the bulk MgO. The higher activity exhibited by 5% MgO supported on mesoporous silicalite compared to the one with 1% MgO can be attributed to the large number of weak basic sites observed from the CO2 TPD.

  8. Absolute rate constants for the reaction of hypochlorous acid with protein side chains and peptide bonds

    DEFF Research Database (Denmark)

    Pattison, D I; Davies, Michael Jonathan

    2001-01-01

    , absolute second-order rate constants for the reactions of HOCl with protein side chains, model compounds, and backbone amide (peptide) bonds have been determined at physiological pH values. The reactivity of HOCl with potential reactive sites in proteins is summarized by the series: Met (3.8 x 10(7) M(-1......Hypochlorous acid (HOCl) is a potent oxidant, which is produced in vivo by activated phagocytes. This compound is an important antibacterial agent, but excessive or misplaced production has been implicated in a number of human diseases, including atherosclerosis, arthritis, and some cancers....... Proteins are major targets for this oxidant, and such reaction results in side-chain modification, backbone fragmentation, and cross-linking. Despite a wealth of qualitative data for such reactions, little absolute kinetic data is available to rationalize the in vitro and in vivo data. In this study...

  9. Azobenzene side-chain liquid crystalline polyesters with outstanding optical storage properties

    DEFF Research Database (Denmark)

    Hvilsted, Søren; Pedersen, M; Holme, NCR

    1998-01-01

    A flexible azobenzene side-chain liquid crystalline (SCLC) polyester architecture employed for reversible optical storage is described. The modular design allows four structural parameters to be individually modified. These parameters: i- the methylene side-chain spacer length, ii- the substituent......,000 are routinely obtained by melt transesterification of the novel diols and selected diacid precursors (parameter iii). Prominent storage features include no prealignment of thin SCLC polyester films prior to the writing process, and sensitivity in a broad laser wavelength window (415-532 nm). Additionally...... sign of fatigue. The non-destructive read out is performed with red light (600-750 nm). Finally, erasing the information can be achieved by heating the polyester film to 80 degrees C or irradiating it briefly with UV-light. In the latter case at least 10,000 write, read and erase cycles are possible...

  10. Electron detachment of the hydrogen-bonded amino acid side-chain guanine complexes

    Science.gov (United States)

    Wang, Jing; Gu, Jiande; Leszczynski, Jerzy

    2007-07-01

    The photoelectron spectra of the hydrogen-bonded amino acid side-chain-guanine complexes has been studied at the partial third order (P3) self-energy approximation of the electron propagator theory. The correlation between the vertical electron detachment energy and the charge distributions on the guanine moiety reveals that the vertical electron detachment energy (VDE) increases as the positive charge distribution on the guanine increases. The low VDE values determined for the negatively charged complexes of the guanine-side-chain-group of Asp/Glu suggest that the influence of the H-bonded anionic groups on the VDE of guanine could be more important than that of the anionic backbone structure. The even lower vertical electron detachment energy for guanine is thus can be expected in the H-bonded protein-DNA systems.

  11. Optimization of the alkyl side chain length of fluorine-18-labeled 7α-alkyl-fluoroestradiol

    International Nuclear Information System (INIS)

    Okamoto, Mayumi; Shibayama, Hiromitsu; Naka, Kyosuke; Kitagawa, Yuya; Ishiwata, Kiichi; Shimizu, Isao; Toyohara, Jun

    2016-01-01

    Introduction: Several lines of evidence suggest that 7α-substituted estradiol derivatives bind to the estrogen receptor (ER). In line with this hypothesis, we designed and synthesized 18 F-labeled 7α-fluoroalkylestradiol (Cn-7α-[ 18 F]FES) derivatives as molecular probes for visualizing ERs. Previously, we successfully synthesized 7α-(3-[ 18 F]fluoropropyl)estradiol (C3-7α-[ 18 F]FES) and showed promising results for quantification of ER density in vivo, although extensive metabolism was observed in rodents. Therefore, optimization of the alkyl side chain length is needed to obtain suitable radioligands based on Cn-7α-substituted estradiol pharmacophores. Methods: We synthesized fluoromethyl (23; C1-7α-[ 18 F]FES) to fluorohexyl (26; C6-7α-[ 18 F]FES) derivatives, except fluoropropyl (C3-7α-[ 18 F]FES) and fluoropentyl derivatives (C5-7α-[ 18 F]FES), which have been previously synthesized. In vitro binding to the α-subtype (ERα) isoform of ERs and in vivo biodistribution studies in mature female mice were carried out. Results: The in vitro IC 50 value of Cn-7α-FES tended to gradually decrease depending on the alkyl side chain length. C1-7α-[ 18 F]FES (23) showed the highest uptake in ER-rich tissues such as the uterus. Uterus uptake also gradually decreased depending on the alkyl side chain length. As a result, in vivo uterus uptake reflected the in vitro ERα affinity of each compound. Bone uptake, which indicates de-fluorination, was marked in 7α-(2-[ 18 F]fluoroethyl)estradiol (C2-7α-[ 18 F]FES) (24) and 7α-(4-[ 18 F]fluorobutyl)estradiol (C4-7α-[ 18 F]FES) (25) derivatives. However, C1-7α-[ 18 F]FES (23) and C6-7α-[ 18 F]FES (26) showed limited uptake in bone. As a result, in vivo bone uptake (de-fluorination) showed a bell-shaped pattern, depending on the alkyl side chain length. C1-7α-[ 18 F]FES (23) showed the same levels of uptake in uterus and bone compared with those of 16α-[ 18 F]fluoro-17β-estradiol. Conclusions: The optimal alkyl

  12. Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.

    Science.gov (United States)

    Gaines, J C; Acebes, S; Virrueta, A; Butler, M; Regan, L; O'Hern, C S

    2018-05-01

    We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins. © 2018 Wiley Periodicals, Inc.

  13. Topological side-chain classification of beta-turns: ideal motifs for peptidomimetic development.

    Science.gov (United States)

    Tran, Tran Trung; McKie, Jim; Meutermans, Wim D F; Bourne, Gregory T; Andrews, Peter R; Smythe, Mark L

    2005-08-01

    Beta-turns are important topological motifs for biological recognition of proteins and peptides. Organic molecules that sample the side chain positions of beta-turns have shown broad binding capacity to multiple different receptors, for example benzodiazepines. Beta-turns have traditionally been classified into various types based on the backbone dihedral angles (phi2, psi2, phi3 and psi3). Indeed, 57-68% of beta-turns are currently classified into 8 different backbone families (Type I, Type II, Type I', Type II', Type VIII, Type VIa1, Type VIa2 and Type VIb and Type IV which represents unclassified beta-turns). Although this classification of beta-turns has been useful, the resulting beta-turn types are not ideal for the design of beta-turn mimetics as they do not reflect topological features of the recognition elements, the side chains. To overcome this, we have extracted beta-turns from a data set of non-homologous and high-resolution protein crystal structures. The side chain positions, as defined by C(alpha)-C(beta) vectors, of these turns have been clustered using the kth nearest neighbor clustering and filtered nearest centroid sorting algorithms. Nine clusters were obtained that cluster 90% of the data, and the average intra-cluster RMSD of the four C(alpha)-C(beta) vectors is 0.36. The nine clusters therefore represent the topology of the side chain scaffold architecture of the vast majority of beta-turns. The mean structures of the nine clusters are useful for the development of beta-turn mimetics and as biological descriptors for focusing combinatorial chemistry towards biologically relevant topological space.

  14. An exceptional series of phase transitions in hydrophobic amino acids with linear side chains

    Czech Academy of Sciences Publication Activity Database

    Görbitz, C.H.; Karen, P.; Dušek, Michal; Petříček, Václav

    2016-01-01

    Roč. 3, Sep (2016), s. 341-353 ISSN 2052-2525 R&D Projects: GA MŠk LO1603 EU Projects: European Commission(XE) CZ.2.16/3.1.00/24510 Institutional support: RVO:68378271 Keywords : amino acids * disorder * hydrogen bonding * modulated phases * phase transitions * side-chain stacking * polymorphism * molecular crystals Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 5.793, year: 2016

  15. Side-chain liquid-crystalline polyesters for optical information storage

    DEFF Research Database (Denmark)

    Hvilsted, Søren; Andruzzi, F.; Ramanujam, P.S.

    1992-01-01

    We report erasable holographic recording with a resolution of at least 2500 lines/mm on unoriented films of side-chain liquid-crystalline polyesters. Recording energies of approximately 1 J/cm2 have been used. We have obtained a diffraction efficiency of approximately 30% with polarization record...... recording of holograms. The holograms can be erased by heating them to approximately 80-degrees-C for approximately 2 min and are available for rerecording....

  16. Mesogenic polybuthadiene diols with thiol side-chain units: synthesis and thermal behaviour

    Czech Academy of Sciences Publication Activity Database

    Bubnov, Alexej; Kašpar, Miroslav; Sedláková, Zdeňka

    2010-01-01

    Roč. 83, č. 1 (2010), 16-27 ISSN 0141-1594 R&D Projects: GA AV ČR IAA100100911; GA AV ČR(CZ) GA202/09/0047; GA MŠk OC 175 Institutional research plan: CEZ:AV0Z10100520; CEZ:AV0Z40500505 Keywords : mesogenic polymer * phase transition * polybutadiene diol * side -chain polymer Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.006, year: 2010

  17. Exploiting the CNC side chain in heterocyclic rearrangements: synthesis of 4(5)-acylamino-imidazoles.

    Science.gov (United States)

    Piccionello, Antonio Palumbo; Buscemi, Silvestre; Vivona, Nicolò; Pace, Andrea

    2010-08-06

    A new variation on the Boulton-Katritzky reaction is reported, namely, involving use of a CNC side chain. A novel Montmorillonite-K10 catalyzed nonreductive transamination of a 3-benzoyl-1,2,4-oxadiazole afforded a 3-(alpha-aminobenzyl)-1,2,4-oxadiazole, which was condensed with benzaldehydes to afford the corresponding imines. In the presence of strong base, these imines underwent Boulton-Katritzky-type rearrangement to afford novel 4(5)-acylaminoimidazoles.

  18. Synthesis of side-chain polystyrenes for all organic solution processed OLEDs

    OpenAIRE

    Lorente Sánchez, Alejandro Jose (Dr.)

    2017-01-01

    In the present work side-chain polystyrenes were synthesized and characterized, in order to be applied in multilayer OLEDs fabricated by solution process techniques. Manufacture of optoelectronic devices by solution process techniques is meant to decrease significantly fabrication cost and allow large scale production of such devices. This dissertation focusses in three series, enveloped in two material classes. The two classes differ to each other in the type of charge transport exhibited...

  19. Contribution of cutinase serine 42 side chain to the stabilization of the oxyanion transition state.

    Science.gov (United States)

    Nicolas, A; Egmond, M; Verrips, C T; de Vlieg, J; Longhi, S; Cambillau, C; Martinez, C

    1996-01-16

    Cutinase from the fungus Fusarium solani pisi is a lipolytic enzyme able to hydrolyze both aggregated and soluble substrates. It therefore provides a powerful tool for probing the mechanisms underlying lipid hydrolysis. Lipolytic enzymes have a catalytic machinery similar to those present in serine proteinases. It is characterized by the triad Ser, His, and Asp (Glu) residues, by an oxyanion binding site that stabilizes the transition state via hydrogen bonds with two main chain amide groups, and possibly by other determinants. It has been suggested on the basis of a covalently bond inhibitor that the cutinase oxyanion hole may consist not only of two main chain amide groups but also of the Ser42 O gamma side chain. Among the esterases and the serine and the cysteine proteases, only Streptomyces scabies esterase, subtilisin, and papain, respectively, have a side chain residue which is involved in the oxyanion hole formation. The position of the cutinase Ser42 side chain is structurally conserved in Rhizomucor miehei lipase with Ser82 O gamma, in Rhizopus delemar lipase with Thr83 O gamma 1, and in Candida antartica B lipase with Thr40 O gamma 1. To evaluate the increase in the tetrahedral intermediate stability provided by Ser42 O gamma, we mutated Ser42 into Ala. Furthermore, since the proper orientation of Ser42 O gamma is directed by Asn84, we mutated Asn84 into Ala, Leu, Asp, and Trp, respectively, to investigate the contribution of this indirect interaction to the stabilization of the oxyanion hole. The S42A mutation resulted in a drastic decrease in the activity (450-fold) without significantly perturbing the three-dimensional structure. The N84A and N84L mutations had milder kinetic effects and did not disrupt the structure of the active site, whereas the N84W and N84D mutations abolished the enzymatic activity due to drastic steric and electrostatic effects, respectively.

  20. Utilizing alkoxyphenyl substituents for side-chain engineering of efficient benzo[1,2-b:4,5-b ']dithiophene-based small molecule organic solar cells

    DEFF Research Database (Denmark)

    Du, Zhengkun; Chen, Weichao; Qiu, Meng

    2015-01-01

    -processed organic solar cells (OSCs) as an electron donor material, in which an alkoxyphenyl group was introduced as a weak electrondonating side chain of the BDT moiety. The DCA3TBDTP molecule exhibited good solubility, a deep highest occupied molecular orbital (HOMO) level (-5.25 eV), an appropriate optical band......-gap (1.82 eV) and a high decomposition temperature (362 degrees C). By applying the simple solution spin-coating fabrication process, the bulk heterojunction (BHJ) OSCs based on DCA3TBDTP and [6,6]-phenyl-C-61-butyric acid methyl ester (PC61BM) exhibited a good power conversion efficiency (PCE) of 4...

  1. Improving proton conduction pathways in di- and triblock copolymer membranes: Branched versus linear side chains

    Science.gov (United States)

    Dorenbos, G.

    2017-06-01

    Phase separation within a series of polymer membranes in the presence of water is studied by dissipative particle dynamics. Each polymer contains hydrophobic A beads and hydrophilic C beads. Three parent architectures are constructed from a backbone composed of connected hydrophobic A beads to which short ([C]), long ([A3C]), or symmetrically branched A5[AC][AC] side chains spring off. Three di-block copolymer derivatives are constructed by covalently bonding an A30 block to each parent architecture. Also three tri-blocks with A15 blocks attached to both ends of each parent architecture are modeled. Monte Carlo tracer diffusion calculations through the water containing pores for 1226 morphologies reveal that water diffusion for parent architectures is slowest and diffusion through the di-blocks is fastest. Furthermore, diffusion increases with side chain length and is highest for branched side chains. This is explained by the increase of water pore size with , which is the average number of bonds that A beads are separated from a nearest C bead. Optimization of within the amphiphilic parent architecture is expected to be essential in improving proton conduction in polymer electrolyte membranes.

  2. The dominant role of side chains in supramolecular double helical organisation in synthetic tripeptides

    Science.gov (United States)

    Sharma, Ankita; Tiwari, Priyanka; Dutt Konar, Anita

    2018-06-01

    Peptide self-assembled nanostructures have attracted attention recently owing to their promising applications in diversified avenues. To validate the importance of sidechains in supramolecular architectural stabilization, herein this report describes the self-assembly propensities involving weak interactions in a series of model tripeptides Boc-Xaa-Aib-Yaa-OMe I-IV, (where Xaa = 4-F-Phe/NMeSer/Ile & Yaa = Tyr in peptide I-III respectively and Xaa = 4-F-Phe & Yaa = Ile in peptide IV) differing in terminal side chains. The solid state structural analysis reveals that tripeptide (I) displays supramolecular preference for double helical architecture. However, when slight modification has been introduced in the N-terminal side chains disfavour the double helical organisation (Peptide II and III). Indeed the peptides display sheet like ensemble within the framework. Besides replacement of C-terminal Tyr by Ile in peptide I even do not promote the architecture, emphasizing the dominant role of balance of side chains in stabilizing double helical organisation. The CD measurements, concentration dependant studies, NMR titrations and ROESY spectra are well in agreement with the solid state conformational investigation. Moreover the morphological experiments utilizing FE-SEM, support the heterogeneity present in the peptides. Thus this work may not only hold future promise in understanding the structure and function of neurodegenerative diseases but also assist in rational design of protein modification in biologically active peptides.

  3. Systematic and efficient side chain optimization for molecular docking using a cheapest-path procedure.

    Science.gov (United States)

    Schumann, Marcel; Armen, Roger S

    2013-05-30

    Molecular docking of small-molecules is an important procedure for computer-aided drug design. Modeling receptor side chain flexibility is often important or even crucial, as it allows the receptor to adopt new conformations as induced by ligand binding. However, the accurate and efficient incorporation of receptor side chain flexibility has proven to be a challenge due to the huge computational complexity required to adequately address this problem. Here we describe a new docking approach with a very fast, graph-based optimization algorithm for assignment of the near-optimal set of residue rotamers. We extensively validate our approach using the 40 DUD target benchmarks commonly used to assess virtual screening performance and demonstrate a large improvement using the developed side chain optimization over rigid receptor docking (average ROC AUC of 0.693 vs. 0.623). Compared to numerous benchmarks, the overall performance is better than nearly all other commonly used procedures. Furthermore, we provide a detailed analysis of the level of receptor flexibility observed in docking results for different classes of residues and elucidate potential avenues for further improvement. Copyright © 2013 Wiley Periodicals, Inc.

  4. An exceptional series of phase transitions in hydrophobic amino acids with linear side chains

    Directory of Open Access Journals (Sweden)

    Carl Henrik Görbitz

    2016-09-01

    Full Text Available The solid-state phase transitions and intermediate structures of S-2-aminobutanoic acid (l-2-aminobutyric acid, S-2-aminopentanoic acid (l-norvaline, S-2-aminohexanoic acid (l-norleucine and l-methionine between 100 and 470 K, identified by differential scanning calorimetry, have been characterized in a comprehensive single-crystal X-ray diffraction investigation. Unlike other enantiomeric amino acids investigated until now, this group featuring linear side chains displays up to five distinct phases. The multiple transitions between them involve a number of different processes: alteration of the hydrogen-bond pattern, to our knowledge the first example of this observed for an amino acid, sliding of molecular bilayers, seen previously only for racemates and quasiracemates, concerted side-chain rearrangements and abrupt as well as gradual modifications of the side-chain disorder. Ordering of l-norleucine upon cooling even proceeds via an incommensurately modulated structure. l-Methionine has previously been described as being fully ordered at room temperature. An accurate refinement now reveals extensive disorder for both molecules in the asymmetric unit, while two previously unknown phases occur above room temperature.

  5. Boosting the ambipolar performance of solution-processable polymer semiconductors via hybrid side-chain engineering.

    Science.gov (United States)

    Lee, Junghoon; Han, A-Reum; Yu, Hojeong; Shin, Tae Joo; Yang, Changduk; Oh, Joon Hak

    2013-06-26

    Ambipolar polymer semiconductors are highly suited for use in flexible, printable, and large-area electronics as they exhibit both n-type (electron-transporting) and p-type (hole-transporting) operations within a single layer. This allows for cost-effective fabrication of complementary circuits with high noise immunity and operational stability. Currently, the performance of ambipolar polymer semiconductors lags behind that of their unipolar counterparts. Here, we report on the side-chain engineering of conjugated, alternating electron donor-acceptor (D-A) polymers using diketopyrrolopyrrole-selenophene copolymers with hybrid siloxane-solubilizing groups (PTDPPSe-Si) to enhance ambipolar performance. The alkyl spacer length of the hybrid side chains was systematically tuned to boost ambipolar performance. The optimized three-dimensional (3-D) charge transport of PTDPPSe-Si with pentyl spacers yielded unprecedentedly high hole and electron mobilities of 8.84 and 4.34 cm(2) V(-1) s(-1), respectively. These results provide guidelines for the molecular design of semiconducting polymers with hybrid side chains.

  6. Controlling the mode of operation of organic transistors through side-chain engineering

    KAUST Repository

    Giovannitti, Alexander

    2016-10-11

    Electrolyte-gated organic transistors offer low bias operation facilitated by direct contact of the transistor channel with an electrolyte. Their operation mode is generally defined by the dimensionality of charge transport, where a field-effect transistor allows for electrostatic charge accumulation at the electrolyte/semiconductor interface, whereas an organic electrochemical transistor (OECT) facilitates penetration of ions into the bulk of the channel, considered a slow process, leading to volumetric doping and electronic transport. Conducting polymer OECTs allow for fast switching and high currents through incorporation of excess, hygroscopic ionic phases, but operate in depletion mode. Here, we show that the use of glycolated side chains on a thiophene backbone can result in accumulation mode OECTs with high currents, transconductance, and sharp subthreshold switching, while maintaining fast switching speeds. Compared with alkylated analogs of the same backbone, the triethylene glycol side chains shift the mode of operation of aqueous electrolyte-gated transistors from interfacial to bulk doping/transport and show complete and reversible electrochromism and high volumetric capacitance at low operating biases. We propose that the glycol side chains facilitate hydration and ion penetration, without compromising electronic mobility, and suggest that this synthetic approach can be used to guide the design of organic mixed conductors.

  7. Controlling the mode of operation of organic transistors through side-chain engineering

    Science.gov (United States)

    Giovannitti, Alexander; Sbircea, Dan-Tiberiu; Inal, Sahika; Nielsen, Christian B.; Bandiello, Enrico; Hanifi, David A.; Sessolo, Michele; Malliaras, George G.; McCulloch, Iain; Rivnay, Jonathan

    2016-01-01

    Electrolyte-gated organic transistors offer low bias operation facilitated by direct contact of the transistor channel with an electrolyte. Their operation mode is generally defined by the dimensionality of charge transport, where a field-effect transistor allows for electrostatic charge accumulation at the electrolyte/semiconductor interface, whereas an organic electrochemical transistor (OECT) facilitates penetration of ions into the bulk of the channel, considered a slow process, leading to volumetric doping and electronic transport. Conducting polymer OECTs allow for fast switching and high currents through incorporation of excess, hygroscopic ionic phases, but operate in depletion mode. Here, we show that the use of glycolated side chains on a thiophene backbone can result in accumulation mode OECTs with high currents, transconductance, and sharp subthreshold switching, while maintaining fast switching speeds. Compared with alkylated analogs of the same backbone, the triethylene glycol side chains shift the mode of operation of aqueous electrolyte-gated transistors from interfacial to bulk doping/transport and show complete and reversible electrochromism and high volumetric capacitance at low operating biases. We propose that the glycol side chains facilitate hydration and ion penetration, without compromising electronic mobility, and suggest that this synthetic approach can be used to guide the design of organic mixed conductors. PMID:27790983

  8. Cylindrical polymer brushes with dendritic side chains by iterative anionic reactions

    KAUST Repository

    Zhang, Hefeng

    2015-05-01

    We report in this paper an easy method for the synthesis of cylindrical polymer brushes with dendritic side chains through anionic reaction. The synthesis is accomplished by iteratively grafting a living block copolymer, polyisoprene-. b-polystyrenyllithium (PI-. b-PSLi), to the main chain and subsequently to the branches in a divergent way. PI segment is short and serves as a precursor for multifunctional branching unit. The grafting reaction involves two successive steps: i) epoxidation of internal double bonds of PI segments, either in main chain or side chains; ii) ring-opening addition to the resulting epoxy group by the living PI-. b-PSLi. Repeating the two steps affords a series of cylindrical polymer brushes with up to 3rd generation and extremely high molecular weight. The branching multiplicity depends on the average number of oxirane groups per PI segment, usually ca. 8 in the present work. The high branching multiplicity leads to tremendous increase in molecular weights of the cylindrical products with generation growth. Several series of cylindrical polymer brushes with tunable aspect ratios are prepared using backbones and branches with controlled lengths. Shape anisotropy is investigated in dilute solution using light scattering technique. Worm-like single molecular morphology with large persistence length is observed on different substrates by atomic force microscopy.

  9. A possibility for generation of two species of charge carriers along main-chain and side-chains for a π-conjugated polymer

    International Nuclear Information System (INIS)

    Kudo, Yuki; Kawabata, Kohsuke; Goto, Hiromasa

    2013-01-01

    Iodide doping produces charge carriers in π-conjugated polymers. Solitons can be generated in the case of polyacetylene, and polarons in the case of aromatic-type conjugated polymers. We synthesized a conjugated main-chain/side-chain polymer, which consists of polyene in the main-chain and aromatic-type conjugated units in the side-chains. Based on the SSH (Su, Schrieffer, Heeger) theoretical model of solitons in one-dimensional conjugated polymers, we experimentally carried out chemical doping to the main-chain/side-chains conjugated polymer. Generation of the charge carriers was examined by electron spin resonance spectroscopy. This study may lead to realization of a dual doping system of solitons and polarons in π-conjugation expanded to two-dimensional directions in polymers.

  10. Semi-crystalline photovoltaic polymers with siloxane-terminated hybrid side-chains

    Institute of Scientific and Technical Information of China (English)

    Yuxiang Li; Seyeong Song; Song Yi Park; Jin Young Kim; Han Young Woo

    2017-01-01

    Three types of semi-cry stalline photovoltaic polymers were synthesized by incorporating a siloxane-terminated organic/inorganic hybrid side-chain and changing the number of fluorine substituents.A branch point away from a polymer main backbone in the siloxane-containing side-chains and the intra-and/or interchain noncovalent coulombic interactions enhance a chain planarity and facile interchain organization.The resulting polymers formed strongly agglomerated films with high roughness,suggesting strong intermolecular interactions.The optical band gap of ca.1.7 eV was measured for all polymers with a pronounced shoulder peak due to tight π-π stacking.With increasing the fluorine substituents,the frontier energy levels decreased and preferential face-on orientation was observed.The siloxane-terminated side-chains and fluorine substitution promoted the intermolecular packing,showing well resolved lamellar scatterings up to(300) for this series of polymers in the grazing incidence wide angle X-ray scattering measurements.The PPsiDTBT,PPsiDTFBT and PPsiDT2 FBT devices showed a power conversion efficiency of 3.16%,4.40%and 5.65%,respectively,by blending with PC71BM.Langevin-type bimolecular charge recombination was similar for three polymeric solar cells.The main loss in the photocurrent generation for PPsiDTBT:PC71BM was interpreted to originate from the trap assisted charge recombination by measuring light-intensity dependent short-circuit current density(JSC) and open-circuit voltage(VOc).Our results provide a new insight into the rational selection of solubilizing substituents for optimizing crystalline interchain packing with appropriate miscibility with PC71 BM for further optimizing polymer solar cells.

  11. Semi-crystalline photovoltaic polymers with siloxane-terminated hybrid side-chains

    Institute of Scientific and Technical Information of China (English)

    Yuxiang Li; Seyeong Song; Song Yi Park; Jin Young Kim; Han Young Woo

    2017-01-01

    Three types of semi-crystalline photovoltaic polymers were synthesized by incorporating a siloxane-terminated organic/inorganic hybrid side-chain and changing the number of fluorine substituents.A branch point away from a polymer main backbone in the siloxane-containing side-chains and the intra-and/or interchain noncovalent coulombic interactions enhance a chain planarity and facile interchain organization.The resulting polymers formed strongly agglomerated films with high roughness,suggesting strong intermolecular interactions.The optical band gap of ca.1.7 eV was measured for all polymers with a pronounced shoulder peak due to tight π-π stacking.With increasing the fluorine substituents,the frontier energy levels decreased and preferential face-on orientation was observed.The siloxane-terminated side-chains and fluorine substitution promoted the intermolecular packing,showing well resolved lamellar scatterings up to (300) for this series of polymers in the grazing incidence wide angle X-ray scattering measurements.The PPsiDTBT,PPsiDTFBT and PPsiDT2FBT devices showed a power conversion efficiency of 3.16%,4.40% and 5.65%,respectively,by blending with PC71BM.Langevin-type bimolecular charge recombination was similar for three polymeric solar cells.The main loss in the photocurrent generation for PPsiDTBT:PC71BM was interpreted to originate from the trap assisted charge recombination by measuring light-intensity dependent short-circuit current density (Jsc) and open-circuit voltage (Voc).Our results provide a new insight into the rational selection of solubilizing substituents for optimizing crystalline interchain packing with appropriate miscibility with PC71BM for further optimizing polymer solar cells.

  12. Peramivir analogues bearing hydrophilic side chains exhibit higher activities against H275Y mutant than wild-type influenza virus.

    Science.gov (United States)

    Chiu, Din-Chi; Lin, Tzu-Chen; Huang, Wen-I; Cheng, Ting-Jen; Tsai, Keng-Chang; Fang, Jim-Min

    2017-11-29

    Peramivir is an effective anti-influenza drug in the clinical treatment of influenza, but its efficacy toward the H275Y mutant is reduced. The previously reported cocrystal structures of inhibitors in the mutant neuraminidase (NA) suggest that the hydrophobic side chain should be at the origin of reduced binding affinity. In contrast, zanamivir having a hydrophilic glycerol side chain still possesses high affinity toward the H275Y NA. We thus designed five peramivir analogues (5-9) carrying hydrophilic glycol or glycerol side chains, and evaluated their roles in anti-influenza activity, especially for the H275Y mutant. The synthetic sequence involves a key step of (3 + 2) cycloaddition reactions between alkenes and nitrile oxides to construct the scaffold of peramivir carrying the desired hydrophilic side chains and other appropriate functional groups. The molecular docking experiments reveal that the hydrophilic side chain can provide extra hydrogen bonding with the translocated Glu-276 residue in the H275Y NA active site. Thus, the H275Y mutant may be even more sensitive than wild-type virus toward the peramivir analogues bearing hydrophilic side chains. Notably, the peramivir analogue bearing a glycerol side chain inhibits the H275Y mutant with an IC 50 value of 35 nM, which is better than the WSN virus by 9 fold.

  13. Structural and kinetic mapping of side-chain exposure onto the protein energy landscape.

    Science.gov (United States)

    Bernstein, Rachel; Schmidt, Kierstin L; Harbury, Pehr B; Marqusee, Susan

    2011-06-28

    Identification and characterization of structural fluctuations that occur under native conditions is crucial for understanding protein folding and function, but such fluctuations are often rare and transient, making them difficult to study. Native-state hydrogen exchange (NSHX) has been a powerful tool for identifying such rarely populated conformations, but it generally reveals no information about the placement of these species along the folding reaction coordinate or the barriers separating them from the folded state and provides little insight into side-chain packing. To complement such studies, we have performed native-state alkyl-proton exchange, a method analogous to NSHX that monitors cysteine modification rather than backbone amide exchange, to examine the folding landscape of Escherichia coli ribonuclease H, a protein well characterized by hydrogen exchange. We have chosen experimental conditions such that the rate-limiting barrier acts as a kinetic partition: residues that become exposed only upon crossing the unfolding barrier are modified in the EX1 regime (alkylation rates report on the rate of unfolding), while those exposed on the native side of the barrier are modified predominantly in the EX2 regime (alkylation rates report on equilibrium populations). This kinetic partitioning allows for identification and placement of partially unfolded forms along the reaction coordinate. Using this approach we detect previously unidentified, rarely populated conformations residing on the native side of the barrier and identify side chains that are modified only upon crossing the unfolding barrier. Thus, in a single experiment under native conditions, both sides of the rate-limiting barrier are investigated.

  14. Dependence of crystallite formation and preferential backbone orientations on the side chain pattern in PBDTTPD polymers

    KAUST Repository

    El Labban, Abdulrahman

    2014-11-26

    (Figure Presented) Alkyl substituents appended to the π-conjugated main chain account for the solution-processability and film-forming properties of most π-conjugated polymers for organic electronic device applications, including field-effect transistors (FETs) and bulk-heterojunction (BHJ) solar cells. Beyond film-forming properties, recent work has emphasized the determining role that side-chain substituents play on polymer self-assembly and thin-film nanostructural order, and, in turn, on device performance. However, the factors that determine polymer crystallite orientation in thin-films, implying preferential backbone orientation relative to the device substrate, are a matter of some debate, and these structural changes remain difficult to anticipate. In this report, we show how systematic changes in the side-chain pattern of poly(benzo[1,2-b:4,5-b′]dithiophene-alt-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers can (i) influence the propensity of the polymer to order in the π-stacking direction, and (ii) direct the preferential orientation of the polymer crystallites in thin films (e.g., "face-on" vs "edge-on"). Oriented crystallites, specifically crystallites that are well-ordered in the π-stacking direction, are believed to be a key contributor to improved thin-film device performance in both FETs and BHJ solar cells.

  15. Microscopic theory of light-induced deformation in amorphous side-chain azobenzene polymers.

    Science.gov (United States)

    Toshchevikov, V; Saphiannikova, M; Heinrich, G

    2009-04-16

    We propose a microscopic theory of light-induced deformation of side-chain azobenzene polymers taking into account the internal structure of polymer chains. Our theory is based on the fact that interaction of chromophores with the polarized light leads to the orientation anisotropy of azobenzene macromolecules which is accompanied by the appearance of mechanical stress. It is the first microscopic theory which provides the value of the light-induced stress larger than the yield stress. This result explains a possibility for the inscription of surface relief gratings in glassy side-chain azobenzene polymers. For some chemical architectures, elongation of a sample demonstrates a nonmonotonic behavior with the light intensity and can change its sign (a stretched sample starts to be uniaxially compressed), in agreement with experiments. Using a viscoplastic approach, we show that the irreversible strain of a sample, which remains after the light is switched off, decreases with increasing temperature and can disappear at certain temperature below the glass transition temperature. This theoretical prediction is also confirmed by recent experiments.

  16. Amphiphilic polymer based on fluoroalkyl and PEG side chains for fouling release coating

    Science.gov (United States)

    Cong, W. W.; Wang, K.; Yu, X. Y.; Zhang, H. Q.; Lv, Z.; Gui, T. J.

    2017-12-01

    Under static conditions, fouling release coating could not express good release property to marine organisms. Amphiphilic polymer with mixture of fluorinated monomer and short side group of polyethylene glycol (PEG) was synthesized. And also we studied the ability of amphiphilic polymer to influence the surface properties and how it controlled the adhesion of marine organisms to coated surfaces. By incorporating fluorinated monomer and PEG side chain into the polymer, the effect of incorporating both polar and non-polar groups on fouling-release coating could be studied. The dry surface was characterized by three-dimensional digital microscopy and scanning electron microscopy (SEM), and the morphology of the amphiphilic fouling release coating showed just like flaky petal. The amphiphilic polymer in fouling release coating tended to reconstruct in water, and the ability was examined by static contact angle, which was smaller than the PDMS (polydimethylsiloxane) fouling release coating. Also surface energy was calculated by three solvents, and surface energy of amphiphilic fouling release coating was higher than that of the PDMS fouling release coating. To understand more about its fouling release property, seawater exposure method was adopted in gulf of Qingdao port. Fewer diatoms Navicula were found in biofilm after using amphiphilic fouling release coating. In general, coating containing both PEG and fluorinated side chain possessed certain fouling release property.

  17. Enabling high-mobility, ambipolar charge-transport in a DPP-benzotriazole copolymer by side-chain engineering

    DEFF Research Database (Denmark)

    Gruber, Mathias; Jung, Seok-Heon; Schott, Sam

    2015-01-01

    In this article we discuss the synthesis of four new low band-gap co-polymers based on the diketopyrrolopyrrole (DPP) and benzotriazole (BTZ) monomer unit. We demonstrate that the BTZ unit allows for additional solubilizing side-chains on the co-monomer and show that the introduction of a linear...... side-chain on the DPP-unit leads to an increase in thin-film order and charge-carrier mobility if a sufficiently solubilizing, branched, side chain is attached to the BTZ. We compare two different synthetic routes, direct arylation and Suzuki-polycondensation, by a direct comparison of polymers...

  18. Revealing the Supramolecular Nature of Side-Chain Terpyridine-Functionalized Polymer Networks

    Directory of Open Access Journals (Sweden)

    Jérémy Brassinne

    2015-01-01

    Full Text Available Nowadays, finely controlling the mechanical properties of polymeric materials is possible by incorporating supramolecular motifs into their architecture. In this context, the synthesis of a side-chain terpyridine-functionalized poly(2-(dimethylaminoethyl methacrylate is reported via reversible addition-fragmentation chain transfer polymerization. By addition of transition metal ions, concentrated aqueous solutions of this polymer turn into metallo-supramolecular hydrogels whose dynamic mechanical properties are investigated by rotational rheometry. Hence, the possibility for the material to relax mechanical constrains via dissociation of transient cross-links is brought into light. In addition, the complex phenomena occurring under large oscillatory shear are interpreted in the context of transient networks.

  19. Influence of water solubility, side chain degradability and side chain configuration on the degradation of phthalic acid esters under methanogenic conditions

    Energy Technology Data Exchange (ETDEWEB)

    Alnervik, M.

    1996-12-31

    Water solubility and degradability of side chains estrifying phthalic acid are factors possible to influence the degradation of phthalic acid esters (PAEs). To investigate the importance of these factors degradation of butyl 2-ethylhexyl phthalate (BEHP), bis(2-ethylhexyl) phthalate (DEHP), dibutyl phthalate (DBP), dihexyl phthalate (DHP), dioctyl phthalate (DOP) and didecyl phthalate (DDP) were examined under methanogenic conditions as well as was the degradability of the alcohols estrifying these PAEs. We also investigated if the degradation of resistant PAEs could be stimulated by the addition of a degradable PAE. Synthesis of degradation intermediates and two methods for PAE analyses are presented. The investigation showed that all alcohols were degraded to methane and carbon dioxide and that the degradation of PAE occurred in incubations amended with BBP, BEHP, DHP and DBP, whilst DEHP, DOP and DDP were unaffected throughout the experimental period. BBP added to incubations with DEHP, could not stimulate DEHP degradation. In conclusion, the degradability of alcohols estrifying phthalic acid in this study does not affect the anaerobic degradability of PAEs. Water solubility of a PAE can not be rejected as a factor limiting phthalate degradation under methanogenic conditions. Anaerobic degradation of persistent PAEs can not be stimulated by mixing it with a degradable phthalate. 23 refs, 11 figs, 2 tabs

  20. Ion-Exchange Membranes Based on Polynorbornenes with Fluorinated Imide Side Chain Groups

    Directory of Open Access Journals (Sweden)

    Arlette A. Santiago

    2012-01-01

    Full Text Available The electrochemical characteristics of cation-exchange membranes based on polynorbornenes with fluorinated and sulfonated dicarboximide side chain groups were reported. This study was extended to a block copolymer containing structural units with phenyl and 4-oxybenzenesulfonic acid, 2,3,5,6-tetrafluorophenyl moieties replacing the hydrogen atom of the dicarboximide group. A thorough study on the electrochemical characteristics of the membranes involving electromotive forces of concentration cells and proton conductivity is reported. The proton permselectivity of the membranes is also discussed.

  1. Synthesis and Intramolecular [4+2] Cycloaddition Reactions of 4-Pyridazinecarbonitriles with Alkyne Side Chains

    Directory of Open Access Journals (Sweden)

    Norbert Haider

    1998-01-01

    Full Text Available The preparation of a series of new 3-(alkynyl-X-substituted 4-pyridazinecarbonitriles 2-5 (X = O, NH is described. The compounds are shown to undergo thermally induced intramolecular Diels-Alder reactions with inverse electron demand, affording the fused benzonitriles 6-8. Incorporation of a 1,2-phenylene unit into the side chain, as in the case of compounds 10 and 13, results in a more favorable conformation of the dienophilic substructure and thus to a pronounced acceleration of the [4+2] cycloaddition reaction.

  2. Side Chain and Flexibility Contributions to the Raman Optical Activity Spectra of a Model Cyclic Hexapeptide

    Czech Academy of Sciences Publication Activity Database

    Hudecová, J.; Kapitán, Josef; Baumruk, V.; Hammer, R. P.; Keiderling, T. A.; Bouř, Petr

    2010-01-01

    Roč. 114, č. 28 (2010), s. 7642-7651 ISSN 1089-5639 R&D Projects: GA ČR GA203/06/0420; GA ČR GA202/07/0732; GA AV ČR IAA400550702 Grant - others:GA UK(CZ) 126310 Institutional research plan: CEZ:AV0Z40550506 Keywords : Raman optical activity * ab initio * side chain * flexibility * peptide Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.732, year: 2010

  3. Tuning Thermoresponsive Properties of Cationic Elastin-like Polypeptides by Varying Counterions and Side-Chains.

    Science.gov (United States)

    Petitdemange, Rosine; Garanger, Elisabeth; Bataille, Laure; Bathany, Katell; Garbay, Bertrand; Deming, Timothy J; Lecommandoux, Sébastien

    2017-05-17

    We report the synthesis of methionine-containing recombinant elastin-like polypeptides (ELPs) of different lengths that contain periodically spaced methionine residues. These ELPs were chemoselectively alkylated at all methionine residues to give polycationic derivatives. Some of these samples were found to possess solubility transitions in water, where the temperature of these transitions varied with ELP concentration, nature of the methionine alkylating group, and nature of the sulfonium counterions. These studies show that introduction and controlled spacing of methionine sulfonium residues into ELPs can be used as a means both to tune their solubility transition temperatures in water using a variety of different parameters and to introduce new side-chain functionality.

  4. Mean-field theory of photoinduced molecular reorientation in azobenzene liquid crystalline side-chain polymers

    DEFF Research Database (Denmark)

    Pedersen, T.G.; Johansen, P.M.

    1997-01-01

    . The theory provides an explanation for the high long-term stability of the photoinduced anisotropy as well as a theoretical prediction of the temporal behavior of photoinduced birefringence. The theoretical results agree favorably with measurements in the entire range of writing intensities used......A novel mean-field theory of photoinduced reorientation and optical anisotropy in liquid crystalline side-chain polymers is presented and compared with experiments, The reorientation mechanism is based on photoinduced trans cis isomerization and a multidomain model of the material is introduced...

  5. Mean-field theory of photoinduced formation of surface reliefs in side-chain azobenzene polymers

    DEFF Research Database (Denmark)

    Pedersen, Thomas Garm; Johansen, Per Michael; Holme, N.C.R.

    1998-01-01

    A mean-field model of photoinduced surface reliefs in dye containing side-chain polymers is presented. It is demonstrated that photoinduced ordering of dye molecules subject to anisotropic intermolecular interactions leads to mass transport even when the intensity of the incident light is spatially...... uniform. Theoretical profiles are obtained using a simple variational method and excellent agreement with experimental surface reliefs recorded under various polarization configurations is found. The polarization dependence of both period and shape of the profiles is correctly reproduced by the model....

  6. Asymmetric Meerwein–Ponndorf–Verley reduction of long chain keto alkanoic acid methyl esters

    Directory of Open Access Journals (Sweden)

    AYE YUSUFOGLU

    2007-05-01

    Full Text Available 3-, 7- and 13-Monoketo tetradecanoic acid methyl esters carrying a ketogroup at the ends and at the middle of the chain with 14 carbon atoms were reduced by a Meerwein–Ponndorf–Verley reaction in the presence of R-(+-1,1'-binaphthalene-2,2'-diol, 1,2:5,6-D-di-O-isopropylidene-D-mannitol and L-(–-menthol. The highest enantiomeric purity of 65% ee was found for 13-hydroxy ester isomer. The enantiomeric excess was determined by 1H-NMR shift with Eu(tfc3 and by optical rotation.

  7. Mechanism and Stereochemistry of Polyketide Chain Elongation and Methyl Group Epimerization in Polyether Biosynthesis.

    Science.gov (United States)

    Xie, Xinqiang; Garg, Ashish; Khosla, Chaitan; Cane, David E

    2017-03-01

    The polyketide synthases responsible for the biosynthesis of the polyether antibiotics nanchangmycin (1) and salinomycin (4) harbor a number of redox-inactive ketoreductase (KR 0 ) domains that are implicated in the generation of C2-epimerized (2S)-2-methyl-3-ketoacyl-ACP intermediates. Evidence that the natural substrate for the polyether KR 0 domains is, as predicted, a (2R)-2-methyl-3-ketoacyl-ACP intermediate, came from a newly developed coupled ketosynthase (KS)-ketoreductase (KR) assay that established that the decarboxylative condensation of methylmalonyl-CoA with S-propionyl-N-acetylcysteamine catalyzed by the Nan[KS1][AT1] didomain from module 1 of the nanchangmycin synthase generates exclusively the corresponding (2R)-2-methyl-3-ketopentanoyl-ACP (7a) product. In tandem equilibrium isotope exchange experiments, incubation of [2- 2 H]-(2R,3S)-2-methyl-3-hydroxypentanoyl-ACP (6a) with redox-active, epimerase-inactive EryKR6 from module 6 of the 6-deoxyerythronolide B synthase and catalytic quantities of NADP + in the presence of redox-inactive, recombinant NanKR1 0 or NanKR5 0 , from modules 1 and 5 of the nanchangmycin synthase, or recombinant SalKR7 0 from module 7 of the salinomycin synthase, resulted in first-order, time-dependent washout of deuterium from 6a. Control experiments confirmed that this washout was due to KR 0 -catalyzed isotope exchange of the reversibly generated, transiently formed oxidation product [2- 2 H]-(2R)-2-methyl-3-ketopentanoyl-ACP (7a), consistent with the proposed epimerase activity of each of the KR 0 domains. Although they belong to the superfamily of short chain dehydrogenase-reductases, the epimerase-active KR 0 domains from polyether synthases lack one or both residues of the conserved Tyr-Ser dyad that has previously been implicated in KR-catalyzed epimerizations.

  8. A Solid-State Deuterium NMR and SFG Study of the Side Chain Dynamics of Peptides Adsorbed onto Surfaces

    Science.gov (United States)

    Breen, Nicholas F.; Weidner, Tobias; Li, Kun; Castner, David G.; Drobny, Gary P.

    2011-01-01

    The artificial amphiphilic peptide LKα14 adopts a helical structure at interfaces, with opposite orientation of its leucine (L, hydrophobic) and lysine (K, hydrophilic) side chains. When adsorbed onto surfaces, different residue side chains necessarily have different proximities to the surface, depending on both their position in the helix and the composition of the surface itself. Deuterating the individual leucine residues (isopropyl-d7) permits the use of solid-state deuterium NMR as a site-specific probe of side chain dynamics. In conjunction with SFG as a probe of the peptide binding face, we demonstrate that the mobility of specific leucine side chains at the interface is quantifiable in terms of their surface proximity. PMID:19764755

  9. A new series of two-ring-based side chain liquid crystalline polymers: synthesis and mesophase characterization

    CSIR Research Space (South Africa)

    Reddy, GSM

    2013-05-01

    Full Text Available A new series of side chain liquid crystalline polymers containing a core, a butamethylenoxy spacer, ester groups, and terminal alkoxy groups were synthesised and their structures were confirmed. The core was constructed with two phenyl rings...

  10. Oxidative stress and alterations in DNA methylation: two sides of the same coin in reproduction.

    Science.gov (United States)

    Menezo, Yves J R; Silvestris, Erica; Dale, Brian; Elder, Kay

    2016-12-01

    The negative effect of oxidative stress on the human reproductive process is no longer a matter for debate. Oxidative stress affects female and male gametes and the developmental capacity of embryos. Its effect can continue through late stages of pregnancy. Metabolic disorders and psychiatric problems can also be caued by DNA methylation and epigenetic errors. Age has a negative effect on oxidative stress and DNA methylation, and recent observations suggest that older men are at risk of transmitting epigenetic disorders to their offspring. Environmental endocrine disruptors can also increase oxidative stress and methylation errors. Oxidative stress and DNA methylation feature a common denominator: the one carbon cycle. This important metabolic pathway stimulates glutathione synthesis and recycles homocysteine, a molecule that interferes with the process of methylation. Glutathione plays a pivotal role during oocyte activation, protecting against reactive oxygen species. Assisted reproductive techniques may exacerbate defects in methylation and epigenesis. Antioxidant supplements are proposed to reduce the risk of potentially harmful effects, but their use has failed to prevent problems and may sometimes be detrimental. New concepts reveal a significant correlation between oxidative stress, methylation processes and epigenesis, and have led to changes in media composition with positive preliminary clinical consequences. Copyright © 2016 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

  11. Synthesis and property characterization of two novel side-chain isoindigo copolymers for polymer solar cells

    Directory of Open Access Journals (Sweden)

    X. Liu

    2015-11-01

    Full Text Available Two novel side-chain conjugated polymers, PTBT-TID and PTBT-TTID, based on the new synthetic thiophene-benzne-thiophene (TBT unit, side-chain isoindigo (ID unit, and the introduced thiophene π-bridge, have been designed and synthesized. The photophysical, electrochemical and photovoltaic properties of the two polymers have been systematically investigated. The two polymers possess relatively good solubility as well as excellent thermal stability up to 380°C, and all of the polymer solar cell (PSC devices based on the two polymers obtain high open circuit voltage (Voc of about 0.8 V. The polymer solar cells based on the polymer PTBT-TID show relatively higher efficiencies than the PTBT-TTID-based ones, due to the broader absorption spectrum, a relatively higher hole mobility, a lower HOMO (the highest occupied molecular orbital energy level, a stronger IPCE (the incident photon to current conversion efficiency response and a better microphase separation, Consequently, the device based on PTBT-TID:PC61BM (1:2, by weight gives the best power conversion efficiency (PCE of 2.04%, with a short-circuit current density (Jsc of 5.39 mA·cm–2, an open-circuit voltage (Voc of 0.83 V, and a fill factor (FF of 0.45.

  12. Subcritical Water Hydrolysis of Peptides: Amino Acid Side-Chain Modifications

    Science.gov (United States)

    Powell, Thomas; Bowra, Steve; Cooper, Helen J.

    2017-09-01

    Previously we have shown that subcritical water may be used as an alternative to enzymatic digestion in the proteolysis of proteins for bottom-up proteomics. Subcritical water hydrolysis of proteins was shown to result in protein sequence coverages greater than or equal to that obtained following digestion with trypsin; however, the percentage of peptide spectral matches for the samples treated with trypsin were consistently greater than for those treated with subcritical water. This observation suggests that in addition to cleavage of the peptide bond, subcritical water treatment results in other hydrolysis products, possibly due to modifications of amino acid side chains. Here, a model peptide comprising all common amino acid residues (VQSIKCADFLHYMENPTWGR) and two further model peptides (VCFQYMDRGDR and VQSIKADFLHYENPTWGR) were treated with subcritical water with the aim of probing any induced amino acid side-chain modifications. The hydrolysis products were analyzed by direct infusion electrospray tandem mass spectrometry, either collision-induced dissociation or electron transfer dissociation, and liquid chromatography collision-induced dissociation tandem mass spectrometry. The results show preferential oxidation of cysteine to sulfinic and sulfonic acid, and oxidation of methionine. In the absence of cysteine and methionine, oxidation of tryptophan was observed. In addition, water loss from aspartic acid and C-terminal amidation were observed in harsher subcritical water conditions. [Figure not available: see fulltext.

  13. Novel Random PBS-Based Copolymers Containing Aliphatic Side Chains for Sustainable Flexible Food Packaging

    Directory of Open Access Journals (Sweden)

    Giulia Guidotti

    2017-12-01

    Full Text Available In the last decade, there has been an increased interest from the food packaging industry toward the development and application of biodegradable and biobased plastics, to contribute to the sustainable economy and to reduce the huge environmental problem afflicting the planet. In this framework, the present paper describes the synthesis of novel PBS (poly(butylene succinate-based random copolymers with different composition containing glycol sub-units characterized by alkyl pendant groups of different length. The prepared samples were subjected to molecular, thermal, diffractometric and mechanical characterization. The barrier performances to O2, CO2 and N2 gases were also evaluated, envisioning for these new materials an application in food packaging. The presence of the side alkyl groups did not alter the thermal stability, whereas it significantly reduced the sample crystallinity degree, making these materials more flexible. The barrier properties were found to be worse than PBS; however, some of them were comparable to, or even better than, those of Low Density Polyethylene (LDPE, widely employed for flexible food packaging. The entity of variations in the final properties due to copolymerization were more modest in the case of the co-unit with short side methyl groups, which, when included in the PBS crystal lattice, causes a more modest decrement of crystallinity degree.

  14. Branched-chain dicationic ionic liquids for fatty acid methyl ester assessment by gas chromatography.

    Science.gov (United States)

    Talebi, Mohsen; Patil, Rahul A; Sidisky, Leonard M; Berthod, Alain; Armstrong, Daniel W

    2017-12-06

    Twelve bis- or dicationic ionic liquids (ILs) including eight based on imidazolium, a single one based on phosphonium, and three based on pyrrolidinium cationic units were prepared with the bis(trifluoromethyl sulfonyl) imide anion. The two identical cationic moieties were attached by different alkyl spacers having three or five carbons and differing alkyl substituents attached to the spacer. The SLB-IL111 column, as the most polar commercial stationary phase known, was included in the study for comparison. Isothermal separations of a rapeseed oil fatty acid methyl ester (FAME) sample were used to study and compare the 12 IL-based column performances and selectivities. The retention times of the most retained methyl esters of lignoceric (C24:0) and erucic (C22:1) acids were used to estimate the IL polarity. The phosphonium dicationic IL column was, by far, the least polar. Imidazolium-based dicationic IL columns were the most polar. Polarity and selectivity for the FAME separation were somewhat related. The separation of a 37-FAME standard mixture allowed the investigation of selectivity variations observed on the 12 IL-based columns under temperature gradients up to 230 °C. The remarkable selectivity of the IL-based columns is demonstrated by the detailed analysis of the cis/trans C18:1 isomers of a partially hydrogenated vegetable oil sample on 30-m columns, separations competing with that done following an "official method" performed on a 100-m column. Graphical abstract Separation of fatty acid methyl esters on a 30-m 3m 2 C 5 (mpy) 2 . 2NTf 2 branched-chain dicationic IL-based column. Branched chain dicationic ILs show great selectivity for separation of cis/trans, ω-3/ω-6, and detailed analysis of cis/trans fats.

  15. Controlling the morphology and efficiency of hybrid ZnO: Polythiophene solar cells via side chain functionalization

    NARCIS (Netherlands)

    Oosterhout, S.D.; Koster, L.J.A.; Bavel, van S.S.; Loos, J.; Stenzel, O.; Thiedmann, R.; Schmidt, V.; Campo, B.J.; Cleij, T.J.; Lutzen, L.; Vanderzande, D.J.M.; Wienk, M.M.; Janssen, R.A.J.

    2011-01-01

    The efficiency of polymer – metal oxide hybrid solar cells depends critically on the intimacy of mixing of the two semiconductors. The effect of side chain functionalization on the morphology and performance of conjugated polymer:ZnO solar cells is investigated. Using an ester-functionalized side

  16. Controlling the Morphology and Efficiency of Hybrid ZnO : Polythiophene Solar Cells Via Side Chain Functionalization

    NARCIS (Netherlands)

    Oosterhout, Stefan D.; Koster, L. Jan Anton; van Bavel, Svetlana S.; Loos, Joachim; Stenzel, Ole; Thiedmann, Ralf; Schmidt, Volker; Campo, Bert; Cleij, Thomas J.; Lutzen, Laurence; Vanderzande, Dirk; Wienk, Martijn M.; Janssen, Rene A. J.

    2011-01-01

    The efficiency of polymer - metal oxide hybrid solar cells depends critically on the intimacy of mixing of the two semiconductors. The effect of side chain functionalization on the morphology and performance of conjugated polymer:ZnO solar cells is investigated. Using an ester-functionalized side

  17. Structural characterization of saturated branched chain fatty acid methyl esters by collisional dissociation of molecular ions generated by electron ionization[S

    Science.gov (United States)

    Ran-Ressler, Rinat R.; Lawrence, Peter; Brenna, J. Thomas

    2012-01-01

    Saturated branched chain fatty acids (BCFA) are present as complex mixtures in numerous biological samples. The traditional method for structure elucidation, electron ionization (EI) mass spectrometry, sometimes does not unambiguously enable assignment of branching in isomeric BCFA. Zirrolli and Murphy (Zirrolli , J. A. , and R. A. Murphy. 1993. Low-energy tandem mass spectrometry of the molecular ion derived from fatty acid methyl esters: a novel method for analysis of branched-chain fatty acids. J. Am. Soc. Mass Spectrom. 4: 223–229.) showed that the molecular ions of four BCFA methyl ester (BCFAME) yield highly characteristic fragments upon collisional dissociation using a triple quadrupole instrument. Here, we confirm and extend these results by analysis using a tabletop 3-D ion trap for activated molecular ion EI-MS/MS to 30 BCFAME. iso-BCFAME produces a prominent ion (30-100% of base peak) for [M-43] (M-C3H7), corresponding to the terminal isopropyl moiety in the original iso-BCFAME. Anteiso-FAME yield prominent ions (20-100% of base peak) corresponding to losses on both side of the methyl branch, [M-29] and [M-57], and tend to produce more prominent m/z 115 peaks corresponding to a cyclization product around the ester. Dimethyl and tetramethyl FAME, with branches separated by at least one methylene group, yield fragment on both sides of the sites of methyl branches that are more than 6 C away from the carboxyl carbon. EI-MS/MS yields uniquely specific ions that enable highly confident structural identification and quantification of BCFAME. PMID:22021637

  18. Different DNA methylation patterns detected by the Amplified Methylation Polymorphism Polymerase Chain Reaction (AMP PCR technique among various cell types of bulls

    Directory of Open Access Journals (Sweden)

    Carroll Bernie

    2010-03-01

    Full Text Available Abstract Background The purpose of this study was to apply an arbitrarily primed methylation sensitive polymerase chain reaction (PCR assay called Amplified Methylation Polymorphism Polymerase Chain Reaction (AMP PCR to investigate the methylation profiles of somatic and germ cells obtained from Holstein bulls. Methods Genomic DNA was extracted from sperm, leukocytes and fibroblasts obtained from three bulls and digested with a methylation sensitive endonuclease (HpaII. The native genomic and enzyme treated DNA samples were used as templates in an arbitrarily primed-PCR assay with 30 sets of single short oligonucleotide primer. The PCR products were separated on silver stained denaturing polyacrylamide gels. Three types of PCR markers; digestion resistant-, digestion sensitive-, and digestion dependent markers, were analyzed based on the presence/absence polymorphism of the markers between the two templates. Results Approximately 1,000 PCR markers per sample were produced from 27 sets of primer and most of them (>90% were digestion resistant markers. The highest percentage of digestion resistant markers was found in leukocytic DNA (94.8% and the lowest in fibroblastic DNA (92.3%, P ≤ 0.05. Spermatozoa contained a higher number of digestion sensitive markers when compared with the others (3.6% vs. 2.2% and 2.6% in leukocytes and fibroblasts respectively, P ≤ 0.05. Conclusions The powerfulness of the AMP PCR assay was the generation of methylation-associated markers without any prior knowledge of the genomic sequence. The data obtained from different primers provided an overview of genome wide DNA methylation content in different cell types. By using this technique, we found that DNA methylation profile is tissue-specific. Male germ cells were hypomethylated at the HpaII locations when compared with somatic cells, while the chromatin of the well-characterized somatic cells was heavily methylated when compared with that of the versatile somatic

  19. A stability study of polymer solar cells using conjugated polymers with different donor or acceptor side chain patterns

    DEFF Research Database (Denmark)

    Heckler, Ilona Maria; Kesters, Jurgen; Defour, Maxime

    2016-01-01

    -phenylethyl group. It is shown that the exchange of the hexyl chain on the DTBT moiety has a negative impact on the stability of the polymer as well as on the performance of the resulting PSCs. On the other hand, partial exchange of the 2-hexyldecyl side chain of the BDT unit by a 2-hydroxyethyl group results......)benzo[c][1,2,5]thiadiazole (DTBT), specifically selected because of its suitability for roll-coating in the ambient environment, is investigated in terms of operational stability via partial exchange (5 or 10%) of the alkyl side chain on either the donor or the acceptor monomer with a 2-hydroxyethyl or 2...

  20. Unusual Photo-Induced Behaviour in a Side Chain Liquid Crystalline Azo-Polyester

    DEFF Research Database (Denmark)

    López, D; Rodríguez, F.J.; Sánchez, C.

    2006-01-01

    An unusual behaviour has been observed in the photo-indueed response of an azobenzene side chain liquid erystalline polyester (P6d4). Room temperature irradiation with linearly polarised 488 nm light does not induce any birefringence (An) in films of this polymer that have been quenehed from...... the isotropie state. However, using the same irradiation conditions An is indueed in quenehed films that have been kept in darkness for a few minutes. Besides, no photo-induced An is observed in films irradiated with 488 nm light that have been previously irradiated with UV light. In this ease, An can...... be reeorded if the UV irradiated films have been kept in darkness for several hours. In another set of experiments performed with the P6d4 polymer, irradiation with high intensity linearly polarised 488 nm light induces an initial increase of An and then it goes back to zero. Subsequent irradiation...

  1. High Performance All-Polymer Solar Cell via Polymer Side-Chain Engineering

    KAUST Repository

    Zhou, Yan; Kurosawa, Tadanori; Ma, Wei; Guo, Yikun; Fang, Lei; Vandewal, Koen; Diao, Ying; Wang, Chenggong; Yan, Qifan; Reinspach, Julia; Mei, Jianguo; Appleton, Anthony Lucas; Koleilat, Ghada I.; Gao, Yongli; Mannsfeld, Stefan C. B.; Salleo, Alberto; Ade, Harald; Zhao, Dahui; Bao, Zhenan

    2014-01-01

    An average PCE of 4.2% for all-polymer solar cells from 20 devices with an average J SC of 8.8 mA cm-2 are obtained with a donor-acceptor pair despite a low LUMO-LUMO energy offset of less than 0.1 eV. Incorporation of polystyrene side chains into the donor polymer is found to assist in reducing the phase separation domain length scale, and results in more than 20% enhancement of PCE. We observe a direct correlation between the short circuit current (J SC) and the length scale of BHJ phase separation, which is obtained by resonance soft X-ray scattering. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Rotator side chains trigger cooperative transition for shape and function memory effect in organic semiconductors.

    Science.gov (United States)

    Chung, Hyunjoong; Dudenko, Dmytro; Zhang, Fengjiao; D'Avino, Gabriele; Ruzié, Christian; Richard, Audrey; Schweicher, Guillaume; Cornil, Jérôme; Beljonne, David; Geerts, Yves; Diao, Ying

    2018-01-18

    Martensitic transition is a solid-state phase transition involving cooperative movement of atoms, mostly studied in metallurgy. The main characteristics are low transition barrier, ultrafast kinetics, and structural reversibility. They are rarely observed in molecular crystals, and hence the origin and mechanism are largely unexplored. Here we report the discovery of martensitic transition in single crystals of two different organic semiconductors. In situ microscopy, single-crystal X-ray diffraction, Raman and nuclear magnetic resonance spectroscopy, and molecular simulations combined indicate that the rotating bulky side chains trigger cooperative transition. Cooperativity enables shape memory effect in single crystals and function memory effect in thin film transistors. We establish a molecular design rule to trigger martensitic transition in organic semiconductors, showing promise for designing next-generation smart multifunctional materials.

  3. Novel side-chain liquid crystalline polyester architecture for reversible optical storage

    DEFF Research Database (Denmark)

    Hvilsted, Søren; Andruzzi, Fulvio; Kulinna, Chrisian

    1995-01-01

    New side-chain liquid crystalline polyesters have been prepared by melt transesterification of diphenyl tetradecanedioate and a series of mesogenic 2-[omega-[4-[(4-cyanophenyl)azo]phenoxyl] alkyl]-1,3-propanediols, where the alkyl spacer is hexa-, octa-, and decamethylene in turn. The polyesters...... have molecular masses in the range 5000-89 000. Solution C-13 NMR spectroscopy has been employed to identify carbons of polyester repeat units and of both types of end groups. Polyester phases and phase transitions have been investigated in detail by polarizing optical microscopy and differential...... scanning calorimetry for the hexamethylene spacer architecture with different molecular masses. Using FTIR polarization spectroscopy, the segmental orientation in unoriented polyester films induced by argon ion laser irradiation has been followed and an irradiation-dependent order parameter...

  4. Side chain and backbone contributions of Phe508 to CFTR folding

    Energy Technology Data Exchange (ETDEWEB)

    Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J. (U. of Texas-SMED)

    2010-12-07

    Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an integral membrane protein, cause cystic fibrosis (CF). The most common CF-causing mutant, deletion of Phe508, fails to properly fold. To elucidate the role Phe508 plays in the folding of CFTR, missense mutations at this position were generated. Only one missense mutation had a pronounced effect on the stability and folding of the isolated domain in vitro. In contrast, many substitutions, including those of charged and bulky residues, disrupted folding of full-length CFTR in cells. Structures of two mutant nucleotide-binding domains (NBDs) reveal only local alterations of the surface near position 508. These results suggest that the peptide backbone plays a role in the proper folding of the domain, whereas the side chain plays a role in defining a surface of NBD1 that potentially interacts with other domains during the maturation of intact CFTR.

  5. Lithiated short side chain perfluorinated sulfonic ionomeric membranes: Water content and conductivity

    Science.gov (United States)

    Navarrini, Walter; Scrosati, Bruno; Panero, Stefania; Ghielmi, Alessandro; Sanguineti, Aldo; Geniram, Giuliana

    In view of possible applications as single-ion electrolyte for lithium batteries, some aspects of the lithium form of Hyflon Ion ionomer, a sulfonic short side chain (SSC) electrolyte, have been investigated. The synthesis of the ionomer and the successive membrane preparation is reported. An appropriate methodology for the direct salification of the ionomeric membrane from the SO 2F form to lithium salt, using lithium hydroxide in absence of organic solvent has been found. Utilizing these SSC lithium ionomer membranes and though a particular methodology for the dehydration of the lithium ion membrane in non-aqueous media, it has been possible to achieve an ionic conductivity of 10 -3 S cm -1 at room temperature [W. Navarrini, S. Panero, B. Scrosati, A. Sanguineti, European Patent 1,403,958 A1 (2003)]. Surprisingly it was observed that the membrane ionic conductivity depends on the dehydration methodologies adopted.

  6. High Performance All-Polymer Solar Cell via Polymer Side-Chain Engineering

    KAUST Repository

    Zhou, Yan

    2014-03-24

    An average PCE of 4.2% for all-polymer solar cells from 20 devices with an average J SC of 8.8 mA cm-2 are obtained with a donor-acceptor pair despite a low LUMO-LUMO energy offset of less than 0.1 eV. Incorporation of polystyrene side chains into the donor polymer is found to assist in reducing the phase separation domain length scale, and results in more than 20% enhancement of PCE. We observe a direct correlation between the short circuit current (J SC) and the length scale of BHJ phase separation, which is obtained by resonance soft X-ray scattering. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. White emission from liquid-crystalline copolymers containing oxadiazole moieties in the side chain

    Science.gov (United States)

    Kawamoto, Masuki; Tsukamoto, Takuji; Kinoshita, Motoi; Ikeda, Tomiki

    2006-09-01

    A liquid-crystalline polymer in the side chain was synthesized through copolymerization of a bipolar carrier-transporting monomer with a liquid-crystalline monomer containing oxadiazole moieties substituted with trifluoromethyl groups. A single-layer light-emitting diode of indium tin oxide (ITO)/copolymer/MgAg emitted white light with a maximum luminous efficiency of 0.1cd/A. The origin of the white emission in the copolymer is the electroplex between bipolar carrier-transporting moieties and strong electron-withdrawing moieties. Furthermore, a simple multilayer device with configuration of ITO/poly(3,4-ethylenedioxythiophene)/poly(styrenesulfonic acid)/copolymer/MgAg device showed white emission with CIE 1931 chromaticity coordinates (x,y): (0.30, 0.33).

  8. Diffraction from polarization holographic gratings with surface relief in side-chain azobenzene polyesters

    DEFF Research Database (Denmark)

    Naydenova, I; Nikolova, L; Todorov, T

    1998-01-01

    We investigate the polarization properties of holographic gratings in side-chain azobenzene polyesters in which an anisotropic grating that is due to photoinduced linear and circular birefringence is recorded in the volume of the material and a relief grating appears on the surface. A theoretical...... model is proposed to explain the experimental results, making it possible to understand the influence of the different photoinduced effects. It is shown that at low intensity the polarization properties of the diffraction at these gratings are determined by the interaction of the linear and circular...... photobirefringences, and at larger intensity the influence of the surface relief dominates the effect of the circular anisotropy. Owing to the high recording efficiency of the polyesters, the +/-1-order diffracted waves change the polarization interference pattern during the holographic recording, resulting...

  9. Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions

    Directory of Open Access Journals (Sweden)

    Inbar Yuval

    2010-07-01

    Full Text Available Abstract Background Accurate evaluation and modelling of residue-residue interactions within and between proteins is a key aspect of computational structure prediction including homology modelling, protein-protein docking, refinement of low-resolution structures, and computational protein design. Results Here we introduce a method for accurate protein structure modelling and evaluation based on a novel 4-distance description of residue-residue interaction geometry. Statistical 4-distance preferences were extracted from high-resolution protein structures and were used as a basis for a knowledge-based potential, called Hunter. We demonstrate that 4-distance description of side chain interactions can be used reliably to discriminate the native structure from a set of decoys. Hunter ranked the native structure as the top one in 217 out of 220 high-resolution decoy sets, in 25 out of 28 "Decoys 'R' Us" decoy sets and in 24 out of 27 high-resolution CASP7/8 decoy sets. The same concept was applied to side chain modelling in protein structures. On a set of very high-resolution protein structures the average RMSD was 1.47 Å for all residues and 0.73 Å for buried residues, which is in the range of attainable accuracy for a model. Finally, we show that Hunter performs as good or better than other top methods in homology modelling based on results from the CASP7 experiment. The supporting web site http://bioinfo.weizmann.ac.il/hunter/ was developed to enable the use of Hunter and for visualization and interactive exploration of 4-distance distributions. Conclusions Our results suggest that Hunter can be used as a tool for evaluation and for accurate modelling of residue-residue interactions in protein structures. The same methodology is applicable to other areas involving high-resolution modelling of biomolecules.

  10. Energetically Unfavorable Amide Conformations for N6-Acetyllysine Side Chains in Refined Protein Structures

    Science.gov (United States)

    Genshaft, Alexander; Moser, Joe-Ann S.; D'Antonio, Edward L.; Bowman, Christine M.; Christianson, David W.

    2013-01-01

    The reversible acetylation of lysine to form N6-acetyllysine in the regulation of protein function is a hallmark of epigenetics. Acetylation of the positively charged amino group of the lysine side chain generates a neutral N-alkylacetamide moiety that serves as a molecular “switch” for the modulation of protein function and protein-protein interactions. We now report the analysis of 381 N6-acetyllysine side chain amide conformations as found in 79 protein crystal structures and 11 protein NMR structures deposited in the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics. We find that only 74.3% of N6-acetyllysine residues in protein crystal structures and 46.5% in protein NMR structures contain amide groups with energetically preferred trans or generously trans conformations. Surprisingly, 17.6% of N6-acetyllysine residues in protein crystal structures and 5.3% in protein NMR structures contain amide groups with energetically unfavorable cis or generously cis conformations. Even more surprisingly, 8.1% of N6-acetyllysine residues in protein crystal structures and 48.2% in NMR structures contain amide groups with energetically prohibitive twisted conformations that approach the transition state structure for cis-trans isomerization. In contrast, 109 unique N-alkylacetamide groups contained in 84 highly-accurate small molecule crystal structures retrieved from the Cambridge Structural Database exclusively adopt energetically preferred trans conformations. Therefore, we conclude that cis and twisted N6-acetyllysine amides in protein structures deposited in the PDB are erroneously modeled due to their energetically unfavorable or prohibitive conformations. PMID:23401043

  11. Computational mining for hypothetical patterns of amino acid side chains in protein data bank (PDB)

    Science.gov (United States)

    Ghani, Nur Syatila Ab; Firdaus-Raih, Mohd

    2018-04-01

    The three-dimensional structure of a protein can provide insights regarding its function. Functional relationship between proteins can be inferred from fold and sequence similarities. In certain cases, sequence or fold comparison fails to conclude homology between proteins with similar mechanism. Since the structure is more conserved than the sequence, a constellation of functional residues can be similarly arranged among proteins of similar mechanism. Local structural similarity searches are able to detect such constellation of amino acids among distinct proteins, which can be useful to annotate proteins of unknown function. Detection of such patterns of amino acids on a large scale can increase the repertoire of important 3D motifs since available known 3D motifs currently, could not compensate the ever-increasing numbers of uncharacterized proteins to be annotated. Here, a computational platform for an automated detection of 3D motifs is described. A fuzzy-pattern searching algorithm derived from IMagine an Amino Acid 3D Arrangement search EnGINE (IMAAAGINE) was implemented to develop an automated method for searching of hypothetical patterns of amino acid side chains in Protein Data Bank (PDB), without the need for prior knowledge on related sequence or structure of pattern of interest. We present an example of the searches, which is the detection of a hypothetical pattern derived from known structural motif of C2H2 structural pattern from zinc fingers. The conservation of particular patterns of amino acid side chains in unrelated proteins is highlighted. This approach can act as a complementary method for available structure- and sequence-based platforms and may contribute in improving functional association between proteins.

  12. Side-chain-controlled self-assembly of polystyrene-polypeptide miktoarm star copolymers

    KAUST Repository

    Junnila, Susanna

    2012-03-27

    We show how the self-assembly of miktoarm star copolymers can be controlled by modifying the side chains of their polypeptide arms, using A 2B and A 2B 2 type polymer/polypeptide hybrids (macromolecular chimeras). Initially synthesized PS 2PBLL and PS 2PBLL 2 (PS, polystyrene; PBLL, poly(ε-tert-butyloxycarbonyl-l-lysine) ) miktoarms were first deprotected to PS 2PLLHCl and PS 2PLLHCl 2 miktoarms (PLLHCl, poly(l-lysine hydrochloride)) and then complexed ionically with sodium dodecyl sulfonate (DS) to give the supramolecular complexes PS 2PLL(DS) and PS 2(PLL(DS)) 2. The solid-state self-assemblies of these six miktoarm systems were studied by transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and small- and wide-angle X-ray scattering (SAXS, WAXS). The side chains of the polypeptide arms were observed to have a large effect on the solubility, polypeptide conformation, and self-assembly of the miktoarms. Three main categories were observed: (i) lamellar self-assemblies at the block copolymer length scale with packed layers of α-helices in PS 2PBLL and PS 2PBLL 2; (ii) charge-clustered polypeptide micelles with less-defined conformations in a nonordered lattice within a PS matrix in PS 2PLLHCl and PS 2PLLHCl 2; (iii) lamellar polypeptide-surfactant self-assemblies with β-sheet conformation in PS 2PLL(DS) and PS 2(PLL(DS)) 2 which dominate over the formation of block copolymer scale structures. Differences between the 3- and 4-arm systems illustrate how packing frustration between the coil-like PS arms and rigid polypeptide conformations can be relieved by the right number of arms, leading to differences in the extent of order. © 2012 American Chemical Society.

  13. Methylation of hemoglobin to enhance flocculant performance

    Science.gov (United States)

    An inexpensive bioflocculant, bovine hemoglobin (Hb), has been covalently modified through methylation of the side chain carboxyl groups of aspartic and glutamic acid residues to improve its flocculation activity. Potentiometric titration of the recovered products showed approximately 28% degree of ...

  14. DMFC Performance of Polymer Electrolyte Membranes Prepared from a Graft-Copolymer Consisting of a Polysulfone Main Chain and Styrene Sulfonic Acid Side Chains

    Directory of Open Access Journals (Sweden)

    Nobutaka Endo

    2016-08-01

    Full Text Available Polymer electrolyte membranes (PEMs for direct methanol fuel cell (DMFC applications were prepared from a graft-copolymer (PSF-g-PSSA consisting of a polysulfone (PSF main chain and poly(styrene sulfonic acid (PSSA side chains with various average distances between side chains (Lav and side chain lengths (Lsc. The polymers were synthesized by grafting ethyl p-styrenesulfonate (EtSS on macro-initiators of chloromethylated polysulfone with different contents of chloromethyl (CM groups, and by changing EtSS content in the copolymers by using atom transfer radical polymerization (ATRP. The DMFC performance tests using membrane electrode assemblis (MEAs with the three types of the PEMs revealed that: a PSF-g-PSSA PEM (SF-6 prepared from a graft copolymer with short average distances between side chains (Lav and medium Lsc had higher DMFC performance than PEMs with long Lav and long Lsc or with short Lav and short Lsc. SF-6 had about two times higher PDmax (68.4 mW/cm2 than Nafion® 112 at 30 wt % of methanol concentration. Furthermore, it had 58.2 mW/cm2 of PDmax at 50 wt % of methanol concentration because of it has the highest proton selectivity during DMFC operation of all the PSF-g-PSSA PEMs and Nafion® 112.

  15. Multi-functionalized side-chain supramolecular polymers: A methodology towards tunable functional materials

    Science.gov (United States)

    Nair, Kamlesh Prabhakaran

    Even as we see a significant growth in the field of supramolecular polymers in the last ten years, multi-functionalized systems have been scarcely studied. Noncovalent multi-functionalization provides unique advantages such as rapid materials optimization via reversible functionalization as well as for the tuning of materials properties by exploiting the differences in the nature of these reversible interactions. This thesis involves the design principles, synthesis & methodology of supramolecular side-chain multi-functionalized polymers. The combination of a functionally tolerant & controlled polymerization technique such as ROMP with multiple noncovalent interactions such as hydrogen bonding, metal coordination and ionic interactions has been successfully used to synthesize these polymers. Furthermore, the orthogonality between the above interactions in block/random copolymers has been studied in detail. It has been found that the studied interactions were orthogonal to each other. To validate the viability of this methodology using multiple orthogonal interactions towards materials design noncovalent crosslinking of polymers has been used as a potential application. Three classes of networks have been studied: complementary multiple hydrogen bonded networks, metal crosslinked networks, & multi-functionalized hydrogen bonded and metal coordinated networks. The first room temperature decrosslinking by exclusive complementary hydrogen bonded interactions has been successfully achieved. Furthermore network properties have been successfully tuned by varying the network micro-structure which in turn was tuned by the hydrogen bonding motifs used for inter-chain crosslinking. By combining two different noncovalent interactions used for inter-chain crosslinking, it was possible to make multi-functionalized materials whose properties could be controlled by varying the crosslinking strategy. Hence by employing multi-functionalization methodology, important materials

  16. The power of hard-sphere models: explaining side-chain dihedral angle distributions of Thr and Val.

    Science.gov (United States)

    Zhou, Alice Qinhua; O'Hern, Corey S; Regan, Lynne

    2012-05-16

    The energy functions used to predict protein structures typically include both molecular-mechanics and knowledge-based terms. In contrast, our approach is to develop robust physics- and geometry-based methods. Here, we investigate to what extent simple hard-sphere models can be used to predict side-chain conformations. The distributions of the side-chain dihedral angle χ(1) of Val and Thr in proteins of known structure show distinctive features: Val side chains predominantly adopt χ(1) = 180°, whereas Thr side chains typically adopt χ(1) = 60° and 300° (i.e., χ(1) = ±60° or g- and g(+) configurations). Several hypotheses have been proposed to explain these differences, including interresidue steric clashes and hydrogen-bonding interactions. In contrast, we show that the observed side-chain dihedral angle distributions for both Val and Thr can be explained using only local steric interactions in a dipeptide mimetic. Our results emphasize the power of simple physical approaches and their importance for future advances in protein engineering and design. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  17. Characterization of threonine side chain dynamics in an antifreeze protein using natural abundance {sup 13}C NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Daley, Margaret E.; Sykes, Brian D. [University of Alberta, Department of Biochemistry, CIHR Group in Protein Structure and Function and Protein Engineering Network of Centres of Excellence (Canada)

    2004-06-15

    The dynamics of threonine side chains of the Tenebrio molitor antifreeze protein (TmAFP) were investigated using natural abundance {sup 13}C NMR. In TmAFP, the array of threonine residues on one face of the protein is responsible for conferring its ability to bind crystalline ice and inhibit its growth. Heteronuclear longitudinal and transverse relaxation rates and the {sup 1}H-{sup 13}C NOE were determined in this study. The C{alpha}H relaxation measurements were compared to the previously measured {sup 15}N backbone parameters and these are found to be in agreement. For the analysis of the threonine side chain motions, the model of restricted rotational diffusion about the {chi}{sub 1} dihedral angle was employed [London and Avitabile (1978) J. Am. Chem. Soc., 100, 7159-7165]. We demonstrate that the motion experienced by the ice binding threonine side chains is highly restricted, with an approximate upper limit of less than {+-}25 deg.

  18. Characterization of threonine side chain dynamics in an antifreeze protein using natural abundance 13C NMR spectroscopy

    International Nuclear Information System (INIS)

    Daley, Margaret E.; Sykes, Brian D.

    2004-01-01

    The dynamics of threonine side chains of the Tenebrio molitor antifreeze protein (TmAFP) were investigated using natural abundance 13 C NMR. In TmAFP, the array of threonine residues on one face of the protein is responsible for conferring its ability to bind crystalline ice and inhibit its growth. Heteronuclear longitudinal and transverse relaxation rates and the 1 H- 13 C NOE were determined in this study. The CαH relaxation measurements were compared to the previously measured 15 N backbone parameters and these are found to be in agreement. For the analysis of the threonine side chain motions, the model of restricted rotational diffusion about the χ 1 dihedral angle was employed [London and Avitabile (1978) J. Am. Chem. Soc., 100, 7159-7165]. We demonstrate that the motion experienced by the ice binding threonine side chains is highly restricted, with an approximate upper limit of less than ±25 deg

  19. From Semi- to Full-Two-Dimensional Conjugated Side-Chain Design: A Way toward Comprehensive Solar Energy Absorption

    Energy Technology Data Exchange (ETDEWEB)

    Chao, Pengjie [Department; School; Wang, Huan [Department; Qu, Shiwei [Department; Mo, Daize [Department; Meng, Hong [School; Chen, Wei [Materials; Institute; He, Feng [Department

    2017-12-05

    Two polymers with fully two-dimensional (2D) conjugated side chains, 2D-PTB-Th and 2D-PTB-TTh, were synthesized and characterized through simultaneously integrating the 2D-TT and the 2D-BDT monomers onto the polymer backbone. Resulting from the synergistic effect from the conjugated side chains on both monomers, the two polymers showed remarkably efficient absorption of the sunlight and improved pi-pi intermolecular interactions for efficient charge carrier transport. The optimized bulk heterojunction device based on 2D-PTB-Th and PC71BM shows a higher PCE of 9.13% compared to PTB7-Th with a PCE of 8.26%, which corresponds to an approximately 10% improvement in solar energy conversion. The fully 2D-conjugated side-chain concept reported here developed a new molecular design strategy for polymer materials with enhanced sunlight absorption and efficient solar energy conversion.

  20. Role of Side-Chain Molecular Features in Tuning Lower Critical Solution Temperatures (LCSTs) of Oligoethylene Glycol Modified Polypeptides.

    Science.gov (United States)

    Gharakhanian, Eric G; Deming, Timothy J

    2016-07-07

    A series of thermoresponsive polypeptides has been synthesized using a methodology that allowed facile adjustment of side-chain functional groups. The lower critical solution temperature (LCST) properties of these polymers in water were then evaluated relative to systematic molecular modifications in their side-chains. It was found that in addition to the number of ethylene glycol repeats in the side-chains, terminal and linker groups also have substantial and predictable effects on cloud point temperatures (Tcp). In particular, we found that the structure of these polypeptides allowed for inclusion of polar hydroxyl groups, which significantly increased their hydrophilicity and decreased the need to use long oligoethylene glycol repeats to obtain LCSTs. The thioether linkages in these polypeptides were found to provide an additional structural feature for reversible switching of both polypeptide conformation and thermoresponsive properties.

  1. Structural effects of a light emitting copolymer having perylene moieties in the side chain on the electroluminescent characteristics

    International Nuclear Information System (INIS)

    Lee, Chang Ho; Ryu, Seung Hoon; Jang, Hee Dong; Oh, Se Young

    2004-01-01

    We have synthesized a novel side chain light emitting copolymer. The side chain light emitting copolymer has a perylene moiety as an emitting unit and methylmethacrylate (MMA) as a spacer to decrease the concentration quenching of light emitting site in the polymer intrachain. These polymers are very soluble in most organic solvents such as monochlorobenzene, tetrahydrofuran, chloroform and benzene. The single-layered electroluminescent (EL) device consisting of ITO/carrier transporting copolymer and light emitting copolymer/Al was manufactured. The carrier transporting copolymer has triphenylamine moiety as a hole transporting unit and triazine moiety as an electron transporting unit in the polymer side chain. This device exhibits maximum external quantum efficiency when the MMA contents of light emitting copolymer is 30 wt.%. In particular, the device emits more blue light as MMA contents increase

  2. The Influence of Conjugated Polymer Side Chain Manipulation on the Efficiency and Stability of Polymer Solar Cells

    DEFF Research Database (Denmark)

    Heckler, Ilona Maria; Kesters, Jurgen; Defour, Maxime

    2016-01-01

    ]thiazole (TzTz) acceptor units, were selected toward effective device scalability by roll-coating. The influence of the partial exchange (5% or 10%) of the solubilizing 2-hexyldecyloxy by alternative 2-phenylethoxy groups on efficiency and stability was investigated. With an increasing 2-phenylethoxy ratio...... studies under constant sun irradiance showed a diminishing initial degradation rate for the BT-based devices upon including the alternative side chains, whereas the (more stable) TzTz-based devices degraded at a faster rate from the start of the experiment upon partly exchanging the side chains. No clear......The stability of polymer solar cells (PSCs) can be influenced by the introduction of particular moieties on the conjugated polymer side chains. In this study, two series of donor-acceptor copolymers, based on bis(thienyl)dialkoxybenzene donor and benzo[c][1,2,5]thiadiazole (BT) or thiazolo[5,4-d...

  3. Novel Pyridinium Surfactants with Unsaturated Alkyl Chains : Aggregation Behavior and Interactions with Methyl Orange in Aqueous Solution

    NARCIS (Netherlands)

    Kuiper, Johanna M.; Buwalda, Rixt T.; Hulst, Ron; Engberts, Jan B.F.N.

    2001-01-01

    This paper presents the synthesis and a study of the aggregation behavior of 4-undecyl-1-methyl- and 4-undecenyl-1-methylpyridinium iodide surfactants. The effect of the position of the double bond in the alkyl chain of the surfactant on the critical micelle concentration (cmc), degree of counterion

  4. Introduction of a methoxymethyl side chain into p-phenylenediamine attenuates its sensitizing potency and reduces the risk of allergy induction

    Energy Technology Data Exchange (ETDEWEB)

    Goebel, Carsten, E-mail: goebel.c.1@pg.com [The Procter and Gamble Co., Central Product Safety and Communications, Darmstadt (Germany); Troutman, John [The Procter and Gamble Co., Central Product Safety, Cincinnati, OH (United States); Hennen, Jenny [Dept. of Environmental Toxicology, Trier University, Trier (Germany); Rothe, Helga; Schlatter, Harald [The Procter and Gamble Co., Central Product Safety and Communications, Darmstadt (Germany); Gerberick, G. Frank [The Procter and Gamble Co., Central Product Safety, Cincinnati, OH (United States); Blömeke, Brunhilde [Dept. of Environmental Toxicology, Trier University, Trier (Germany)

    2014-02-01

    The strong sensitizing potencies of the most important primary intermediates of oxidative hair dyes, p-phenylenediamine (PPD) and p-toluylenediamine (PTD, i.e. 2-methyl-PPD) are well established. They are considered as the key sensitizers in hair dye allergic contact dermatitis. While modification of their molecular structure is expected to alter their sensitizing properties, it may also impair their color performance. With introduction of a methoxymethyl side chain we found the primary intermediate 2-methoxymethyl-p-phenylenediamine (ME-PPD) with excellent hair coloring performance but significantly reduced sensitizing properties compared to PPD and PTD: In vitro, ME-PPD showed an attenuated innate immune response when analyzed for its protein reactivity and dendritic cell activation potential. In vivo, the effective concentration of ME-PPD necessary to induce an immune response 3-fold above vehicle control (EC3 value) in the local lymph node assay (LLNA) was 4.3%, indicating a moderate skin sensitizing potency compared to values of 0.1 and 0.17% for PPD and PTD, respectively. Finally, assessing the skin sensitizing potency of ME-PPD under consumer hair dye usage conditions through a quantitative risk assessment (QRA) indicated an allergy induction risk negligible compared to PPD or PTD. - Highlights: • Methoxymethyl side chain in p-phenylenediamine reduces its strong skin sensitizing properties. • Reduced protein reactivity and dendritic cell activation. • Reduced skin sensitizing potency in local lymph node assay (LLNA). • Negligible allergy induction risk under hair dye usage conditions.

  5. Introduction of a methoxymethyl side chain into p-phenylenediamine attenuates its sensitizing potency and reduces the risk of allergy induction

    International Nuclear Information System (INIS)

    Goebel, Carsten; Troutman, John; Hennen, Jenny; Rothe, Helga; Schlatter, Harald; Gerberick, G. Frank; Blömeke, Brunhilde

    2014-01-01

    The strong sensitizing potencies of the most important primary intermediates of oxidative hair dyes, p-phenylenediamine (PPD) and p-toluylenediamine (PTD, i.e. 2-methyl-PPD) are well established. They are considered as the key sensitizers in hair dye allergic contact dermatitis. While modification of their molecular structure is expected to alter their sensitizing properties, it may also impair their color performance. With introduction of a methoxymethyl side chain we found the primary intermediate 2-methoxymethyl-p-phenylenediamine (ME-PPD) with excellent hair coloring performance but significantly reduced sensitizing properties compared to PPD and PTD: In vitro, ME-PPD showed an attenuated innate immune response when analyzed for its protein reactivity and dendritic cell activation potential. In vivo, the effective concentration of ME-PPD necessary to induce an immune response 3-fold above vehicle control (EC3 value) in the local lymph node assay (LLNA) was 4.3%, indicating a moderate skin sensitizing potency compared to values of 0.1 and 0.17% for PPD and PTD, respectively. Finally, assessing the skin sensitizing potency of ME-PPD under consumer hair dye usage conditions through a quantitative risk assessment (QRA) indicated an allergy induction risk negligible compared to PPD or PTD. - Highlights: • Methoxymethyl side chain in p-phenylenediamine reduces its strong skin sensitizing properties. • Reduced protein reactivity and dendritic cell activation. • Reduced skin sensitizing potency in local lymph node assay (LLNA). • Negligible allergy induction risk under hair dye usage conditions

  6. Regioselectively nucleus and/or side-chain fluorinated 2-(Phenanthryl)propionic acids by an effective combination of radical and organometallic chemistry.

    Science.gov (United States)

    Ricci, Giacomo; Ruzziconi, Renzo

    2005-01-21

    Regioselectively nucleus and/or side-chain fluorinated 2-(phenanthr-1-yl)- and 2-(phenanthr-2-yl)propionic acids 1-5 were prepared using phenanthren-1(2H)-ones 6a-c as key intermediates. Thus, ethyl 2-(fluorophenanthryl)propionates 11 were obtained in good yields by Reformatsky reaction of 6a-c with ethyl 2-bromopropionate followed by dehydratation and DDQ-promoted aromatization of the resulting beta-hydroxyesters. Side-chain alkyl 2-hydroxy-2-(phenanthr-1-yl)propionates 14 were obtained by bromine/lithium permutation of dihydrophenanthryl bromides 12a-c with butyllithium followed by quenching of the lithiated intermediates with methyl pyruvate or ethyl 3,3,3-trifluoropyruvate and subsequent DDQ-promoted aromatization. The alkyl 2-hydroxy-2-(phenanthr-1-yl)propionates 25 were prepared by reacting 8-bromo-1,3-difluorophenanthrene 24 with butyllithium for 10 seconds at -110 degrees C and subsequent addition of the suitable pyruvate to the lithiated intermediates. Alkyl 2-hydroxy-2-(phenanthr-2-yl)propionates 26 and 29 were suitably obtained by site-selective metalation of 1,3-difluorophenanthrene 28 and the bromophenanthrene 24, respectively, with LDA followed by quenching of the metalated intermediates with the suitable alkyl pyruvate. Fluorination of the above alpha-hydroxypropionates with DAST, followed by the alkaline hydrolysis, allowed the expected 2-(phenanthryl)propionic acids 1-5 to be obtained in satisfactory overall yields.

  7. Unique contributions of an arginine side chain to ligand recognition in a glutamate-gated chloride channel

    DEFF Research Database (Denmark)

    Lynagh, Timothy; Komnatnyy, Vitaly V; Pless, Stephan A

    2017-01-01

    Glutamate recognition by neurotransmitter receptors often relies on arginine (Arg) residues in the binding site, leading to the assumption that charge-charge interactions underlie ligand recognition. However, assessing the precise chemical contribution of Arg side chains to protein function......-gated chloride channel from the nematode Haemonchus contortus. Our data unveil a surprisingly small contribution of charge at a conserved arginine side chain previously suggested to form a salt bridge with the ligand, glutamate. Instead, our data show that Arg contributes crucially to ligand sensitivity via...

  8. Fabrication of narrow surface relief features in a side-chain azobenzene polyester with a scanning near-field microscope

    DEFF Research Database (Denmark)

    Ramanujam, P.S.; Holme, N. C. R.; Pedersen, M.

    2001-01-01

    We show that it is possible to fabricate topographic submicron features in a side-chain azobenzene polyester with a scanning near-field optical microscope, Through irradiation at a wavelength of 488 run at intensity levels of 12 W/cm(2), topographic features as narrow as 240 nm and as high as 6 nm...... have been reproducibly recorded in a thin film of the polyester. These observations are consistent with the fact that at low intensities peaks are produced evolving into formation of trenches at high intensities in the case of amorphous side-chain azobenzene polyesters. This may find applications...

  9. Proton conducting graft copolymers with tunable length and density of phosphonated side chains for fuel cell membranes

    DEFF Research Database (Denmark)

    Dimitrov, Ivaylo; Takamuku, Shogo; Jankova Atanasova, Katja

    2014-01-01

    Polysulfones functionalized with highly phosphonated poly(pentafluorostyrene) side chains of different lengths were synthesized applying controlled polymerization and modification methods. The graft copolymers' thermal properties were evaluated by differential scanning calorimetry and thermal...... gravimetrical analyses. The proton conductivity of membrane prepared from the graft copolymer with the shortest phosphonated side chains was 134 mS cm(-1) at 100 degrees C under fully immersed conditions. The graft copolymer TEM image shows a nanophase separation of ion-rich segments within the polysulfone...

  10. Structure and isotopic ratios of aliphatic side chains in the insoluble organic matter of the Murchison carbonaceous chondrite

    Science.gov (United States)

    Huang, Yongsong; Alexandre, Marcelo R.; Wang, Yi

    2007-07-01

    We report in this paper the first molecular and isotopic characterization of individual aliphatic side chains from the insoluble organic matter (IOM) in the Murchison carbonaceous chondrite using a novel combined approach of RuO 4 oxidation and solid phase microextraction (SPME). The aliphatic side chains in the IOM of Murchison were first released by oxidizing aromatic structures using RuO 4. Because the IOM of carbonaceous chondrites contains predominantly short (C 1 to C 9) aliphatic substitutions, the resulting low molecular weight monocarboxylic acids (MCAs) are highly volatile and water-soluble. The conventional aqueous extraction and derivatization procedures following RuO 4 oxidation are unable to recover MCAs for subsequent analyses. We overcame this problem by employing SPME to directly capture the MCAs from the aqueous solution. We selected a SPME fiber with greater affinity for longer chain monoacids to compensate for the exponential decline of monoacid concentrations with increasing carbon numbers in meteorite IOM, allowing more accurate identification and quantification for the less abundant monoacids. We also determined the carbon and hydrogen isotopic ratios of individual MCAs derived from Murchinson IOM. Our results reveal significant similarity in both molecular structures and hydrogen isotopic ratios between the IOM aliphatic side chains and water-soluble MCAs in Murchison, suggesting that these compounds had common precursors. Our combined new approach of RuO 4 oxidation-SPME provides a new way to probe the molecular and isotopic characteristics of aliphatic side chains in carbonaceous chondrites.

  11. Effect of side chain length and degree of polymerization on the decomposition and crystallization behaviour of chlorinated poly(vinyl ester) oligomers

    International Nuclear Information System (INIS)

    Heinze, D.; Mang, Th.; Popescu, C.; Weichold, O.

    2016-01-01

    Highlights: • Thermal behaviour of telomerized polyvinyl esters is investigated. • Thermal stability relies mainly on the contribution of side chains. • At equal molecular weights thermal stability is dictated by length of side chain. • Increasing the length of side chains improves also the packing degree of polymer. - Abstract: Four members of a homologous series of chlorinated poly(vinyl ester) oligomers CCl_3–(CH_2CH (OCO(CH_2)_mCH_3))_n–Cl with degrees of polymerization of 10 and 20 were prepared by telomerisation using carbon tetrachloride. The number of side chain carbon atoms ranges from 2 (poly(vinyl acetate) to 18 (poly(vinyl stearate)). The effect of the n-alkyl side chain length and of the degree of polymerization on the thermal stability and crystallization behaviour of the synthesized compounds was investigated. All oligomers degrade in two major steps by first losing HCl and side chains with subsequent breakdown of the backbone. The members with short side chains, up to poly(vinyl octanoate), are amorphous and show internal plasticization, whereas those with high number of side chain carbon atoms are semi-crystalline due to side-chain crystallization. A better packing for poly(vinyl stearate) is also noticeable. The glass transition and melting temperatures as well as the onset temperature of decomposition are influenced to a larger extent by the side chain length than by the degree of polymerization. Thermal stability is improved if both the size and number of side chains increase, but only a long side chain causes a significant increase of the resistance to degradation. This results in a stabilization of PVAc so that oligomers from poly(vinyl octanoate) on are stable under atmospheric conditions. Thus, the way to design stable, chlorinated PVEs oligomers is to use a long n-alkyl side chain.

  12. Effect of side chain length and degree of polymerization on the decomposition and crystallization behaviour of chlorinated poly(vinyl ester) oligomers

    Energy Technology Data Exchange (ETDEWEB)

    Heinze, D.; Mang, Th. [Aachen University of Applied Sciences, Heinrich-Mussmann-Str. 1, 52428 Jülich (Germany); Popescu, C., E-mail: crisan.popescu@kao.com [KAO Germany GmbH, Pfungstädterstr. 98-100, 64297 Darmstadt (Germany); Weichold, O., E-mail: weichold@ibac.rwth-aachen.de [Institute of Building Materials Research, Schinkelstr. 3, 52062 Aachen (Germany)

    2016-08-10

    Highlights: • Thermal behaviour of telomerized polyvinyl esters is investigated. • Thermal stability relies mainly on the contribution of side chains. • At equal molecular weights thermal stability is dictated by length of side chain. • Increasing the length of side chains improves also the packing degree of polymer. - Abstract: Four members of a homologous series of chlorinated poly(vinyl ester) oligomers CCl{sub 3}–(CH{sub 2}CH (OCO(CH{sub 2}){sub m}CH{sub 3})){sub n}–Cl with degrees of polymerization of 10 and 20 were prepared by telomerisation using carbon tetrachloride. The number of side chain carbon atoms ranges from 2 (poly(vinyl acetate) to 18 (poly(vinyl stearate)). The effect of the n-alkyl side chain length and of the degree of polymerization on the thermal stability and crystallization behaviour of the synthesized compounds was investigated. All oligomers degrade in two major steps by first losing HCl and side chains with subsequent breakdown of the backbone. The members with short side chains, up to poly(vinyl octanoate), are amorphous and show internal plasticization, whereas those with high number of side chain carbon atoms are semi-crystalline due to side-chain crystallization. A better packing for poly(vinyl stearate) is also noticeable. The glass transition and melting temperatures as well as the onset temperature of decomposition are influenced to a larger extent by the side chain length than by the degree of polymerization. Thermal stability is improved if both the size and number of side chains increase, but only a long side chain causes a significant increase of the resistance to degradation. This results in a stabilization of PVAc so that oligomers from poly(vinyl octanoate) on are stable under atmospheric conditions. Thus, the way to design stable, chlorinated PVEs oligomers is to use a long n-alkyl side chain.

  13. The role of side chain conformational flexibility in surface recognition by Tenebrio molitor antifreeze protein

    Science.gov (United States)

    Daley, Margaret E.; Sykes, Brian D.

    2003-01-01

    Two-dimensional nuclear magnetic resonance spectroscopy was used to investigate the flexibility of the threonine side chains in the β-helical Tenebrio molitor antifreeze protein (TmAFP) at low temperatures. From measurement of the 3Jαβ 1H-1H scalar coupling constants, the χ1 angles and preferred rotamer populations can be calculated. It was determined that the threonines on the ice-binding face of the protein adopt a preferred rotameric conformation at near freezing temperatures, whereas the threonines not on the ice-binding face sample many rotameric states. This suggests that TmAFP maintains a preformed ice-binding conformation in solution, wherein the rigid array of threonines that form the AFP-ice interface matches the ice crystal lattice. A key factor in binding to the ice surface and inhibition of ice crystal growth appears to be the close surface-to-surface complementarity between the AFP and crystalline ice, and the lack of an entropic penalty associated with freezing out motions in a flexible ligand. PMID:12824479

  14. Anti-Biofouling Properties of Comblike Block Copolymers with Amphiphilic Side Chains

    International Nuclear Information System (INIS)

    Krishnan, S.; Ayothi, R.; Hexemer, A.; Finlay, J.; Sohn, K.; Perry, R.; Ober, C.; Kramer, E.; Callow, M.

    2006-01-01

    Surfaces of novel block copolymers with amphiphilic side chains were studied for their ability to influence the adhesion of marine organisms. The surface-active polymer, obtained by grafting fluorinated molecules with hydrophobic and hydrophilic blocks to a block copolymer precursor, showed interesting bioadhesion properties. Two different algal species, one of which adhered strongly to hydrophobic surfaces, and the other, to hydrophilic surfaces, showed notably weak adhesion to the amphiphilic surfaces. Both organisms are known to secrete adhesive macromolecules, with apparently different wetting characteristics, to attach to underwater surfaces. The ability of the amphiphilic surface to undergo an environment-dependent transformation in surface chemistry when in contact with the extracellular polymeric substances is a possible reason for its antifouling nature. Near-edge X-ray absorption fine structure spectroscopy (NEXAFS) was used, in a new approach based on angle-resolved X-ray photoelectron spectroscopy (XPS), to determine the variation in chemical composition within the top few nanometers of the surface and also to study the surface segregation of the amphiphilic block. A mathematical model to extract depth-profile information from the normalized NEXAFS partial electron yield is developed

  15. Kerr effect in the isotropic phase of a side-chain polymeric liquid crystal

    Science.gov (United States)

    Reys, V.; Dormoy, Y.; Collin, D.; Keller, P.; Martinoty, P.

    1992-02-01

    The birefringence induced by a pulsed electrical field was used to study the pretransitional effects associated with the isotropic phase of a side-chain polysiloxane. The results obtained show that these effects are characterised by a conventional value of the static exponent and an abnormal value of the dynamic exponent, which shows that the dynamic theory of low molecular weight liquid crystals does not apply. The results also reveal competition between the dipolar moments induced by the electrical field and the permanent moments of the mesogenic molecules. La biréfringence induite par un champ électrique impulsionnel a été utilisée pour étudier les effets prétransitionnels associés à la phase isotrope d'un polysiloxane à chaînes latérales. Les résultats obtenus montrent que ces effets sont caractérisés par une valeur classique de l'exposant statique et une valeur anormale de l'exposant dynamique. Ce dernier résultat montre que la théorie dynamique des cristaux liquides de bas poids moléculaire n'est pas applicable au cas présent. Les expériences mettent également en évidence une compétition entre les moments dipolaires induits par le champ électrique et les moments permanents des molécules mésogènes.

  16. Effect of alkyl side chain location and cyclicity on the aerobic biotransformation of naphthenic acids.

    Science.gov (United States)

    Misiti, Teresa M; Tezel, Ulas; Pavlostathis, Spyros G

    2014-07-15

    Aerobic biodegradation of naphthenic acids is of importance to the oil industry for the long-term management and environmental impact of process water and wastewater. The effect of structure, particularly the location of the alkyl side chain as well as cyclicity, on the aerobic biotransformation of 10 model naphthenic acids (NAs) was investigated. Using an aerobic, mixed culture, enriched with a commercial NA mixture (NA sodium salt; TCI Chemicals), batch biotransformation assays were conducted with individual model NAs, including eight 8-carbon isomers. It was shown that NAs with a quaternary carbon at the α- or β-position or a tertiary carbon at the β- and/or β'-position are recalcitrant or have limited biodegradability. In addition, branched NAs exhibited lag periods and lower degradation rates than nonbranched or simple cyclic NAs. Two NA isomers used in a closed bottle, aerobic biodegradation assay were mineralized, while 21 and 35% of the parent compound carbon was incorporated into the biomass. The NA biodegradation probability estimated by two widely used models (BIOWIN 2 and 6) and a recently developed model (OCHEM) was compared to the biodegradability of the 10 model NAs tested in this study as well as other related NAs. The biodegradation probability estimated by the OCHEM model agreed best with the experimental data and was best correlated with the measured NA biodegradation rate.

  17. Poly(Amido Amine)s Containing Agmatine and Butanol Side Chains as Efficient Gene Carriers.

    Science.gov (United States)

    Won, Young-Wook; Ankoné, Marc; Engbersen, Johan F J; Feijen, Jan; Kim, Sung Wan

    2016-04-01

    A new type of bioreducible poly(amido amine) copolymer is synthesized by the Michael addition polymerization of cystamine bisacrylamide (CBA) with 4-aminobutylguanidine (agmatine, AGM) and 4-aminobutanol (ABOL). Since the positively charged guanidinium groups of AGM and the hydroxybutyl groups of ABOL in the side chains have shown to improve the overall transfection efficiency of poly(amido amine)s, it is hypothesized that poly(CBA-ABOL/AGM) synthesized at the optimal ratio of both components would result in high transfection efficiency and minimal toxicity. In this study, a series of the poly(CBA-ABOL/AGM) copolymers is synthesized as gene carriers. The polymers are characterized and luciferase transfection efficiencies of the polymers in various cell lines are investigated to select the ideal ratio between AGM and ABOL. The poly(CBA-ABOL/AGM) containing 80% AGM and 20% ABOL has shown the best transfection efficiency with the lowest cytotoxicity, indicating that this polymer is very promising as a potent and nontoxic gene carrier. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. A rigid disulfide-linked nitroxide side chain simplifies the quantitative analysis of PRE data

    Energy Technology Data Exchange (ETDEWEB)

    Fawzi, Nicolas L. [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Fleissner, Mark R. [University of California, Jules Stein Eye Institute and Department of Chemistry and Biochemistry (United States); Anthis, Nicholas J. [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Kalai, Tamas; Hideg, Kalman [University of Pecs, Institute of Organic and Medicinal Chemistry (Hungary); Hubbell, Wayne L., E-mail: hubbellw@jsei.ucla.edu [University of California, Jules Stein Eye Institute and Department of Chemistry and Biochemistry (United States); Clore, G. Marius, E-mail: mariusc@mail.nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2011-09-15

    The measurement of {sup 1}H transverse paramagnetic relaxation enhancement (PRE) has been used in biomolecular systems to determine long-range distance restraints and to visualize sparsely-populated transient states. The intrinsic flexibility of most nitroxide and metal-chelating paramagnetic spin-labels, however, complicates the quantitative interpretation of PREs due to delocalization of the paramagnetic center. Here, we present a novel, disulfide-linked nitroxide spin label, R1p, as an alternative to these flexible labels for PRE studies. When introduced at solvent-exposed {alpha}-helical positions in two model proteins, calmodulin (CaM) and T4 lysozyme (T4L), EPR measurements show that the R1p side chain exhibits dramatically reduced internal motion compared to the commonly used R1 spin label (generated by reacting cysteine with the spin labeling compound often referred to as MTSL). Further, only a single nitroxide position is necessary to account for the PREs arising from CaM S17R1p, while an ensemble comprising multiple conformations is necessary for those observed for CaM S17R1. Together, these observations suggest that the nitroxide adopts a single, fixed position when R1p is placed at solvent-exposed {alpha}-helical positions, greatly simplifying the interpretation of PRE data by removing the need to account for the intrinsic flexibility of the spin label.

  19. A rigid disulfide-linked nitroxide side chain simplifies the quantitative analysis of PRE data

    International Nuclear Information System (INIS)

    Fawzi, Nicolas L.; Fleissner, Mark R.; Anthis, Nicholas J.; Kálai, Tamás; Hideg, Kálmán; Hubbell, Wayne L.; Clore, G. Marius

    2011-01-01

    The measurement of 1 H transverse paramagnetic relaxation enhancement (PRE) has been used in biomolecular systems to determine long-range distance restraints and to visualize sparsely-populated transient states. The intrinsic flexibility of most nitroxide and metal-chelating paramagnetic spin-labels, however, complicates the quantitative interpretation of PREs due to delocalization of the paramagnetic center. Here, we present a novel, disulfide-linked nitroxide spin label, R1p, as an alternative to these flexible labels for PRE studies. When introduced at solvent-exposed α-helical positions in two model proteins, calmodulin (CaM) and T4 lysozyme (T4L), EPR measurements show that the R1p side chain exhibits dramatically reduced internal motion compared to the commonly used R1 spin label (generated by reacting cysteine with the spin labeling compound often referred to as MTSL). Further, only a single nitroxide position is necessary to account for the PREs arising from CaM S17R1p, while an ensemble comprising multiple conformations is necessary for those observed for CaM S17R1. Together, these observations suggest that the nitroxide adopts a single, fixed position when R1p is placed at solvent-exposed α-helical positions, greatly simplifying the interpretation of PRE data by removing the need to account for the intrinsic flexibility of the spin label.

  20. Synthesis and Antiplasmodial Activity of Novel Chloroquine Analogues with Bulky Basic Side Chains.

    Science.gov (United States)

    Tasso, Bruno; Novelli, Federica; Tonelli, Michele; Barteselli, Anna; Basilico, Nicoletta; Parapini, Silvia; Taramelli, Donatella; Sparatore, Anna; Sparatore, Fabio

    2015-09-01

    Chloroquine is commonly used in the treatment and prevention of malaria, but Plasmodium falciparum, the main species responsible for malaria-related deaths, has developed resistance against this drug. Twenty-seven novel chloroquine (CQ) analogues characterized by a side chain terminated with a bulky basic head group, i.e., octahydro-2H-quinolizine and 1,2,3,4,5,6-hexahydro-1,5-methano-8H-pyrido[1,2-a][1,5]diazocin-8-one, were synthesized and tested for activity against D-10 (CQ-susceptible) and W-2 (CQ-resistant) strains of P. falciparum. Most compounds were found to be active against both strains with nanomolar or sub-micromolar IC50 values. Eleven compounds were found to be 2.7- to 13.4-fold more potent than CQ against the W-2 strain; among them, four cytisine derivatives appear to be of particular interest, as they combine high potency with low cytotoxicity against two human cell lines (HMEC-1 and HepG2) along with easier synthetic accessibility. Replacement of the 4-NH group with a sulfur bridge maintained antiplasmodial activity at a lower level, but produced an improvement in the resistance factor. These compounds warrant further investigation as potential drugs for use in the fight against malaria. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. QSAR studies of some side chain modified 7-chloro-4-aminoquinolines as antimalarial agents

    Directory of Open Access Journals (Sweden)

    Nitendra K. Sahu

    2014-11-01

    Full Text Available The quantitative structure–activity relationship (QSAR analyses were carried out for a series of new side chain modified 4-amino-7-chloroquinolines to find out the structural requirements of their antimalarial activities against both chloroquine sensitive (HB3 and resistant (Dd2 Plasmodium falciparum strain. The statistically significant best 2D QSAR models for Dd2, having correlation coefficient (r2 = 0.9188 and cross validated squared correlation coefficient (q2 = 0.8349 with external predictive ability (pred_r2 = 0.7258 and for HB3, having r2 = 0.9024, q2 = 0.8089 and pred_r2 = 0.7463 were developed by multiple linear regression coupled with genetic algorithm (GA–MLR and stepwise (SW–MLR forward algorithm, respectively. The results of the present study may be useful on the designing of more potent analogues as antimalarial agents.

  2. UV resonance Raman finds peptide bond-Arg side chain electronic interactions.

    Science.gov (United States)

    Sharma, Bhavya; Asher, Sanford A

    2011-05-12

    We measured the UV resonance Raman excitation profiles and Raman depolarization ratios of the arginine (Arg) vibrations of the amino acid monomer as well as Arg in the 21-residue predominantly alanine peptide AAAAA(AAARA)(3)A (AP) between 194 and 218 nm. Excitation within the π → π* peptide bond electronic transitions result in UVRR spectra dominated by amide peptide bond vibrations. The Raman cross sections and excitation profiles indicate that the Arg side chain electronic transitions mix with the AP peptide bond electronic transitions. The Arg Raman bands in AP exhibit Raman excitation profiles similar to those of the amide bands in AP which are conformation specific. These Arg excitation profiles distinctly differ from the Arg monomer. The Raman depolarization ratios of Arg in monomeric solution are quite simple with ρ = 0.33 indicating enhancement by a single electronic transition. In contrast, we see very complex depolarization ratios of Arg in AP that indicate that the Arg residues are resonance enhanced by multiple electronic transitions.

  3. DISTRIBUTION OF GBM HEPARAN-SULFATE PROTEOGLYCAN CORE PROTEIN AND SIDE-CHAINS IN HUMAN GLOMERULAR-DISEASES

    NARCIS (Netherlands)

    VANDENBORN, J; VANDENHEUVEL, LPWJ; BAKKER, MAH; VEERKAMP, JH; ASSMANN, KJM; WEENING, JJ; BERDEN, JHM

    Using monoclonal antibodies (mAbs) recognizing either the core protein or the heparan sulfate (HS) side chain of human GBM heparan sulfate proteoglycan (HSPG), we investigated their glomerular distribution on cryostat sections of human kidney tissues. The study involved 95 biopsies comprising twelve

  4. 26 kDa endochitinase from barley seeds: an interaction of the ionizable side chains essential for catalysis

    DEFF Research Database (Denmark)

    Ohnishi, Tsuneo; Juffer, André H; Tamoi, Masahiro

    2005-01-01

    to be abnormally low (-2.4), suggesting that these side chains may interact with each other. Mutation of Glu203 to alanine (E203A) completely eliminated the enzymatic activity and impaired the thermal stability (deltaT(m) = 6.4 degrees C) of the enzyme. Substrate binding ability was also affected by the Glu203...

  5. Synthesis of deuterium-labeled plant sterols and analysis of their side-chain mobility by solid state deuterium NMR

    International Nuclear Information System (INIS)

    Marsan, M.P.; Muller, I.; Milon, A.

    1996-01-01

    Sitosterol and stigmasterol, plant sterols, were deuterated at specific positions. Orientation and mobility of the deuterated sitosterol and stigmasterol (and two of their diasteromers) on oriented lipid bilayers were analyzed by deuterium NMR spectroscopy. Orientation and mobility of the side chains was revealed by these studies

  6. Enhanced n-Doping Efficiency of a Naphthalenediimide-Based Copolymer through Polar Side Chains for Organic Thermoelectrics

    KAUST Repository

    Kiefer, David; Giovannitti, Alexander; Sun, Hengda; Biskup, Till; Hofmann, Anna; Koopmans, Marten; Cendra, Camila; Weber, Stefan; Anton Koster, L. Jan; Olsson, Eva; Rivnay, Jonathan; Fabiano, Simone; McCulloch, Iain; Mü ller, Christian

    2018-01-01

    (gNDI-gT2) that carries oligoethylene glycol-based side chains and show that the polymer displays superior miscibility with the benzimidazole–dimethylbenzenamine-based n-dopant N-DMBI. The good compatibility of p(gNDI-gT2) and N-DMBI results in a relatively

  7. Effect of Non-fullerene Acceptors' Side Chains on the Morphology and Photovoltaic Performance of Organic Solar Cells.

    Science.gov (United States)

    Zhang, Cai'e; Feng, Shiyu; Liu, Yahui; Hou, Ran; Zhang, Zhe; Xu, Xinjun; Wu, Youzhi; Bo, Zhishan

    2017-10-04

    Three indacenodithieno[3,2-b]thiophene (IT) cored small molecular acceptors (ITIC-SC6, ITIC-SC8, and ITIC-SC2C6) were synthesized, and the influence of side chains on their performances in solar cells was systematically probed. Our investigations have demonstrated the variation of side chains greatly affects the charge dissociation, charge mobility, and morphology of the donor:acceptor blend films. ITIC-SC2C6 with four branched side chains showed improved solubility, which can ensure the polymer donor to form favorable fibrous nanostructure during the drying of the blend film. Consequently, devices based on PBDB-ST:ITIC-SC2C6 demonstrated higher charge mobility, more effective exciton dissociation, and the optimal power conversion efficiency up to 9.16% with an FF of 0.63, a J sc of 15.81 mA cm -2 , and a V oc of 0.92 V. These results reveal that the side chain engineering is a valid way of tuning the morphology of blend films and further improving PCE in polymer solar cells.

  8. Conjugation of diisocyanate side chains to dimethacrylate reduces polymerization shrinkage and increases the hardness of composite resins.

    Science.gov (United States)

    Jan, Yih-Dean; Lee, Bor-Shiunn; Lin, Chun-Pin; Tseng, Wan-Yu

    2014-04-01

    Polymerization shrinkage is one of the main causes of dental restoration failure. This study tried to conjugate two diisocyanate side chains to dimethacrylate resins in order to reduce polymerization shrinkage and increase the hardness of composite resins. Diisocyanate, 2-hydroxyethyl methacrylate, and bisphenol A dimethacrylate were reacted in different ratios to form urethane-modified new resin matrices, and then mixed with 50 wt.% silica fillers. The viscosities of matrices, polymerization shrinkage, surface hardness, and degrees of conversion of experimental composite resins were then evaluated and compared with a non-modified control group. The viscosities of resin matrices increased with increasing diisocyanate side chain density. Polymerization shrinkage and degree of conversion, however, decreased with increasing diisocyanate side chain density. The surface hardness of all diisocyanate-modified groups was equal to or significantly higher than that of the control group. Conjugation of diisocyanate side chains to dimethacrylate represents an effective means of reducing polymerization shrinkage and increasing the surface hardness of dental composite resins. Copyright © 2012. Published by Elsevier B.V.

  9. Siloxane-Terminated Solubilizing Side Chains: Bringing Conjugated Polymer Backbones Closer and Boosting Hole Mobilities in Thin-Film Transistors

    KAUST Repository

    Mei, Jianguo; Kim, Do Hwan; Ayzner, Alexander L.; Toney, Michael F.; Bao, Zhenan

    2011-01-01

    We introduce a novel siloxane-terminated solubilizing group and demonstrate its effectiveness as a side chain in an isoindigo-based conjugated polymer. An average hole mobility of 2.00 cm 2 V -1 s -1 (with a maximum mobility of 2.48 cm 2 V -1 s -1

  10. Comparison of the Photovoltaic Characteristics and Nanostructure of Fullerenes Blended with Conjugated Polymers with Siloxane-Terminated and Branched Aliphatic Side Chains

    KAUST Repository

    Kim, Do Hwan

    2013-02-12

    All-organic bulk heterojunction solar cells based on blends of conjugated polymers with fullerenes have recently surpassed the 8% efficiency mark and are well on their way to the industrially relevant ∼15% threshold. Using a low band-gap conjugated polymer, we have recently shown that polymer side chain engineering can lead to dramatic improvement in the in-plane charge carrier mobility. In this article, we investigate the effectiveness of siloxy side chain derivatization in controlling the photovoltaic performance of polymer:[6,6]-phenyl-C[71]-butyric acid methyl ester (PC71BM) blends and hence its influence on charge transport in the out-of-plane direction relevant for organic solar cells. We find that, in neat blends, the photocurrent of the polymer with siloxy side chains (PII2T-Si) is 4 times greater than that in blends using the polymer with branched aliphatic side chains (PII2T-ref). This difference is due to a larger out-of-plane hole mobility for PII2T-Si brought about by a largely face-on crystallite orientation as well as more optimal nanoscale polymer:PC71BM mixing. However, upon incorporating a common processing additive, 1,8-diiodooctane (DIO), into the spin-casting blend solution and following optimization, the PII2T-ref:PC71BM OPV device performance undergoes a large improvement and becomes the better-performing device, almost independent of DIO concentration (>1%). We find that the precise amount of DIO plays a larger role in determining the efficiency of PII2T-Si:PC71BM, and even at its maximum, the device performance lags behind optimized PII2T-ref:PC71BM blends. Using a combination of atomic force microscopy and small- and wide-angle X-ray scattering, we are able to elucidate the morphological modifications associated with the DIO-induced changes in both the nanoscale morphology and the molecular packing in blend films. © 2012 American Chemical Society.

  11. A Study on Copolymer Systems of Styrene with Diethanolamine Side Group and Methyl Methacrylate

    Directory of Open Access Journals (Sweden)

    Aslisah Acikses

    2018-01-01

    Full Text Available 4-Diethanolaminomethyl styrene (DEAMSt monomer was prepared by the modification of 4-chloromethyl styrene with diethanolamine. The copolymers in different combinations (0.11, 0.19, and 0.30 by mole of DEAMSt and methyl methacrylate (MMA were prepared by free radical polymerization method at 60°C in the presence of 1,4-dioxane and AIBN as initiator. The structures of DEAMSt and DEAMSt-MMA copolymer were characterized by FT-IR and 1H-NMR. The glass transition temperature (Tg of the copolymers was measured by DSC. Thermal decomposition behavior of the copolymers was investigated by TGA. The average molecular weights of the copolymers were determined by GPC. The dye uptaking properties of the copolymers were investigated using bromocresol green. Then, the dielectric constant, dielectric loss factor, and conductivity of copolymers were investigated as a function of temperature and frequency. The activation energies (Ea of the copolymers were determined by impedance analyzer.

  12. Molecular dynamics simulation of radiation grafted FEP films as proton exchange membranes: Effects of the side chain length

    DEFF Research Database (Denmark)

    Li, Xue; Zhao, Yang; Li, Weiwei

    2017-01-01

    In order to study the microstructure of the prepared potential proton exchange membrane (PEM), molecular dynamics (MD) simulations were used to lucubrate the transport behavior of water molecules and hydronium ions inside the hydrated sulfonated styrene grafted fluorinated ethylene propylene (FEP...... whereas larger water clusters formed. The results of the mean square displacements (MSDs) show that the proton conductivities of the membranes with the proposed side chain lengths were about three fifths of the experimental data, of which the membrane with side chain length of 7 sulfonic styrene units...... was supposed to exhibit the highest proton conductivity, that is 115.69 mS cm-1. All of the supposed membrane models presented good proton conductivity that could definitely meet the application requirements of the proton exchange membranes. The MD simulations can provide an insight to the chain structure...

  13. CONCERNING CHAIN GROWTH SPECIFIC REACTION RATE AS A PART OF THE PROCESS OF METHYL METHACRYLATE MASS RADICAL POLYMERIZATION

    Directory of Open Access Journals (Sweden)

    A. A. Sultanova

    2017-02-01

    Full Text Available It is the chain growth specific reaction rate that was determined for the process of methyl methacrylate mass radical polymerization within the temperature range of 40–900 С in quasi-steady approximation by means of Monte Carlo method. The theoretical model of radical polymerization was developed taking the gel effect into account. Computer software was developed that enables to imitate radical polymerization process taking gel effect into account within the minimum run time. The programme was tested on asymptotic examples as well as was applied for methyl methacrylate mass radical polymerization. The programme makes it possible to calculate monomer conversion, molecular mass variation, molecular-mass distribution, etc.

  14. Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase.

    Science.gov (United States)

    Zhai, Xiang; Amyes, Tina L; Richard, John P

    2015-12-09

    The side chains of Y208 and S211 from loop 7 of triosephosphate isomerase (TIM) form hydrogen bonds to backbone amides and carbonyls from loop 6 to stabilize the caged enzyme-substrate complex. The effect of seven mutations [Y208T, Y208S, Y208A, Y208F, S211G, S211A, Y208T/S211G] on the kinetic parameters for TIM catalyzed reactions of the whole substrates dihydroxyacetone phosphate and d-glyceraldehyde 3-phosphate [(k(cat)/K(m))(GAP) and (k(cat)/K(m))DHAP] and of the substrate pieces glycolaldehyde and phosphite dianion (k(cat)/K(HPi)K(GA)) are reported. The linear logarithmic correlation between these kinetic parameters, with slope of 1.04 ± 0.03, shows that most mutations of TIM result in an identical change in the activation barriers for the catalyzed reactions of whole substrate and substrate pieces, so that the transition states for these reactions are stabilized by similar interactions with the protein catalyst. The second linear logarithmic correlation [slope = 0.53 ± 0.16] between k(cat) for isomerization of GAP and K(d)(⧧) for phosphite dianion binding to the transition state for wildtype and many mutant TIM-catalyzed reactions of substrate pieces shows that ca. 50% of the wildtype TIM dianion binding energy, eliminated by these mutations, is expressed at the wildtype Michaelis complex, and ca. 50% is only expressed at the wildtype transition state. Negative deviations from this correlation are observed when the mutation results in a decrease in enzyme reactivity at the catalytic site. The main effect of Y208T, Y208S, and Y208A mutations is to cause a reduction in the total intrinsic dianion binding energy, but the effect of Y208F extends to the catalytic site.

  15. Molecular Design for Preparation of Hexagonal-Ordered Porous Films Based on Side-chain Type Liquid-Crystalline Star Polymer.

    Science.gov (United States)

    Naka, Yumiko; Takayama, Hiromu; Koyama, Teruhisa; Le, Khoa V; Sasaki, Takeo

    2018-05-02

    Fabrication of regularly porous films by the breath-figure method has attracted much attention. The simple, low-cost technique uses the condensation of water droplets to produce these structures, but the phenomenon itself is complex, requiring control over many interacting parameters that change throughout the process. Developing a unified understanding for the molecular design of polymers to prepare ordered porous films is challenging, but required for further advancements. In this article, the effects of the chemical structure of polymers in the breath-figure technique were systematically explored using side-chain type liquid-crystalline (LC) star polymers. The formation of porous films was affected by the structure of the polymers. Although the entire film surface of poly(11-[4-(4-cyanobiphenyl)oxy]undecyl methacrylate) (P11CB) had a hexagonal ordered porous structure over a certain Mn value, regularly arranged holes did not easily form in poly(methyl methacrylate) (PMMA), even though the main chain of PMMA is similar to that of P11CB. Comparing P11CB and poly(11-[(1,1'-biphenyl)-4-yloxy]undecyl methacrylate) (P11B) (P11CB without cyano groups) showed that the local polar groups in hydrophobic polymers promoted the formation of ordered porous films. No holes formed in poly(4-cyanobiphenyl methacrylate) (P0CB) (P11CB without alkyl spacers) films due to its hydrophilicity. The introduction of alkyl chains in P0CB allowed the preparation of honeycomb-structured films by increasing the internal tension. However, alkyl chains in the side chain alone did not result in a porous structure, as in the case of poly(11-[(1,1'-biphenyl)-4-yloxy]undecyl methacrylate) (P11). Aromatic rings are also required to increase the Tg and improve film formability. In the present study, suitable molecular designs of polymers were found, specifically hydrophobic polymers with local polar groups, to form a regularly porous structure. Development of clear guidelines for the molecular

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

    Science.gov (United States)

    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.

  17. "There is a chain of connections": using syndemics theory to understand HIV treatment side effects.

    Science.gov (United States)

    Gagnon, Marilou

    2018-07-01

    Side effects are central to the experience of living longer with HIV but rarely have they been studied alone. Unlike other aspects of that experience, like quality of life, treatment adherence, chronicity, episodic disability, aging, health, and viral load suppression, side effects have not benefited from the same level of empirical and theoretical engagement from qualitative researchers. In this paper, we draw on syndemics theory and 50 qualitative interviews to better understand the experience of HIV treatment side effects. Two main categories were identified in the data: side effects as a product and side effects as a risk factor. The first category suggests that side effects are not just the product of taking antiretroviral drugs. They are also the product of particular conditions and tend to cluster with other health problems. The second category puts forward the idea that side effects can act as a syndemic risk factor by exposing PLWH to a greater risk of developing health problems and creating conditions in which psychosocial issues are more likely to emerge. The paper concludes by calling for more research on the complex nature of side effects and for the development of comprehensive approaches for the assessment and management of side effects.

  18. Siloxane-Terminated Solubilizing Side Chains: Bringing Conjugated Polymer Backbones Closer and Boosting Hole Mobilities in Thin-Film Transistors

    KAUST Repository

    Mei, Jianguo

    2011-12-21

    We introduce a novel siloxane-terminated solubilizing group and demonstrate its effectiveness as a side chain in an isoindigo-based conjugated polymer. An average hole mobility of 2.00 cm 2 V -1 s -1 (with a maximum mobility of 2.48 cm 2 V -1 s -1), was obtained from solution-processed thin-film transistors, one of the highest mobilities reported to date. In contrast, the reference polymer with a branched alkyl side chain gave an average hole mobility of 0.30 cm 2 V -1 s -1 and a maximum mobility of 0.57 cm 2 V -1 s -1. This is largely explained by the polymer packing: our new polymer exhibited a π-π stacking distance of 3.58 Å, while the reference polymer showed a distance of 3.76 Å. © 2011 American Chemical Society.

  19. Fused-Ring Acceptors with Asymmetric Side Chains for High-Performance Thick-Film Organic Solar Cells.

    Science.gov (United States)

    Feng, Shiyu; Zhang, Cai'e; Liu, Yahui; Bi, Zhaozhao; Zhang, Zhe; Xu, Xinjun; Ma, Wei; Bo, Zhishan

    2017-11-01

    A kind of new fused-ring electron acceptor, IDT-OB, bearing asymmetric side chains, is synthesized for high-efficiency thick-film organic solar cells. The introduction of asymmetric side chains can increase the solubility of acceptor molecules, enable the acceptor molecules to pack closely in a dislocated way, and form favorable phase separation when blended with PBDB-T. As expected, PBDB-T:IDT-OB-based devices exhibit high and balanced hole and electron mobility and give a high power conversion efficiency (PCE) of 10.12%. More importantly, the IDT-OB-based devices are not very sensitive to the film thickness, a PCE of 9.17% can still be obtained even the thickness of active layer is up to 210 nm. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. ω-Turn: a novel β-turn mimic in globular proteins stabilized by main-chain to side-chain C−H···O interaction.

    Science.gov (United States)

    Dhar, Jesmita; Chakrabarti, Pinak; Saini, Harpreet; Raghava, Gajendra Pal Singh; Kishore, Raghuvansh

    2015-02-01

    Mimicry of structural motifs is a common feature in proteins. The 10-membered hydrogen-bonded ring involving the main-chain C − O in a β-turn can be formed using a side-chain carbonyl group leading to Asx-turn. We show that the N − H component of hydrogen bond can be replaced by a C(γ) -H group in the side chain, culminating in a nonconventional C − H···O interaction. Because of its shape this β-turn mimic is designated as ω-turn, which is found to occur ∼ three times per 100 residues. Three residues (i to i + 2) constitute the turn with the C − H···O interaction occurring between the terminal residues, constraining the torsion angles ϕi + 1, ψi + 1, ϕi + 2 and χ'1(i + 2) (using the interacting C(γ) atom). Based on these angles there are two types of ω-turns, each of which can be further divided into two groups. C(β) -branched side-chains, and Met and Gln have high propensities to occur at i + 2; for the last two residues the carbonyl oxygen may participate in an additional interaction involving the S and amino group, respectively. With Cys occupying the i + 1 position, such turns are found in the metal-binding sites. N-linked glycosylation occurs at the consensus pattern Asn-Xaa-Ser/Thr; with Thr at i + 2, the sequence can adopt the secondary structure of a ω-turn, which may be the recognition site for protein modification. Location between two β-strands is the most common occurrence in protein tertiary structure, and being generally exposed ω-turn may constitute the antigenic determinant site. It is a stable scaffold and may be used in protein engineering and peptide design. © 2014 Wiley Periodicals, Inc.

  1. A salt water battery with high stability and charging rates made from solution processed conjugated polymers with polar side chains

    KAUST Repository

    Moia, Davide; Giovannitti, Alexander; Szumska, Anna A.; Schnurr, Martin; Rezasoltani, Elham; Maria, Iuliana P.; Barnes, Piers R. F.; McCulloch, Iain; Nelson, Jenny

    2017-01-01

    conjugated polymer backbones, allowed the films to maintain constant capacity at high charge and discharge rates (>1000 C-rate). The electrodes also show good stability during electrochemical cycling (less than 30% decrease in capacity over >1000 cycles) and an output voltage up to 1.4 V. The performance of these semiconducting polymers with polar side-chains demonstrates the potential of this material class for fast-charging, water based electrochemical energy storage devices.

  2. Improvement in carrier mobility and photovoltaic performance through random distribution of segments of linear and branched side chains

    Energy Technology Data Exchange (ETDEWEB)

    Egbe, Daniel A.M.; Adam, Getachew; Pivrikas, Almantas; Ulbricht, Christoph; Ramil, Alberto M.; Sariciftci, Niyazi Serdar [Johannes Kepler Univ., Linz (AT). Linz Inst. for Organic Solar Cells (LIOS); Hoppe, Harald [Technische Univ. Ilmenau (Germany). Inst. of Physics and Inst. of Micro- and Nanotechnologies; Rathgeber, Silke [Mainz Univ. (Germany). Inst. of Physics

    2010-07-01

    The random distribution of segments of linear octyloxy side chains and of branched 2-ethylhexyloxy side chains, on the backbone of anthracene containing poly(p-phenylene-ethynylene)-alt-poly(p-phenylene-vinylene) (PPE-PPV) has resulted in a side chain based statistical copolymer, denoted AnE-PVstat, showing optimized features as compared to the well defined homologues AnE-PVaa, -ab, -ba and -bb, whose constitutional units are incorporated into its backbone. WAXS studies on AnE-P's demonstrate the highest degree of order at the self-assembly state of AnE-PVstat, which is confirmed by its highly structured thin film absorption band. Electric field independent charge carrier mobility ({mu}{sub hole}) for AnE-PVstat was demonstrated by CELIV and OFET measurements, both methods resulting in similar {mu}{sub hole} values of up to 5.43 x 10{sup -4} cm{sup 2}/Vs. Upon comparison, our results show that charge carrier mobility as measured by CELIV technique is predominantly an intrachain process and less an interchain one, which is in line with past photoconductivity results from PPE-PPV based materials. The present side chain distribution favors efficient solar cell active layer phase separation. As a result, a smaller amount of PC{sub 60}BM is needed to achieve relatively high energy conversion efficiencies above 3 %. The efficiency of {eta}{sub AM1.5} {approx} 3.8 % obtained for AnE-PVstat:PC{sub 60}BM blend is presently the state-of-art value for PPV-based materials. (orig.)

  3. Aromatic Side Chain Water-to-Lipid Transfer Free Energies Show a Depth Dependence across the Membrane Normal.

    Science.gov (United States)

    McDonald, Sarah K; Fleming, Karen G

    2016-06-29

    Quantitating and understanding the physical forces responsible for the interactions of biomolecules are fundamental to the biological sciences. This is especially challenging for membrane proteins because they are embedded within cellular bilayers that provide a unique medium in which hydrophobic sequences must fold. Knowledge of the energetics of protein-lipid interactions is thus vital to understand cellular processes involving membrane proteins. Here we used a host-guest mutational strategy to calculate the Gibbs free energy changes of water-to-lipid transfer for the aromatic side chains Trp, Tyr, and Phe as a function of depth in the membrane. This work reveals an energetic gradient in the transfer free energies for Trp and Tyr, where transfer was most favorable to the membrane interfacial region and comparatively less favorable into the bilayer center. The transfer energetics follows the concentration gradient of polar atoms across the bilayer normal that naturally occurs in biological membranes. Additional measurements revealed nearest-neighbor coupling in the data set are influenced by a network of aromatic side chains in the host protein. Taken together, these results show that aromatic side chains contribute significantly to membrane protein stability through either aromatic-aromatic interactions or placement at the membrane interface.

  4. The Influence of Conjugated Polymer Side Chain Manipulation on the Efficiency and Stability of Polymer Solar Cells.

    Science.gov (United States)

    Heckler, Ilona M; Kesters, Jurgen; Defour, Maxime; Madsen, Morten V; Penxten, Huguette; D'Haen, Jan; Van Mele, Bruno; Maes, Wouter; Bundgaard, Eva

    2016-03-09

    The stability of polymer solar cells (PSCs) can be influenced by the introduction of particular moieties on the conjugated polymer side chains. In this study, two series of donor-acceptor copolymers, based on bis(thienyl)dialkoxybenzene donor and benzo[ c ][1,2,5]thiadiazole (BT) or thiazolo[5,4- d ]thiazole (TzTz) acceptor units, were selected toward effective device scalability by roll-coating. The influence of the partial exchange (5% or 10%) of the solubilizing 2-hexyldecyloxy by alternative 2-phenylethoxy groups on efficiency and stability was investigated. With an increasing 2-phenylethoxy ratio, a decrease in solar cell efficiency was observed for the BT-based series, whereas the efficiencies for the devices based on the TzTz polymers remained approximately the same. The photochemical degradation rate for PSCs based on the TzTz polymers decreased with an increasing 2-phenylethoxy ratio. Lifetime studies under constant sun irradiance showed a diminishing initial degradation rate for the BT-based devices upon including the alternative side chains, whereas the (more stable) TzTz-based devices degraded at a faster rate from the start of the experiment upon partly exchanging the side chains. No clear trends in the degradation behavior, linked to the copolymer structural changes, could be established at this point, evidencing the complex interplay of events determining PSCs' lifetime.

  5. The Influence of Conjugated Polymer Side Chain Manipulation on the Efficiency and Stability of Polymer Solar Cells

    Directory of Open Access Journals (Sweden)

    Ilona M. Heckler

    2016-03-01

    Full Text Available The stability of polymer solar cells (PSCs can be influenced by the introduction of particular moieties on the conjugated polymer side chains. In this study, two series of donor-acceptor copolymers, based on bis(thienyldialkoxybenzene donor and benzo[c][1,2,5]thiadiazole (BT or thiazolo[5,4-d]thiazole (TzTz acceptor units, were selected toward effective device scalability by roll-coating. The influence of the partial exchange (5% or 10% of the solubilizing 2-hexyldecyloxy by alternative 2-phenylethoxy groups on efficiency and stability was investigated. With an increasing 2-phenylethoxy ratio, a decrease in solar cell efficiency was observed for the BT-based series, whereas the efficiencies for the devices based on the TzTz polymers remained approximately the same. The photochemical degradation rate for PSCs based on the TzTz polymers decreased with an increasing 2-phenylethoxy ratio. Lifetime studies under constant sun irradiance showed a diminishing initial degradation rate for the BT-based devices upon including the alternative side chains, whereas the (more stable TzTz-based devices degraded at a faster rate from the start of the experiment upon partly exchanging the side chains. No clear trends in the degradation behavior, linked to the copolymer structural changes, could be established at this point, evidencing the complex interplay of events determining PSCs’ lifetime.

  6. Fluorinated polyimides grafted with poly(ethylene glycol) side chains by the RAFT-mediated process and their membranes

    International Nuclear Information System (INIS)

    Chen Yiwang; Chen Lie; Nie Huarong; Kang, E.T.; Vora, R.H.

    2005-01-01

    Graft polymerization of poly(ethylene glycol) methyl ether methacrylate (PEGMA) from fluorinated polyimide (FPI) was carried out by the reversible addition-fragmentation chain transfer (RAFT)-mediated process. The peroxides generated by the ozone treatment on FPI facilitated the thermally-initiated graft copolymerization from FPI backbone. The 'living' character of the graft chain growing was ascertained in the subsequent chain extension of PEGMA. Nuclear magnetic resonance (NMR) and molecular weight measurements were used to characterize the chemical composition and structure of the copolymers. Microfiltration (MF) membranes were fabricated from the FPI-g-PEGMA comb copolymers by phase inversion in aqueous media. Surface composition analysis of the membranes scanned by X-ray photoelectron spectroscopy (XPS) revealed a substantial surface enrichment of the hydrophilic components. The pore size distribution of the resulting membranes was found to be much more uniform than that of the corresponding membranes cast from FPI-g-PEGMA prepared by the conventional radical polymerization process in the absence of the chain transfer agent. The morphology of the membranes was characterized by scanning electron microscopy (SEM)

  7. Fine-tuning blend morphology via alkylthio side chain engineering towards high performance non-fullerene polymer solar cells

    Science.gov (United States)

    Li, Ling; Feng, Liuliu; Yuan, Jun; Peng, Hongjian; Zou, Yingping; Li, Yongfang

    2018-03-01

    Two medium bandgap polymers (ffQx-TS1, ffQx-TS2) were designed and synthesized to investigate the influence of different alkylthio side chain on the morphology and photovoltaic performance of non-fullerene polymer solar cells (PSCs). Both polymers exhibit similar molecular weights and comparable the highest occupied molecular orbital (HOMO) energy level. However, the polymer with straight alkylthio chain delivers a root-mean-square (RMS) of 0.86 nm, which is slightly lower than that with branched chain (1.40 nm). The lower RMS benefits the ohmic contact between the active lay and interface layer, thus enhanced short circuit current (Jsc) (from 13.54 mA cm-1 to 15.25 mA cm-1) could be obtained. Due to the enhancement of Jsc, better power conversion efficiency (PCE) of 7.69% for ffQx-TS2 could be realized. These results indicated that alkylthio side chain engineering is a promising method to improve photovoltaic performance.

  8. Methylation effect on the ohmic resistance of a poly-GC DNA-like chain

    Energy Technology Data Exchange (ETDEWEB)

    Moura, F.A.B.F. de, E-mail: fidelis@fis.ufal.br [Instituto de Física, Universidade Federal de Alagoas, Maceió AL 57072-970 (Brazil); Lyra, M.L. [Instituto de Física, Universidade Federal de Alagoas, Maceió AL 57072-970 (Brazil); Almeida, M.L. de; Ourique, G.S.; Fulco, U.L.; Albuquerque, E.L. [Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN (Brazil)

    2016-10-14

    We determine, by using a tight-binding model Hamiltonian, the characteristic current–voltage (IxV) curves of a 5-methylated cytosine single strand poly-GC DNA-like finite segment, considering the methyl groups attached laterally to a random fraction of the cytosine basis. Striking, we found that the methylation significantly impacts the ohmic resistance (R) of the DNA-like segments, indicating that measurements of R can be used as a biosensor tool to probe the presence of anomalous methylation. - Highlights: • Ohmic resistance of finite segments of poly-CG DNA-like segments. • Possibility for the development of biosensor devices. • Methylation effect and electronic transport in DNA-like segments.

  9. Effect of the different chain transfer agents on molecular weight and optical properties of poly(methyl methacrylate)

    Science.gov (United States)

    Çetinkaya, Onur; Demirci, Gökhan; Mergo, Paweł

    2017-08-01

    Investigation of molecular weight and optical properties of poly(methyl metacrylate) (PMMA) polymerized in house with different chain transfer agents was studied. Isopropyl alcohol (IPA), n-butyl mercaptan (nBMC) and pentamethyl disilane (PMDS) were used as chain transfer agents. The molecular weight (Mw) of PMMA samples were measured by Ostwald viscometer. Mw of bulk polymer samples were decreased with increase the concentration of chain transfer agents (CTA). Since reactivity of used CTAs is not same, molecular weights of samples which were produced with different type of CTA but same concentration of CTA was varied. Higher concentration of n-BMC showed higher scattering. Transmission of samples could not be correlated with different concentration of CTA. Refractive index of samples was not affected by concentration of CTA nevertheless higher molecular weight of CTA showed higher refractive index.

  10. Influence of the side chain and substrate on polythiophene thin film surface, bulk, and buried interfacial structures.

    Science.gov (United States)

    Xiao, Minyu; Jasensky, Joshua; Zhang, Xiaoxian; Li, Yaoxin; Pichan, Cayla; Lu, Xiaolin; Chen, Zhan

    2016-08-10

    The molecular structures of organic semiconducting thin films mediate the performance of various devices composed of such materials. To fully understand how the structures of organic semiconductors alter on substrates due to different polymer side chains and different interfacial interactions, thin films of two kinds of polythiophene derivatives with different side-chains, poly(3-hexylthiophene) (P3HT) and poly(3-potassium-6-hexanoate thiophene) (P3KHT), were deposited and compared on various surfaces. A combination of analytical tools was applied in this research: contact angle goniometry and X-ray photoelectron spectroscopy (XPS) were used to characterize substrate dielectric surfaces with varied hydrophobicity for polymer film deposition; X-ray diffraction and UV-vis spectroscopy were used to examine the polythiophene film bulk structure; sum frequency generation (SFG) vibrational spectroscopy was utilized to probe the molecular structures of polymer film surfaces in air and buried solid/solid interfaces. Both side-chain hydrophobicity and substrate hydrophobicity were found to mediate the crystallinity of the polythiophene film, as well as the orientation of the thiophene ring within the polymer backbone at the buried polymer/substrate interface and the polymer thin film surface in air. For the same type of polythiophene film deposited on different substrates, a more hydrophobic substrate surface induced thiophene ring alignment with the surface normal at both the buried interface and on the surface in air. For different films (P3HT vs. P3KHT) deposited on the same dielectric substrate, a more hydrophobic polythiophene side chain caused the thiophene ring to align more towards the surface at the buried polymer/substrate interface and on the surface in air. We believe that the polythiophene surface, bulk, and buried interfacial molecular structures all influence the hole mobility within the polythiophene film. Successful characterization of an organic conducting

  11. Influence of the substituent on azobenzene side-chain polyester optical storage materials

    DEFF Research Database (Denmark)

    Pedersen, M; Hvilsted, Søren; Holme, NCR

    1999-01-01

    , chloro, and bromo. C-13 NMR spectroscopic and molecular mass investigations substantiate good film forming characteristics. The optical storage performance of thin polyester films are investigated through polarization holography. The resulting diffraction efficiency is mapped and discussed as a function...... of irradiation power and exposure time. Polytetradecanedioates with cyano-, nitro-, methyl-, fluoro-, or trinuoromethyl-azobenzene reach more than 50% diffraction efficiency. Investigations of anisotropy induced at different temperatures reveal that the polyesters are only photosensitive in a narrow temperature...

  12. Side-Chain Supramolecular Polymers Employing Conformer Independent Triple Hydrogen Bonding Arrays

    OpenAIRE

    Gooch, Adam; Murphy, Natasha S.; Thomson, Neil H.; Wilson, Andrew J.

    2013-01-01

    Derivatives of thymine have been extensively used to promote supramolecular materials assembly. Such derivatives can be synthetically challenging to access and may be susceptible to degradation. The current article uses a conformer-independent acceptor-donor-acceptor array (ureidopyrimidine) which forms moderate affinity interactions with diamidopyridine derivatives to effect supramolecular blend formation between polystyrene and poly(methyl methacrylate) polymers obtained by RAFT which have ...

  13. Thermoresponsive Poly(2-oxazoline) Molecular Brushes by Living Ionic Polymerization: Kinetic Investigations of Pendant Chain Grafting and Cloud Point Modulation by Backbone and Side Chain Length Variation

    KAUST Repository

    Zhang, Ning

    2012-04-17

    Molecular brushes of poly(2-oxazoline)s were prepared by living anionic polymerization of 2-iso-propenyl-2-oxazoline to form the backbone and subsequent living cationic ring-opening polymerization of 2-n- or 2-iso-propyl-2-oxazoline for pendant chain grafting. In situ kinetic studies indicate that the initiation efficiency and polymerization rates are independent from the number of initiator functions per initiator molecule. This was attributed to the high efficiency of oxazolinium salt and the stretched conformation of the backbone, which is caused by the electrostatic repulsion of the oxazolinium moieties along the macroinitiator. The resulting molecular brushes showed thermoresponsive properties, that is, having a defined cloud point (CP). The dependence of the CP as a function of backbone and side chain length as well as concentration was studied. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Substituted group and side chain effects for the porphyrin and zinc(II)–porphyrin derivatives: A DFT and TD-DFT study

    International Nuclear Information System (INIS)

    Tai, Chin-Kuen; Chuang, Wen-Hua; Wang, Bo-Cheng

    2013-01-01

    The DFT/B3LYP/LANL2DZ and TD-DFT calculations have been performed to generate the optimized structures, electronic and photo-physical properties for the porphyrin and zinc(II)–porphyrin (metalloporphyrin) derivatives. The substituted group and side chain effects for these derivatives are discussed in this study. According to the calculation results, the side chain moiety extends the π-delocalization length from the porphyrin core to the side chain moiety. The substituted group with a stronger electron-donating ability increases the energy level of highest occupied molecular orbital (E HOMO ). The side chain moiety with a lower resonance energy decreases E HOMO , the energy level of the lowest unoccupied molecular orbital (E LUMO ), and the energy gap (E g ) between HOMO and LUMO in the porphyrin and zinc(II)–porphyrin derivatives. The natural bonding orbital (NBO) analysis determines the possible electron transfer mechanism from the electron-donating to -withdrawing groups (the side chain moiety) in these porphyrin derivatives. The projected density of state (PDOS) analysis shows that the electron-donating group affects the electron density distribution in both HOMO and LUMO, and the side chain moiety influence the electron density distribution in LUMO. The calculated photo-physical properties (absorption wavelengths and the related oscillator strength, f) in dichloromethane environment for porphyrin and zinc(II)–porphyrin derivatives have been simulated by using the TD-DFT method within the Polarizable Continuum Model (PCM). The present of both of the substituted group and the side chain moiety in these derivatives results in a red shift and broadening of the range of the absorption peaks of the Q/Soret band as compared to porphin. -- Highlights: • Side chain moiety extends the π-delocalization for the porphyrins. • Substituted group increases the energy of highest occupied molecular orbital. • Side chain moiety influences the Q/Soret band of

  15. Modification of eucalyptus pulp fiber using silane coupling agents with aliphatic side chains of different length

    Science.gov (United States)

    The objective of this work was to evaluate the effect of three silane coupling agents with different aliphatic chain lengths on the hydrophobicity of eucalyptus pulp fiber. The three silanes coupling agents used (isobutyltrimethoxysilane, methyltrimethoxysilane, and n-octyltriethoxysilane [OTES]) we...

  16. effect of side chain length on the stability and structural properties of 3

    African Journals Online (AJOL)

    Preferred Customer

    We report on the effect of the alkoxy chain length on the thermodynamic ... studied by Hartree-Fock (HF) and Density Functional Theory (DFT) methods. ..... with longer alkoxy substituents on the phenyl ring have lesser value of change in Gibbs ...

  17. Evaluation of branched chain fatty acid, BMIPP [β-methyl-ω-(p-iodophenyl)-pentadecanoic acid] for the myocardial imaging

    International Nuclear Information System (INIS)

    Kawamura, Yasuaki; Morishita, Takeshi; Yamazaki, Junichi

    1988-01-01

    Iodine-123 labeled branched chain fatty acid BMIPP [ β -methyl-ω-(p-iodophenyl)-pentadecanoic acid] was evaluated for the myocardial imaging experimentally. 123 I-BMIPP was accumulated in the heart at 2 - 4 minutes after injection and retention in the heart was remarkable at 30 minutes. In the acute canine infarction model, infarcted area was recognized as a defect. Furthermore, in comparison between 123 I-BMIPP and 201 Tl-Cl, discrepancy between these images was recognized in the ischemic and infarcted area. BMIPP is of use in not only cardiomyopathy and hypertension, but ischemic heart desease. (author)

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

    Science.gov (United States)

    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.

  19. Is buffer a good proxy for a crowded cell-like environment? A comparative NMR study of calmodulin side-chain dynamics in buffer and E. coli lysate.

    Directory of Open Access Journals (Sweden)

    Michael P Latham

    Full Text Available Biophysical studies of protein structure and dynamics are typically performed in a highly controlled manner involving only the protein(s of interest. Comparatively fewer such studies have been carried out in the context of a cellular environment that typically involves many biomolecules, ions and metabolites. Recently, solution NMR spectroscopy, focusing primarily on backbone amide groups as reporters, has emerged as a powerful technique for investigating protein structure and dynamics in vivo and in crowded "cell-like" environments. Here we extend these studies through a comparative analysis of Ile, Leu, Val and Met methyl side-chain motions in apo, Ca(2+-bound and Ca(2+, peptide-bound calmodulin dissolved in aqueous buffer or in E. coli lysate. Deuterium spin relaxation experiments, sensitive to pico- to nano-second time-scale processes and Carr-Purcell-Meiboom-Gill relaxation dispersion experiments, reporting on millisecond dynamics, have been recorded. Both similarities and differences in motional properties are noted for calmodulin dissolved in buffer or in lysate. These results emphasize that while significant insights can be obtained through detailed "test-tube" studies, experiments performed under conditions that are "cell-like" are critical for obtaining a comprehensive understanding of protein motion in vivo and therefore for elucidating the relation between motion and function.

  20. Smectic order and backbone anisotropy of a side-chain liquid crystalline polymer by Small-Angle Neutron Scattering

    Science.gov (United States)

    Noirez, L.; Pépy, G.; Keller, P.; Benguigui, L.

    1991-07-01

    We have simultaneously measured, for the first time, the extension of the polymer backbone of a side-chain liquid crystalline polymer and the intensity of the 001 Bragg reflection, which gives the smectic order parameter Psi as a function of temperature in the smectic phase. We have qualitatively demonstrated that the more the smectic phase is ordered, the more the polymer backbone is localized between the mesogenic layers. It is shown that the Landau theory allows us to relate the radius of gyration parallel to the magnetic field of the polymer backbone to the smectic order parameter. We also show that the Renz-Warner theory is suitable at low temperatures.

  1. Side chain engineering of fused aromatic thienopyrazine based low band-gap polymers for enhanced charge carrier mobility

    KAUST Repository

    Mondal, Rajib

    2011-01-01

    A strategic side-chain engineering approach leads to the two orders of magnitude enhancement of charge carrier mobility in phenanthrene based fused aromatic thienopyrazine polymers. Hole carrier mobility up to 0.012 cm 2/Vs can be obtained in thin film transistor devices. Polymers were also utilized to fabricate bulk heterojunction photovoltaic devices and the maximum PCE obtained in these OPV\\'s was 1.15%. Most importantly, performances of the devices were correlated with thin morphological analysis performed by atomic force microscopy and grazing incidence X-ray scattering. © 2011 The Royal Society of Chemistry.

  2. A salt water battery with high stability and charging rates made from solution processed conjugated polymers with polar side chains

    OpenAIRE

    Moia, Davide; Giovannitti, Alexander; Szumska, Anna A.; Schnurr, Martin; Rezasoltani, Elham; Maria, Iuliana P.; Barnes, Piers R. F.; McCulloch, Iain; Nelson, Jenny

    2017-01-01

    We report a neutral salt water based battery which uses p-type and n-type solution processed polymer films as the cathode and the anode of the cell. The specific capacity of the electrodes (approximately 30 mAh cm-3) is achieved via formation of bipolarons in both the p-type and n-type polymers. By engineering ethylene glycol and zwitterion based side chains attached to the polymer backbone we facilitate rapid ion transport through the non-porous polymer films. This, combined with efficient t...

  3. Synthesis and characterisation of new types of side chain cholesteryl polymers.

    Science.gov (United States)

    Wang, Bin; Du, Haiyan; Zhang, Junhua

    2011-01-01

    A series of cholesterol derivatives have been synthesised via the alkylation reaction of the 3-hydroxyl group with the aliphatic bromide compounds with different chain lengths, namely 3β-alkyloxy-cholesterol. The double bond between the C5 and C6 positions in these cholesterol derivatives was oxidised into epoxy, followed by an epoxy-ring-opening reaction with the treatment with acrylic acid, resulting in a series of 3β-alkyloxy-5α-hydroxy-6β-acryloyloxycholesterol, C(n)OCh (n=1, 2, 4, 6, 8, 10, 12), The acrylate group is connected to the C6 position, which is confirmed by the single crystal structure analysis. The corresponding polymers, PC(n)OCh, were prepared via free radical polymerisation. The structure of monomers and the resulting polymers were characterised with nuclear magnetic resonance (NMR), Fourier transform infrared spectroscopy (FT-IR) and gel permeation chromatography (GPC). The thermal properties of PC(n)OCh were studied using differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). To determine the secondary structure of polymers, circular dichroism (CD) spectra were performed. It was found that not all monomers produce high-molecular-weight polymers because of steric hindrance. However, all polymers have a helical structure, which can be enhanced by increasing the alkoxy chain length. In addition, increasing the alkoxy chain length decreases the glass transition temperature and increases the decomposition temperature of the polymers. Copyright © 2010 Elsevier Inc. All rights reserved.

  4. Total synthesis of a CD-ring: side-chain building block for preparing 17-epi-calcitriol derivatives from the Hajos-Parrish dione.

    Science.gov (United States)

    Michalak, Karol; Wicha, Jerzy

    2011-08-19

    An efficient synthesis of the key building block for 17-epi-calctriol from the Hajos-Parrish dione involving a sequence of diastereoselective transformation of the azulene core and the side-chain construction is presented.

  5. Effect of Side Chains on Molecular Conformation of Anthracene-Ethynylene-Phenylene-Vinylene Oligomers: A Comparative Density Functional Study With and Without Dispersion Interaction.

    Science.gov (United States)

    Dong, Chuanding; Hoppe, Harald; Beenken, Wichard J D

    2016-06-02

    Using density functional calculations with and without dispersion interaction, we studied the effects of linear octyl and branched 2-ethylhexyl side chains on the oligomer conformation of the conjugated copolymer poly(p-anthracene-ethynylene)-alt-poly(p-phenylene-vinylene). With dispersion included, the branched side chains can cause significant bending of the oligomer backbone, while without dispersion they induce mainly torsional disorder. The oligomers with mainly linear side chains keep good planarity when optimized with and without dispersion. Despite their dramatically different conformations, the calculated absorption spectra of the oligomers with various side chain combinations are very similar, indicating that the conformation of the copolymer is not the main reason for the experimentally observed different spectra of ordered and disordered phases.

  6. Self-assembly of long chain fatty acids: Effect of a methyl branch

    DEFF Research Database (Denmark)

    Liljeblad, Jonathan F. D.; Tyrode, Eric; Thormann, Esben

    2014-01-01

    chains of the straight chain fatty acids appear to be oriented perpendicular to the sample surface, based on an orientational analysis of VSFS data and the odd/even effect. In addition, the selection of the subphase (neat water or CdCl2 containing water buffered to pH 6.0) used for the LB-deposition has...

  7. 4-N, 4-S & 4-O Chloroquine Analogues: Influence of Side Chain Length and Quinolyl Nitrogen pKa on Activity vs. Chloroquine Resistant Malaria+, #

    OpenAIRE

    Natarajan, Jayakumar K.; Alumasa, John; Yearick, Kimberly; Ekoue-Kovi, Kekeli A.; Casabianca, Leah B.; de Dios, Angel C.; Wolf, Christian; Roepe, Paul D.

    2008-01-01

    Using predictions from heme – quinoline antimalarial complex structures, previous modifications of chloroquine (CQ), and hypotheses for chloroquine resistance (CQR), we synthesize and assay CQ analogues that test structure – function principles. We vary side chain length for both monoethyl and diethyl 4N CQ derivatives. We alter the pKa of the quinolyl N by introducing alkylthio or alkoxy substituents into the 4 position, and vary side chain length for these analogues. We introduce an additio...

  8. Self-Assembly of Amphiphilic Block Copolypeptoids with C 2 -C 5 Side Chains in Aqueous Solution

    KAUST Repository

    Fetsch, Corinna

    2014-12-22

    © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Nowadays, amphiphilic molecules play an important role in our life. In medical applications, amphiphilic block copolymers have attracted much attention as excipients in drug delivery systems. Here, the polymers are used as emulsifiers, micelles, or polymersomes with a hydrophilic corona block and a hydrophobic core or membrane. The aggregation behavior in aqueous solutions of a series of different amphiphilic block copolypeptoids comprising polysarcosine as a hydrophilic part is here reported. The formation of aggregates is investigated with 1H NMR spectroscopy and dynamic light scattering, and the determination of the critical micelle concentration (cmc) is performed using pyrene fluorescence spectroscopy. For the different block copolypeptoids cmc values ranging from 0.6 × 10-6 M to 0.1 × 10-3 M are found. The tendency to form micelles increases with increasing hydrophobicity at the nitrogen side chain in the hydrophobic moiety. Furthermore, in the case of the same hydrophobic side chain, a decreasing hydrophilic/lipophilic balance leads to the formation of larger aggregates. The aggregates formed in the buffer are able to solubilize the hydrophobic model compounds Reichardt\\'s dye and pyrene, and exhibit versatile microenvironments. Final investigations about the cytotoxicity reveal that the block copolypeptoids are well tolerated by mammalian cells up to high concentrations.

  9. Triblock Copolymers with Grafted Fluorine-Free Amphiphilic Non-Ionic Side Chains for Antifouling and Fouling-Release Applications

    Energy Technology Data Exchange (ETDEWEB)

    Y Cho; H Sundaram; C Weinman; M Paik; M Dimitriou; J Finlay; M Callow; J Callow; E Kramer; C Ober

    2011-12-31

    Fluorine-free, amphiphilic, nonionic surface active block copolymers (SABCs) were synthesized through chemical modification of a polystyrene-block-poly(ethylene-ran-butylene)-block-polyisoprene triblock copolymer precursor with selected amphiphilic nonionic Brij and other surfactants. Amphiphilicity was imparted by a hydrophobic aliphatic group combined with a hydrophilic poly(ethylene glycol) (PEG) group-containing moiety. The surfaces were characterized by dynamic water contact angle, atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and near edge X-ray absorption fine structure (NEXAFS) analysis. In biofouling assays, settlement (attachment) of both spores of the green alga Ulva and cells of the diatom Navicula on SABCs modified with Brij nonionic side chains was significantly reduced relative to a PDMS standard, with a nonionic surfactant combining a PEG group and an aliphatic moiety demonstrating the best performance. Additionally, a fouling-release assay using sporelings (young plants) of Ulva and Navicula suggested that the SABC derived from nonionic Brij side chains also out-performed PDMS as a fouling-release material. Good antifouling and fouling-release properties were not demonstrated for the other two amphiphilic surfaces derived from silicone and aromatic group containing nonionic surfactants included in this study. The results suggest that small differences in chemical surface functionality impart more significant changes with respect to the antifouling settlement and fouling-release performance of materials than overall wettability behavior.

  10. A salt water battery with high stability and charging rates made from solution processed conjugated polymers with polar side chains

    KAUST Repository

    Moia, Davide

    2017-11-28

    We report a neutral salt water based battery which uses p-type and n-type solution processed polymer films as the cathode and the anode of the cell. The specific capacity of the electrodes (approximately 30 mAh cm-3) is achieved via formation of bipolarons in both the p-type and n-type polymers. By engineering ethylene glycol and zwitterion based side chains attached to the polymer backbone we facilitate rapid ion transport through the non-porous polymer films. This, combined with efficient transport of electronic charge via the conjugated polymer backbones, allowed the films to maintain constant capacity at high charge and discharge rates (>1000 C-rate). The electrodes also show good stability during electrochemical cycling (less than 30% decrease in capacity over >1000 cycles) and an output voltage up to 1.4 V. The performance of these semiconducting polymers with polar side-chains demonstrates the potential of this material class for fast-charging, water based electrochemical energy storage devices.

  11. Modified melanocortin tetrapeptide Ac-His-dPhe-Arg-Trp-NH at the arginine side chain with ureas and thioureas.

    Science.gov (United States)

    Joseph, C G; Sorensen, N B; Wood, M S; Xiang, Z; Moore, M C; Haskell-Luevano, C

    2005-11-01

    The Ac-His-dPhe-Arg-Trp-NH2 tetrapeptide is a nonselective melanocortin agonist and replacement of Arg in the tetrapeptide with acidic, basic or neutral amino acids results in reduced potency at the melanocortin receptor (MCR) isoforms (MC1R and MC3-5R). To determine the importance of the positive charge and the guanidine moiety for melanocortin activity, a series of urea- and thiourea-substituted tetrapeptides were designed. Replacement of Arg with Lys or ornithine reduced agonist activity at the mouse mMC1 and mMC3-5 receptors, thus supporting the hypothesis that the guanidine moiety is important for receptor potency, particularly at the MC3-5 receptors. The Arg side chain-modified tetrapeptides examined in this study include substituted phenyl, naphthyl, and aliphatic urea and thiourea residues using a Lys side-chain template. These ligands elicit full-agonist pharmacology at the mouse MCRs examined in this study.

  12. Controlling the morphology of side chain liquid crystalline block copolymer thin films through variations in liquid crystalline content.

    Science.gov (United States)

    Verploegen, Eric; Zhang, Tejia; Jung, Yeon Sik; Ross, Caroline; Hammond, Paula T

    2008-10-01

    In this paper, we describe methods for manipulating the morphology of side-chain liquid crystalline block copolymers through variations in the liquid crystalline content. By systematically controlling the covalent attachment of side chain liquid crystals to a block copolymer (BCP) backbone, the morphology of both the liquid crystalline (LC) mesophase and the phase-segregated BCP microstructures can be precisely manipulated. Increases in LC functionalization lead to stronger preferences for the anchoring of the LC mesophase relative to the substrate and the intermaterial dividing surface. By manipulating the strength of these interactions, the arrangement and ordering of the ultrathin film block copolymer nanostructures can be controlled, yielding a range of morphologies that includes perpendicular and parallel cylinders, as well as both perpendicular and parallel lamellae. Additionally, we demonstrate the utilization of selective etching to create a nanoporous liquid crystalline polymer thin film. The unique control over the orientation and order of the self-assembled morphologies with respect to the substrate will allow for the custom design of thin films for specific nanopatterning applications without manipulation of the surface chemistry or the application of external fields.

  13. Improved power conversion efficiency of dye-sensitized solar cells using side chain liquid crystal polymer embedded in polymer electrolytes

    International Nuclear Information System (INIS)

    Cho, Woosum; Lee, Jae Wook; Gal, Yeong-Soon; Kim, Mi-Ra; Jin, Sung Ho

    2014-01-01

    Side chain liquid crystal polymer (SCLCP) embedded in poly(vinylidenefluoride-co-hexafluoropropylene) (PVdF-co-HFP)-based polymer electrolytes (PVdF-co-HFP:side chain liquid crystal polymer (SCLCP)) was prepared for dye-sensitized solar cell (DSSC) application. The polymer electrolytes contained tetrabutylammonium iodide (TBAI), iodine (I 2 ), and 8 wt% PVdF-co-HFP in acetonitrile. DSSCs comprised of PVdF-co-HFP:SCLCP-based polymer electrolytes displayed enhanced redox couple reduction and reduced charge recombination in comparison to those of the conventional PVdF-co-HFP-based polymer electrolyte. The significantly increased short-circuit current density (J sc , 10.75 mA cm −2 ) of the DSSCs with PVdF-co-HFP:SCLCP-based polymer electrolytes afforded a high power conversion efficiency (PCE) of 5.32% and a fill factor (FF) of 0.64 under standard light intensity of 100 mW cm −2 irradiation of AM 1.5 sunlight. - Highlights: • We developed the liquid crystal polymer embedded on polymer electrolyte for DSSCs. • We fabricated the highly efficient DSSCs using polymer electrolyte. • The best PCE achieved for P1 is 5.32% using polymer electrolyte

  14. Improved power conversion efficiency of dye-sensitized solar cells using side chain liquid crystal polymer embedded in polymer electrolytes

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Woosum [Department of Chemistry Education, and Department of Frontier Materials Chemistry, and Institute for Plastic Information and Energy Materials, Pusan National University, Busan 609-735 (Korea, Republic of); Lee, Jae Wook, E-mail: jlee@donga.ac.kr [Department of Chemistry, Dong-A University, Busan 604-714 (Korea, Republic of); Gal, Yeong-Soon [Polymer Chemistry Lab, College of General Education, Kyungil University, Hayang 712-701 (Korea, Republic of); Kim, Mi-Ra, E-mail: mrkim2@pusan.ac.kr [Department of Polymer Science and Engineering, Pusan National University, Busan 609-735 (Korea, Republic of); Jin, Sung Ho, E-mail: shjin@pusan.ac.kr [Department of Chemistry Education, and Department of Frontier Materials Chemistry, and Institute for Plastic Information and Energy Materials, Pusan National University, Busan 609-735 (Korea, Republic of)

    2014-02-14

    Side chain liquid crystal polymer (SCLCP) embedded in poly(vinylidenefluoride-co-hexafluoropropylene) (PVdF-co-HFP)-based polymer electrolytes (PVdF-co-HFP:side chain liquid crystal polymer (SCLCP)) was prepared for dye-sensitized solar cell (DSSC) application. The polymer electrolytes contained tetrabutylammonium iodide (TBAI), iodine (I{sub 2}), and 8 wt% PVdF-co-HFP in acetonitrile. DSSCs comprised of PVdF-co-HFP:SCLCP-based polymer electrolytes displayed enhanced redox couple reduction and reduced charge recombination in comparison to those of the conventional PVdF-co-HFP-based polymer electrolyte. The significantly increased short-circuit current density (J{sub sc}, 10.75 mA cm{sup −2}) of the DSSCs with PVdF-co-HFP:SCLCP-based polymer electrolytes afforded a high power conversion efficiency (PCE) of 5.32% and a fill factor (FF) of 0.64 under standard light intensity of 100 mW cm{sup −2} irradiation of AM 1.5 sunlight. - Highlights: • We developed the liquid crystal polymer embedded on polymer electrolyte for DSSCs. • We fabricated the highly efficient DSSCs using polymer electrolyte. • The best PCE achieved for P1 is 5.32% using polymer electrolyte.

  15. Amide side chain amphiphilic polymers disrupt surface established bacterial bio-films and protect mice from chronic Acinetobacter baumannii infection.

    Science.gov (United States)

    Uppu, Divakara S S M; Samaddar, Sandip; Ghosh, Chandradhish; Paramanandham, Krishnamoorthy; Shome, Bibek R; Haldar, Jayanta

    2016-01-01

    Bacterial biofilms represent the root-cause of chronic or persistent infections in humans. Gram-negative bacterial infections due to nosocomial and opportunistic pathogens such as Acinetobacter baumannii are more difficult to treat because of their inherent and rapidly acquiring resistance to antibiotics. Due to biofilm formation, A. baumannii has been noted for its apparent ability to survive on artificial surfaces for an extended period of time, therefore allowing it to persist in the hospital environment. Here we report, maleic anhydride based novel cationic polymers appended with amide side chains that disrupt surface established multi-drug resistant A. baumannii biofilms. More importantly, these polymers significantly (p polymers also show potent antibacterial efficacy against methicillin resistant Staphylococcus aureus (MRSA), vancomycin resistant Enterococci (VRE) and multi-drug resistant clinical isolates of A. baumannii with minimal toxicity to mammalian cells. We observe that optimal hydrophobicity dependent on the side chain chemical structure of these polymers dictate the selective toxicity to bacteria. Polymers interact with the bacterial cell membranes by causing membrane depolarization, permeabilization and energy depletion. Bacteria develop rapid resistance to erythromycin and colistin whereas no detectable development of resistance occurs against these polymers even after several passages. These results suggest the potential use of these polymeric biomaterials in disinfecting biomedical device surfaces after the infection has become established and also for the topical treatment of chronic bacterial infections. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Side-chain sulfonated poly(ether sulfone)s for PEM applications

    Energy Technology Data Exchange (ETDEWEB)

    Meier-Haack, J.; Butwilowski, W.; Quetschke, A.; Vogel, C. [Leibniz Institute of Polymer Research Dresden, Dresden (Germany)

    2010-07-01

    Copoly(arylene ether sulfone)s from bis-(4-fluoro phenyl)sulfone (DFDPhS), bis(4-trimethylsiloxy phenyl)sulfone (DHDPhS), and 2,5-diphenylhydroquinone trimethylsilylether (Bis-TMS-DPhHQ) were obtained by nucleophilic displacement polycondensation with high molecular weights (M{sub n} up to 70,000 g/mol; {eta}{sub inh} up to 0.93 dl/g) and narrow molecular weight distributions (2.1 - 2.9). All copolymers showed a single glass-transition temperature (T{sub g}) around 230 C. Upon sulfonation with concentrated sulfuric acid, the T{sub g}s (from samples in the protonated form) were shifted to higher temperatures (+ 35 {+-} 5 C). NMR spectra and the determined ion-exchange capacities (IEC; 1.46 - 2.05 mmol/g), which were close to the theoretical values, indicating that only the pendant phenyl rings of the 2,5- diphenylhydroquinone moieties in the polymer backbone were sulfonated. Membranes prepared from N-methyl- 2-pyrrolidone (NMP) solutions were transparent and soft. The water-uptake at room temperature increased from 30% to 80% with increasing IEC. Samples from random copolymers with an IEC {>=} 1.8 mmol/g were soluble in water at 90 C. While the proton conductivity of the low IEC samples (random copolymer) (1.46 mmol/g) was lower than that of Nafion {sup registered}, the conductivities of the high IEC samples were superior to Nafion {sup registered}. In general membranes from blockcopolymers showed lower water-uptake, higher dimensional stability and higher proton conductivities as compared to samples from random copolymers with similar monomer composition and ion-exchange capacities. (orig.)

  17. 5-Ethynyl-2'-deoxycytidine: a DNA building block with a 'clickable' side chain.

    Science.gov (United States)

    Seela, Frank; Mei, Hui; Xiong, Hai; Budow, Simone; Eickmeier, Henning; Reuter, Hans

    2012-10-01

    The title compound [systematic name: 4-amino-1-(2-deoxy-β-D-erythro-pentofuranosyl)-5-ethynylpyrimidin-2(1H)-one], C(11)H(13)N(3)O(4), shows two conformations in the crystalline state. The N-glycosylic bonds of both conformers adopt similar conformations, with χ = -149.2 (1)° for conformer (I-1) and -151.4 (1)° for conformer (I-2), both in the anti range. The sugar residue of (I-1) shows a C2'-endo envelope conformation ((2)E, S-type), with P = 164.7 (1)° and τ(m) = 36.9 (1)°, while (I-2) shows a major C3'-exo sugar pucker (C3'-exo-C2'-endo, (3)T(2), S-type), with P = 189.2 (1)° and τ(m) = 33.3 (1)°. Both conformers participate in the formation of a layered three-dimensional crystal structure with a chain-like arrangement of the conformers. The ethynyl groups do not participate in hydrogen bonding, but are arranged in proximal positions.

  18. Equivalent chain lengths of all C4-C23 saturated monomethyl branched fatty acid methyl esters on methylsilicone OV-1 stationary phase.

    Science.gov (United States)

    Kubinec, Róbert; Blaško, Jaroslav; Górová, Renáta; Addová, Gabriela; Ostrovský, Ivan; Amann, Anton; Soják, Ladislav

    2011-04-01

    Isomer mixtures of monomethyl branched saturated C7-C23 fatty acid methyl esters (FAME) were prepared by performing a methylene insertion reaction to the straight chain FAME and this study model was completed by using commercially available standards of C4-C7 FAME. The equivalent chain lengths (ECL) of all 220 C4-C23 monomethyl branched FAME on OV-1 stationary phase were measured, achieving an average repeatability of ±0.0004 ECL units. The monomethyl branched FAME was identified by GC on the basis of regularity of the fractional chain lengths (FCL) dependence on the number of carbon atoms (C(z)) of individual homologous series of methyl 2-, 3-, …, 21-FAME. The prediction of retention of the first homologues, having the new position of methyl group beginning at higher carbon atoms number, and analogously for the second, third, fourth, and other members of the homologous series, allowed the dependence FCL=f(C(z)) for the first and subsequent members of beginning homologous of monomethyl derivatives of FAME. The identification was confirmed by mass spectrometry. All of the methyl isomers of FAME, which could not be completely separated by gas chromatography due to having a methyl group in surroundings of the middle of the carbon chain, were resolved by mass spectrometry using deconvolution in a SIM-mode. Measured gas chromatographic and mass spectrometric data were applied for identification of the monomethyl branched saturated FAME in tongue coating. Copyright © 2011 Elsevier B.V. All rights reserved.

  19. Role of Side Chains in β-Sheet Self-Assembly into Peptide Fibrils. IR and VCD Spectroscopic Studies of Glutamic Acid-Containing Peptides.

    Science.gov (United States)

    Tobias, Fernando; Keiderling, Timothy A

    2016-05-10

    Poly(glutamic acid) at low pH self-assembles after incubation at higher temperature into fibrils composed of antiparallel sheets that are stacked in a β2-type structure whose amide carbonyls have bifurcated H-bonds involving the side chains from the next sheet. Oligomers of Glu can also form such structures, and isotope labeling has provided insight into their out-of-register antiparallel structure [ Biomacromolecules 2013 , 14 , 3880 - 3891 ]. In this paper we report IR and VCD spectra and transmission electron micrograph (TEM) images for a series of alternately sequenced oligomers, Lys-(Aaa-Glu)5-Lys-NH2, where Aaa was varied over a variety of polar, aliphatic, or aromatic residues. Their spectral and TEM data show that these oligopeptides self-assemble into different structures, both local and morphological, that are dependent on both the nature of the Aaa side chains and growth conditions employed. Such alternate peptides substituted with small or polar residues, Ala and Thr, do not yield fibrils; but with β-branched aliphatic residues, Val and Ile, that could potentially pack with Glu side chains, these oligopeptides do show evidence of β2-stacking. By contrast, for Leu, with longer side chains, only β1-stacking is seen while with even larger Phe side chains, either β-form can be detected separately, depending on preparation conditions. These structures are dependent on high temperature incubation after reducing the pH and in some cases after sonication of initial fibril forms and reincubation. Some of these fibrillar peptides, but not all, show enhanced VCD, which can offer evidence for formation of long, multistrand, often twisted structures. Substitution of Glu with residues having selected side chains yields a variety of morphologies, leading to both β1- and β2-structures, that overall suggests two different packing modes for the hydrophobic side chains depending on size and type.

  20. Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors

    Directory of Open Access Journals (Sweden)

    Zied Gaieb

    Full Text Available Structure and dynamics are essential elements of protein function. Protein structure is constantly fluctuating and undergoing conformational changes, which are captured by molecular dynamics (MD simulations. We introduce a computational framework that provides a compact representation of the dynamic conformational space of biomolecular simulations. This method presents a systematic approach designed to reduce the large MD simulation spatiotemporal datasets into a manageable set in order to guide our understanding of how protein mechanics emerge from side chain organization and dynamic reorganization. We focus on the detection of side chain interactions that undergo rearrangements mediating global domain motions and vice versa. Side chain rearrangements are extracted from side chain interactions that undergo well-defined abrupt and persistent changes in distance time series using Gaussian mixture models, whereas global domain motions are detected using dynamic cross-correlation. Both side chain rearrangements and global domain motions represent the dynamic components of the protein MD simulation, and are both mapped into a network where they are connected based on their degree of coupling. This method allows for the study of allosteric communication in proteins by mapping out the protein dynamics into an intramolecular network to reduce the large simulation data into a manageable set of communities composed of coupled side chain rearrangements and global domain motions. This computational framework is suitable for the study of tightly packed proteins, such as G protein-coupled receptors, and we present an application on a seven microseconds MD trajectory of CC chemokine receptor 7 (CCR7 bound to its ligand CCL21. Keywords: Molecular dynamics, Change-point detection, Side chain reorganization, Helical domain motion, Intramolecular network, Membrane proteins, GPCR, GPCR computational modeling, GPCR allostery

  1. Gamma-radiation induced polymerization of methyl methacrylate in aliphatic hydrocarbons: kinetics and evidence for incorporation of hydrocarbon in the polymer chain

    International Nuclear Information System (INIS)

    Mohan, H.; Iyer, R.M.

    1989-01-01

    On γ-radiolysis, the rate of polymerization of methyl methacrylate in hydrocarbon solvents is observed to decrease. It is explained by hydrocarbon entry into the polymer chains. The hydrocarbon entry into the polymer chains is observed to take place at later stages of polymerization and increases with hydrocarbon chain length. The extent of hydrocarbon entry into the polymer chains is estimated by NMR and GLC analysis. It is observed to be equal to ∼ 12% corresponding to ∼ 97 hexadecane molecules in each polymer chain. The IR, DSC, MW determination and radiation effects on the polymer showed evidences for hydrocarbon entry into the polymer. It is explained by chain transfer from the growing polymer radical to the hydrocarbon molecules. The chain transfer constant is determined to be equal to 1 x 10 -2 . (author)

  2. Side-chain interactions form late and cooperatively in the binding reaction between disordered peptides and PDZ domains

    DEFF Research Database (Denmark)

    Haq, S Raza; Chi, Celestine N; Bach, Anders

    2012-01-01

    Intrinsically disordered proteins are very common and mediate numerous protein-protein and protein-DNA interactions. While it is clear that these interactions are instrumental for the life of the mammalian cell, there is a paucity of data regarding their molecular binding mechanisms. We have here...... used short peptides as a model system for intrinsically disordered proteins. Linear free-energy relationships based on rate and equilibrium constants for the binding of these peptides to ordered target proteins, PDZ domains, demonstrate that native side-chain interactions form mainly after the rate......-limiting barrier for binding, in a cooperative fashion. This finding suggests that these disordered peptides first form a weak encounter complex with non-native interactions. The data do not support the recent notion that the affinities of intrinsically disordered proteins towards their targets are generally...

  3. Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage

    Science.gov (United States)

    Shih, I-hung; Been, Michael D.

    2001-01-01

    Ribozymes of hepatitis delta virus have been proposed to use an active-site cytosine as an acid-base catalyst in the self-cleavage reaction. In this study, we have examined the role of cytosine in more detail with the antigenomic ribozyme. Evidence that proton transfer in the rate-determining step involved cytosine 76 (C76) was obtained from examining cleavage activity of the wild-type and imidazole buffer-rescued C76-deleted (C76Δ) ribozymes in D2O and H2O. In both reactions, a similar kinetic isotope effect and shift in the apparent pKa indicate that the buffer is functionally substituting for the side chain in proton transfer. Proton inventory of the wild-type reaction supported a mechanism of a single proton transfer at the transition state. This proton transfer step was further characterized by exogenous base rescue of a C76Δ mutant with cytosine and imidazole analogues. For the imidazole analogues that rescued activity, the apparent pKa of the rescue reaction, measured under kcat/KM conditions, correlated with the pKa of the base. From these data a Brønsted coefficient (β) of 0.51 was determined for the base-rescued reaction of C76Δ. This value is consistent with that expected for proton transfer in the transition state. Together, these data provide strong support for a mechanism where an RNA side chain participates directly in general acid or general base catalysis of the wild-type ribozyme to facilitate RNA cleavage. PMID:11171978

  4. Rotation of methyl side groups in polymers: A Fourier transform approach to quasielastic neutron scattering. 1: Homopolymers

    International Nuclear Information System (INIS)

    Arrighi, V.; Higgins, J.S.; Howells, W.S.

    1995-01-01

    The rotational motion of the ester methyl group in poly(methyl methacrylate) (PMMA) was investigated using quasielastic neutron scattering (QENS). A comparison between the authors results and the QENS data reported in the literature for PMMA-d 5 indicates that the amount of quasielastic broadening is highly dependent upon the energy resolution of the spectrometer. This anomalous behavior is here attributed to the method of analysis, namely, the use of a single rotational frequency. Such a procedure leads to a non-Arrhenius temperature dependence, to a temperature-dependent elastic incoherent structure factor, and to values of rotational frequency which are resolution dependent. They propose an alternative approach to the analysis of the QENS data which accounts for the existence of a distribution of rotational frequencies. The frequency data are Fourier transformed to the time domain, and the intermediate scattering function is fitted using a stretched exponential or Kohlraush-Williams-Watts function. The excellent overlap between data from different spectrometers leaves no doubt on the adequacy of their procedure. Measurements of the ether methyl group rotation in poly(vinyl methyl ether) (PVME) are also reported. The PVME data confirm that the behavior observed for PMMA-d 5 is likely to be a common feature to all polymeric systems

  5. Oxidation of Peptides by Methyl(trifluoromethyl)dioxirane: the Protecting Group Matters

    Science.gov (United States)

    Rella, Maria Rosaria; Williard, Paul G.

    2011-01-01

    Representative Boc protected and acetyl protected peptide methyl esters bearing alkyl side chains undergo effective oxidation using methyl(trifluoromethyl)dioxirane (1b) under mild conditions. We observe a protecting group dependency in the chemoselectivity displayed by the dioxirane 1b. N-hydroxylation occurs in the case of the Boc protected peptides, side chain hydroxylation takes place in the case of acetyl protected peptides. Both are attractive transformations since they yield derivatized peptides that serve as valuable synthons. PMID:17221970

  6. 4-N-, 4-S-, and 4-O-chloroquine analogues: influence of side chain length and quinolyl nitrogen pKa on activity vs chloroquine resistant malaria.

    Science.gov (United States)

    Natarajan, Jayakumar K; Alumasa, John N; Yearick, Kimberly; Ekoue-Kovi, Kekeli A; Casabianca, Leah B; de Dios, Angel C; Wolf, Christian; Roepe, Paul D

    2008-06-26

    Using predictions from heme-quinoline antimalarial complex structures, previous modifications of chloroquine (CQ), and hypotheses for chloroquine resistance (CQR), we synthesize and assay CQ analogues that test structure-function principles. We vary side chain length for both monoethyl and diethyl 4-N CQ derivatives. We alter the pKa of the quinolyl N by introducing alkylthio or alkoxy substituents into the 4 position and vary side chain length for these analogues. We introduce an additional titratable amino group to the side chain of 4-O analogues with promising CQR strain selectivity and increase activity while retaining selectivity. We solve atomic resolution structures for complexes formed between representative 4-N, 4-S, and 4-O derivatives vs mu-oxo dimeric heme, measure binding constants for monomeric vs dimeric heme, and quantify hemozoin (Hz) formation inhibition in vitro. The data provide additional insight for the design of CQ analogues with improved activity vs CQR malaria.

  7. 4-N, 4-S & 4-O Chloroquine Analogues: Influence of Side Chain Length and Quinolyl Nitrogen pKa on Activity vs. Chloroquine Resistant Malaria+, #

    Science.gov (United States)

    Natarajan, Jayakumar K.; Alumasa, John; Yearick, Kimberly; Ekoue-Kovi, Kekeli A.; Casabianca, Leah B.; de Dios, Angel C.; Wolf, Christian; Roepe, Paul D.

    2009-01-01

    Using predictions from heme – quinoline antimalarial complex structures, previous modifications of chloroquine (CQ), and hypotheses for chloroquine resistance (CQR), we synthesize and assay CQ analogues that test structure – function principles. We vary side chain length for both monoethyl and diethyl 4N CQ derivatives. We alter the pKa of the quinolyl N by introducing alkylthio or alkoxy substituents into the 4 position, and vary side chain length for these analogues. We introduce an additional titratable amino group to the side chain of 4O analogues with promising CQR strain selectivity and increase activity while retaining selectivity. We solve atomic resolution structures for complexes formed between representative 4N, 4S and 4O derivatives vs. μ-oxo dimeric heme, measure binding constants for monomeric vs. dimeric heme, and quantify hemozoin (Hz) formation inhibition in vitro. The data provide additional insight for the design of CQ analogues with improved activity vs. CQR malaria. PMID:18512900

  8. Optical anisotropy of polyimide and polymethacrylate containing photocrosslinkable chalcone group in the side chain under irradiation of a linearly polarized UV light

    CERN Document Server

    Choi, D H

    2002-01-01

    Photocrosslinkable soluble polyimide and polymethacrylate compound were synthesized for studying the optically induced anisotropy of the thin films. Chalcone group was introduced into the side chain unit of two polymers. We observed a photodimerization behavior between the double bonds in the chalcone group and an optical anisotropy of these materials by irradiation of a linearly polarized UV light (LPL). Optical anisotropy of the thin film was also investigated by using polarized UV absorption spectroscopy.The dynamic property of optical anisotropy in photoreactive polyimide was compared to that in polymethacrylate containing chalcone group in the side chain.

  9. Reaction mechanisms in the radiolysis of peptides, polypeptides and proteins II reactions at side-chain loci in model systems

    International Nuclear Information System (INIS)

    Garrison, W.M.

    1983-11-01

    The major emphasis in radiation biology at the molecular level has been on the nucleic acid component of the nucleic acid-protein complex because of its primary genetic importance. But there is increasing evidence that radiation damage to the protein component also has important biological implications. Damage to capsid protein now appears to be a major factor in the radiation inactivation of phage and other viruses. And, there is increasing evidence that radiation-chemical change in the protein component of chromation leads to changes in the stability of the repressor-operator complexes involved in gene expression. Knowledge of the radiation chemistry of protein is also of importance in other fields such as the application of radiation sterilization to foods and drugs. Recent findings that a class of compounds, the α,α'-diaminodicarboxylic acids, not normally present in food proteins, are formed in protein radiolysis is of particular significance since certain of their peptide derivatives have been showing to exhibit immunological activity. The purpose of this review is to bring together and to correlate our present knowledge of products and mechanisms in the radiolysis of peptides, polypeptides and proteins both aqueous and solid-state. In part 1 we presented a discussion of the radiation-induced reactions of the peptide main-chain in model peptide and polypeptide systems. Here in part 2 the emphasis is on the competing radiation chemistry at side-chain loci of peptide derivatives of aliphatic, aromatic-unsaturated and sulfur-containing amino acids in similar systems. Information obtained with the various experimental techniques of product analysis, competition kinetics, spin-trapping, pulse radiolysis, and ESR spectroscopy are included

  10. Enhanced n-Doping Efficiency of a Naphthalenediimide-Based Copolymer through Polar Side Chains for Organic Thermoelectrics

    KAUST Repository

    Kiefer, David

    2018-01-05

    N-doping of conjugated polymers either requires a high dopant fraction or yields a low electrical conductivity because of their poor compatibility with molecular dopants. We explore n-doping of the polar naphthalenediimide–bithiophene copolymer p(gNDI-gT2) that carries oligoethylene glycol-based side chains and show that the polymer displays superior miscibility with the benzimidazole–dimethylbenzenamine-based n-dopant N-DMBI. The good compatibility of p(gNDI-gT2) and N-DMBI results in a relatively high doping efficiency of 13% for n-dopants, which leads to a high electrical conductivity of more than 10–1 S cm–1 for a dopant concentration of only 10 mol % when measured in an inert atmosphere. We find that the doped polymer is able to maintain its electrical conductivity for about 20 min when exposed to air and recovers rapidly when returned to a nitrogen atmosphere. Overall, solution coprocessing of p(gNDI-gT2) and N-DMBI results in a larger thermoelectric power factor of up to 0.4 μW K–2 m–1 compared to other NDI-based polymers.

  11. Factors Governing Intercalation of Fullerenes and Other Small Molecules Between the Side Chains of Semiconducting Polymers Used in Solar Cells

    KAUST Repository

    Miller, Nichole Cates

    2012-08-22

    While recent reports have established signifi cant miscibility in polymer:fullerene blends used in organic solar cells, little is actually known about why polymers and fullerenes mix and how their mixing can be controlled. Here, X-ray diffraction (XRD), differential scanning calorimetry (DSC), and molecular simulations are used to study mixing in a variety of polymer:molecule blends by systematically varying the polymer and smallmolecule properties. It is found that a variety of polymer:fullerene blends mix by forming bimolecular crystals provided there is suffi cient space between the polymer side chains to accommodate a fullerene. Polymer:tetrafl uoro-tetracyanoquinodimethane (F4-TCNQ) bimolecular crystals were also observed, although bimolecular crystals did not form in the other studied polymer:nonfullerene blends, including those with both conjugated and non-conjugated small molecules. DSC and molecular simulations demonstrate that strong polymer-fullerene interactions can exist, and the calculations point to van der Waals interactions as a signifi cant driving force for molecular mixing. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Effect of Side Chain Functional Group on Interactions in Ionic Liquid Systems: Insights from Infinite Dilution Thermodynamic Data.

    Science.gov (United States)

    Paduszyński, Kamil; Królikowska, Marta

    2017-11-02

    Measurements of infinite dilution activity coefficients of 48 molecular solutes (including alkanes, alkenes, alkynes, aromatics, ethers, alcohols, water, ketones, pyridine, thiophene, acetonitrile, and 1-nitropropane) in two ionic liquids (ILs), namely, 1-(2-hydroxyethyl)-3-methylimidazolium dicyanamide and 1-(2-chloroethyl)-3-methylimidazolium dicyanamide, are reported in the temperature range from T = 308.15 to 358.15 K. Comparative analysis of an effect of OH/Cl substitution of terminal carbon in side chains of imidazolium cations is presented and discussed in terms of different types of intermolecular forces acting between ILs and solutes. The new data also are confronted to those published previously for a "plain" counterpart of the studied ILs, namely, 1-ethyl-3-methylimidazolium dicyanamide. Infinite dilution capacity and selectivity of the studied ILs are presented to evaluate them as separating agents in extraction of aromatics from alkanes and sulfur compounds from alkanes. Three modeling approaches, namely, linear solvation energy relationship (LSER), regular solution theory, and conductor-like screening model for real solvents (COSMO-RS), are tested for their capabilities of capturing the substitution effects detected experimentally.

  13. Alanine scan of the peptide antibiotic feglymycin: assessment of amino acid side chains contributing to antimicrobial activity.

    Science.gov (United States)

    Hänchen, Anne; Rausch, Saskia; Landmann, Benjamin; Toti, Luigi; Nusser, Antje; Süssmuth, Roderich D

    2013-03-18

    The antibiotic feglymycin is a linear 13-mer peptide synthesized by the bacterium Streptomyces sp. DSM 11171. It mainly consists of the nonproteinogenic amino acids 4-hydroxyphenylglycine and 3,5-dihydroxyphenylglycine. An alanine scan of feglymycin was performed by solution-phase peptide synthesis in order to assess the significance of individual amino acid side chains for biological activity. Hence, 13 peptides were synthesized from di- and tripeptide building blocks, and subsequently tested for antibacterial activity against Staphylococcus aureus strains. Furthermore we tested the inhibition of peptidoglycan biosynthesis enzymes MurA and MurC, which are inhibited by feglymycin. Whereas the antibacterial activity is significantly based on the three amino acids D-Hpg1, L-Hpg5, and L-Phe12, the inhibitory activity against MurA and MurC depends mainly on L-Asp13. The difference in the position dependence for antibacterial activity and enzyme inhibition suggests multiple molecular targets in the modes of action of feglymycin. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. A stochastic algorithm for global optimization and for best populations: A test case of side chains in proteins

    Science.gov (United States)

    Glick, Meir; Rayan, Anwar; Goldblum, Amiram

    2002-01-01

    The problem of global optimization is pivotal in a variety of scientific fields. Here, we present a robust stochastic search method that is able to find the global minimum for a given cost function, as well as, in most cases, any number of best solutions for very large combinatorial “explosive” systems. The algorithm iteratively eliminates variable values that contribute consistently to the highest end of a cost function's spectrum of values for the full system. Values that have not been eliminated are retained for a full, exhaustive search, allowing the creation of an ordered population of best solutions, which includes the global minimum. We demonstrate the ability of the algorithm to explore the conformational space of side chains in eight proteins, with 54 to 263 residues, to reproduce a population of their low energy conformations. The 1,000 lowest energy solutions are identical in the stochastic (with two different seed numbers) and full, exhaustive searches for six of eight proteins. The others retain the lowest 141 and 213 (of 1,000) conformations, depending on the seed number, and the maximal difference between stochastic and exhaustive is only about 0.15 Kcal/mol. The energy gap between the lowest and highest of the 1,000 low-energy conformers in eight proteins is between 0.55 and 3.64 Kcal/mol. This algorithm offers real opportunities for solving problems of high complexity in structural biology and in other fields of science and technology. PMID:11792838

  15. On the calculation of {sup 3}J{sub {alpha}{beta}}-coupling constants for side chains in proteins

    Energy Technology Data Exchange (ETDEWEB)

    Steiner, Denise [Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH (Switzerland); Allison, Jane R. [Massey University Albany, Centre for Theoretical Chemistry and Physics, Institute for Natural Sciences (New Zealand); Eichenberger, Andreas P.; Gunsteren, Wilfred F. van, E-mail: wfvgn@igc.phys.chem.ethz.ch [Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH (Switzerland)

    2012-07-15

    Structural knowledge about proteins is mainly derived from values of observables, measurable in NMR spectroscopic or X-ray diffraction experiments, i.e. absorbed or scattered intensities, through theoretically derived relationships between structural quantities such as atom positions or torsional angles on the one hand and observable quantities such as squared structure factor amplitudes, NOE intensities or {sup 3}J-coupling constants on the other. The standardly used relation connecting {sup 3}J-couplings to torsional angles is the Karplus relation, which is used in protein structure refinement as well as in the evaluation of simulated properties of proteins. The accuracy of the simple and generalised Karplus relations is investigated using side-chain structural and {sup 3}J{sub {alpha}{beta}}-coupling data for three different proteins, Plastocyanin, Lysozyme, and FKBP, for which such data are available. The results show that the widely used Karplus relations are only a rough estimate for the relation between {sup 3}J{sub {alpha}{beta}}-couplings and the corresponding {chi}{sub 1}-angle in proteins.

  16. Atomic force and optical near-field microscopic investigations of polarization holographic gratings in a liquid crystalline azobenzene side-chain polyester

    DEFF Research Database (Denmark)

    Ramanujam, P.S.; Holme, N.C.R.; Hvilsted, S.

    1996-01-01

    Atomic force and scanning near-field optical microscopic investigations have been carried out on a polarization holographic grating recorded in an azobenzene side-chain Liquid crystalline polyester. It has been found that immediately following laser irradiation, a topographic surface grating...

  17. Synthesis and Catalytic Properties of Non-Cross-Linked and Cross-Linked Poly(alkylmethyldiallylammonium bromides) Having Decyl, Octyl, and Hexyl Side Chains

    NARCIS (Netherlands)

    Wang, G.J; Engberts, J.B.F.N.

    1995-01-01

    A family of non-cross-linked and cross-linked copolymers containing decyl, octyl, and hexyl groups as side chains ((CL)-CopolC1-10, (CL)-CopolC1-8, and (CL)-CopolC1-6, respectively) were synthesized by radical-initiated cyclocopolymerization of alkylmethyldiallylammonium bromide monomers without and

  18. The influence of the side-chain sequence on the structure-activity correlations of immunomodulatory branched polypeptides. Synthesis and conformational analysis of new model polypeptides.

    Science.gov (United States)

    Mezö, G; Hudecz, F; Kajtár, J; Szókán, G; Szekerke, M

    1989-10-01

    New branched polypeptides were synthesized for a detailed study of the influence of the side-chain structure on the conformation and biological properties. The first subset of polypeptides were prepared by coupling of tetrapeptides to poly[L-Lys]. These polymers contain either DL-Ala3-X [poly[Lys-(X-DL-Ala3)n

  19. Positioning of the carboxamide side chain in 11-oxo-11H-indeno[1,2-b]quinolinecarboxamide anticancer agents: effects on cytotoxicity.

    Science.gov (United States)

    Deady, L W; Desneves, J; Kaye, A J; Finlay, G J; Baguley, B C; Denny, W A

    2001-02-01

    A series of 11-oxo-11H-indeno[1,2-b]quinolines bearing a carboxamide-linked cationic side chain at various positions on the chromophore was studied to determine structure-activity relationships between cytotoxicity and the position of the side chain. The compounds were prepared by Pfitzinger synthesis from an appropriate isatin and 1-indanone, followed by various oxidative steps, to generate the required carboxylic acids. The 4- and 6-carboxamides (with the side chain on a terminal ring, off the short axis of the chromophore) were effective cytotoxins. The dimeric 4- and 6-linked analogues were considerably more cytotoxic than the parent monomers, but had broadly similar activities. In contrast, analogues with side chains at the 8-position (on a terminal ring but off the long axis of the chromophore) or 10-position (off the short axis of the chromophore but in a central ring) were drastically less effective. The 4,10- and 6,10-biscarboxamides had activities between those of the corresponding parent monocarboxamides. The first of these showed good activity against advanced subcutaneous colon 38 tumours in mice.

  20. Probing the effects of the ester functional group, alkyl side chain length and anions on the bulk nanostructure of ionic liquids: a computational study.

    Science.gov (United States)

    Fakhraee, Mostafa; Gholami, Mohammad Reza

    2016-04-14

    The effects of ester addition on nanostructural properties of biodegradable ILs composed of 1-alkoxycarbonyl-3-alkyl-imidazolium cations ([C1COOCnC1im](+), n = 1, 2, 4) combined with [Br](-), [NO3](-), [BF4](-), [PF6](-), [TfO](-), and [Tf2N](-) were explored by using the molecular dynamics (MD) simulations and quantum theory of atoms in molecules (QTAIM) analysis at 400 K. Various thermodynamic properties of these ILs were extensively computed in our earlier work (Ind. Eng. Chem. Res., 2015, 54, 11678-11700). Nano-scale segregation analysis demonstrates the formation of a small spherical island-like hydrocarbon within the continuous ionic domain for ILs with short alkyl side chain ([C1COOC1C1im]), and a sponge-like nanostructure for the compound with long alkyl side chain ([C1COOC4C1im]). Ester-functionalized ILs with ethyl side chain ([C1COOC2C1im]) are the turning point between two different morphologies. Non-polar channels were observed for [C1COOC4C1im] ILs composed of smaller anions such as [Br] and [NO3], whereas clustering organization was found for the other anions. Formation of the spherical micelle-like nanostructure was seen for lengthened cations. Finally, the incorporation of an ester group into the alkyl side chain of the cation leads to stronger segregation between charged and uncharged networks, which consequently increased the possibility of self-assembly and micelle formation.

  1. Structural optimization and evaluation of butenolides as potent antifouling agents: modification of the side chain affects the biological activities of compounds

    KAUST Repository

    Li, Yongxin

    2012-09-01

    A recent global ban on the use of organotin compounds as antifouling agents has increased the need for safe and effective antifouling compounds. In this study, a series of new butenolide derivatives with various amine side chains was synthesized and evaluated for their anti-larval settlement activities in the barnacle, Balanus amphitrite. Side chain modification of butenolide resulted in butenolides 3c-3d, which possessed desirable physico-chemical properties and demonstrated highly effective non-toxic anti-larval settlement efficacy. A structure-activity relationship analysis revealed that varying the alkyl side chain had a notable effect on anti-larval settlement activity and that seven to eight carbon alkyl side chains with a tert-butyloxycarbonyl (Boc) substituent on an amine terminal were optimal in terms of bioactivity. Analysis of the physico-chemical profile of butenolide analogues indicated that lipophilicity is a very important physico-chemical parameter contributing to bioactivity. © 2012 Copyright Taylor and Francis Group, LLC.

  2. Collision-Induced Dissociation of Deprotonated Peptides. Relative Abundance of Side-Chain Neutral Losses, Residue-Specific Product Ions, and Comparison with Protonated Peptides.

    Science.gov (United States)

    Liang, Yuxue; Neta, Pedatsur; Yang, Xiaoyu; Stein, Stephen E

    2018-03-01

    High-accuracy MS/MS spectra of deprotonated ions of 390 dipeptides and 137 peptides with three to six residues are studied. Many amino acid residues undergo neutral losses from their side chains. The most abundant is the loss of acetaldehyde from threonine. The abundance of losses from the side chains of other amino acids is estimated relative to that of threonine. While some amino acids lose the whole side chain, others lose only part of it, and some exhibit two or more different losses. Side-chain neutral losses are less abundant in the spectra of protonated peptides, being significant mainly for methionine and arginine. In addition to the neutral losses, many amino acid residues in deprotonated peptides produce specific negative ions after peptide bond cleavage. An expanded list of fragment ions from protonated peptides is also presented and compared with those of deprotonated peptides. Fragment ions are mostly different for these two cases. These lists of fragments are used to annotate peptide mass spectral libraries and to aid in the confirmation of specific amino acids in peptides. Graphical Abstract ᅟ.

  3. Structural optimization and evaluation of butenolides as potent antifouling agents: modification of the side chain affects the biological activities of compounds

    KAUST Repository

    Li, Yongxin; Zhang, Fengying; Xu, Ying; Matsumura, Kiyotaka; Han, Zhuang; Liu, Lingli; Lin, Wenhan; Jia, Yanxing; Qian, Pei Yuan

    2012-01-01

    A recent global ban on the use of organotin compounds as antifouling agents has increased the need for safe and effective antifouling compounds. In this study, a series of new butenolide derivatives with various amine side chains was synthesized and evaluated for their anti-larval settlement activities in the barnacle, Balanus amphitrite. Side chain modification of butenolide resulted in butenolides 3c-3d, which possessed desirable physico-chemical properties and demonstrated highly effective non-toxic anti-larval settlement efficacy. A structure-activity relationship analysis revealed that varying the alkyl side chain had a notable effect on anti-larval settlement activity and that seven to eight carbon alkyl side chains with a tert-butyloxycarbonyl (Boc) substituent on an amine terminal were optimal in terms of bioactivity. Analysis of the physico-chemical profile of butenolide analogues indicated that lipophilicity is a very important physico-chemical parameter contributing to bioactivity. © 2012 Copyright Taylor and Francis Group, LLC.

  4. Application of the Solid-Phase Julia–Lythgoe Olefination in Vitamin D Side-Chain Construction

    Directory of Open Access Journals (Sweden)

    Pierre J. De Clercq

    2006-08-01

    Full Text Available An example of the Julia–Lythgoe attachment of the vitamin D side chain to a solid-phase linked Inhoffen–Lythgoe diol derived CD-ring fragment is reported.

  5. Critical roles of hydrophobicity and orientation of side chains for inactivation of sarcoplasmic reticulum Ca2+-ATPase with thapsigargin and thapsigargin analogs

    DEFF Research Database (Denmark)

    Winther, Anne-Marie Lund; Liu, Huizhen; Sonntag, Yonathan

    2010-01-01

    fluorescence data to show how Tg and chemical analogs of the compound with modified or removed side chains bind to isolated SERCA 1a membranes. This occurs by uptake via the membrane lipid followed by insertion into a resident intramembranous binding site with few adaptative changes. Our binding data indicate...... that a balanced hydrophobicity and accurate positioning of the side chains, provided by the central guaianolide ring structure, defines a pharmacophore of Tg that governs both high affinity and access to the protein-binding site. Tg analogs substituted with long linkers at O-8 extend from the binding site between...... transmembrane segments to the putative N-terminal Ca(2+) entry pathway. The long chain analogs provide a rational basis for the localization of the linker, the presence of which is necessary for enabling prostate-specific antigen to cleave peptide-conjugated prodrugs targeting SERCA of cancer cells (Denmeade, S...

  6. Identification of In-Chain-Functionalized Compounds and Methyl-Branched Alkanes in Cuticular Waxes of Triticum aestivum cv. Bethlehem.

    Directory of Open Access Journals (Sweden)

    Radu C Racovita

    Full Text Available In this work, cuticular waxes from flag leaf blades and peduncles of Triticum aestivum cv. Bethlehem were investigated in search for novel wax compounds. Seven wax compound classes were detected that had previously not been reported, and their structures were elucidated using gas chromatography-mass spectrometry of various derivatives. Six of the classes were identified as series of homologs differing by two methylene units, while the seventh was a homologous series with homologs with single methylene unit differences. In the waxes of flag leaf blades, secondary alcohols (predominantly C27 and C33, primary/secondary diols (predominantly C28 and esters of primary/secondary diols (predominantly C50, combining C28 diol with C22 acid were found, all sharing similar secondary hydroxyl group positions at and around C-12 or ω-12. 7- and 8-hydroxy-2-alkanol esters (predominantly C35, 7- and 8-oxo-2-alkanol esters (predominantly C35, and 4-alkylbutan-4-olides (predominantly C28 were found both in flag leaf and peduncle wax mixtures. Finally, a series of even- and odd-numbered alkane homologs was identified in both leaf and peduncle waxes, with an internal methyl branch preferentially on C-11 and C-13 of homologs with even total carbon number and on C-12 of odd-numbered homologs. Biosynthetic pathways are suggested for all compounds, based on common structural features and matching chain length profiles with other wheat wax compound classes.

  7. The fungal phytotoxin alternariol 9-methyl ether and some of its synthetic analogues inhibit the photosynthetic electron transport chain.

    Science.gov (United States)

    Demuner, Antonio Jacinto; Barbosa, Luiz Cláudio Almeida; Miranda, Ana Cristina Mendes; Geraldo, Guilherme Carvalho; da Silva, Cleiton Moreira; Giberti, Samuele; Bertazzini, Michele; Forlani, Giuseppe

    2013-12-27

    Alternariol and monomethylalternariol are natural phytotoxins produced by some fungal strains, such as Nimbya and Alternaria. These substances confer virulence to phytopathogens, yet no information is available concerning their mode of action. Here we show that in the micromolar range alternariol 9-methyl ether is able to inhibit the electron transport chain (IC50 = 29.1 ± 6.5 μM) in isolated spinach chloroplasts. Since its effectiveness is limited by poor solubility in water, several alternariol analogues were synthesized using different aromatic aldehydes. The synthesized 6H-benzo[c]cromen-6-ones, 5H-chromene[4,3-b]pyridin-5-one, and 5H-chromene[4,3-c]pyridin-5-one also showed inhibitory properties, and three 6H-benzo[c]cromen-6-ones were more effective (IC50 = 12.8-22.8 μM) than the lead compound. Their addition to the culture medium of a cyanobacterial model strain was found to inhibit algal growth, with a relative effectiveness that was consistent with their activity in vitro. In contrast, the growth of a nonphotosynthetic plant cell culture was poorly affected. These compounds may represent a novel lead for the development of new active principles targeting photosynthesis.

  8. Evaluating Force Fields for the Computational Prediction of Ionized Arginine and Lysine Side-Chains Partitioning into Lipid Bilayers and Octanol.

    Science.gov (United States)

    Sun, Delin; Forsman, Jan; Woodward, Clifford E

    2015-04-14

    Abundant peptides and proteins containing arginine (Arg) and lysine (Lys) amino acids can apparently permeate cell membranes with ease. However, the mechanisms by which these peptides and proteins succeed in traversing the free energy barrier imposed by cell membranes remain largely unestablished. Precise thermodynamic studies (both theoretical and experimental) on the interactions of Arg and Lys residues with model lipid bilayers can provide valuable clues to the efficacy of these cationic peptides and proteins. We have carried out molecular dynamics simulations to calculate the interactions of ionized Arg and Lys side-chains with the zwitterionic 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid bilayer for 10 widely used lipid/protein force fields: CHARMM36/CHARMM36, SLIPID/AMBER99SB-ILDN, OPLS-AA/OPLS-AA, Berger/OPLS-AA, Berger/GROMOS87, Berger/GROMOS53A6, GROMOS53A6/GROMOS53A6, nonpolarizable MARTINI, polarizable MARTINI, and BMW MARTINI. We performed umbrella sampling simulations to obtain the potential of mean force for Arg and Lys side-chains partitioning from water to the bilayer interior. We found significant differences between the force fields, both for the interactions between side-chains and bilayer surface, as well as the free energy cost for placing the side-chain at the center of the bilayer. These simulation results were compared with the Wimley-White interfacial scale. We also calculated the free energy cost for transferring ionized Arg and Lys side-chains from water to both dry and wet octanol. Our simulations reveal rapid diffusion of water molecules into octanol whereby the equilibrium mole fraction of water in the wet octanol phase was ∼25%. Surprisingly, our free energy calculations found that the high water content in wet octanol lowered the water-to-octanol partitioning free energies for cationic residues by only 0.6 to 0.7 kcal/mol.

  9. Contributions of a disulfide bond and a reduced cysteine side chain to the intrinsic activity of the high-density lipoprotein receptor SR-BI.

    Science.gov (United States)

    Yu, Miao; Lau, Thomas Y; Carr, Steven A; Krieger, Monty

    2012-12-18

    The high-density lipoprotein (HDL) receptor scavenger receptor class B, type I (SR-BI), binds HDL and mediates selective cholesteryl ester uptake. SR-BI's structure and mechanism are poorly understood. We used mass spectrometry to assign the two disulfide bonds in SR-BI that connect cysteines within the conserved Cys(321)-Pro(322)-Cys(323) (CPC) motif and connect Cys(280) to Cys(334). We used site-specific mutagenesis to evaluate the contributions of the CPC motif and the side chain of extracellular Cys(384) to HDL binding and lipid uptake. The effects of CPC mutations on activity were context-dependent. Full wild-type (WT) activity required Pro(322) and Cys(323) only when Cys(321) was present. Reduced intrinsic activities were observed for CXC and CPX, but not XXC, XPX, or XXX mutants (X ≠ WT residue). Apparently, a free thiol side chain at position 321 that cannot form an intra-CPC disulfide bond with Cys(323) is deleterious, perhaps because of aberrant disulfide bond formation. Pro(322) may stabilize an otherwise strained CPC disulfide bond, thus supporting WT activity, but this disulfide bond is not absolutely required for normal activity. C(384)X (X = S, T, L, Y, G, or A) mutants exhibited altered activities that varied with the side chain's size: larger side chains phenocopied WT SR-BI treated with its thiosemicarbazone inhibitor BLT-1 (enhanced binding, weakened uptake); smaller side chains produced almost inverse effects (increased uptake:binding ratio). C(384)X mutants were BLT-1-resistant, supporting the proposal that Cys(384)'s thiol interacts with BLT-1. We discuss the implications of our findings on the functions of the extracellular loop cysteines in SR-BI and compare our results to those presented by other laboratories.

  10. Solid-State Organization and Ambipolar Field-Effect Transistors of Benzothiadiazole-Cyclopentadithiophene Copolymer with Long Branched Alkyl Side Chains

    Directory of Open Access Journals (Sweden)

    Martin Baumgarten

    2013-06-01

    Full Text Available The solid-state organization of a benzothiadiazole-cyclopentadithiophene copolymer with long, branched decyl-tetradecyl side chains (CDT-BTZ-C14,10 is investigated. The C14,10 substituents are sterically demanding and increase the π-stacking distance to 0.40 nm from 0.37 nm for the same polymer with linear hexadecyls (C16. Despite the bulkiness, the C14,10 side chains tend to crystallize, leading to a small chain-to-chain distance between lamellae stacks and to a crystal-like microstructure in the thin film. Interestingly, field-effect transistors based on solution processed layers of CDT-BTZ-C14,10 show ambipolar behavior in contrast to CDT-BTZ-C16 with linear side chains, for which hole transport was previously observed. Due to the increased π-stacking distance, the mobilities are only 6 × 10−4 cm²/Vs for electrons and 6 × 10−5 cm²/Vs for holes, while CDT-BTZ-C16 leads to values up to 5.5 cm²/Vs. The ambipolarity is attributed to a lateral shift between stacked backbones provoked by the bulky C14,10 side chains. This reorganization is supposed to change the transfer integrals between the C16 and C14,10 substituted polymers. This work shows that the electronic behavior in devices of one single conjugated polymer (in this case CDT-BTZ can be controlled by the right choice of the substituents to place the backbones in the desired packing.

  11. The normally expressed kappa immunoglobulin light chain gene repertoire and somatic mutations studied by single-sided specific polymerase chain reaction (PCR); frequent occurrence of features often assigned to autoimmunity

    DEFF Research Database (Denmark)

    Juul, L; Hougs, L; Andersen, V

    1997-01-01

    The expressed human kappa light chain gene repertoire utilized by healthy individuals was studied by two different single-sided specific PCR techniques to avoid bias for certain V genes. A total of 103 rearranged kappa sequences from peripheral blood mononuclear cells from healthy individuals were...

  12. Effects of hydrophobic helix length and side chain chemistry on biomimicry in peptoid analogues of SP-C.

    Science.gov (United States)

    Brown, Nathan J; Wu, Cindy W; Seurynck-Servoss, Shannon L; Barron, Annelise E

    2008-02-12

    The hydrophobic proteins of lung surfactant (LS), SP-B and SP-C, are critical constituents of an effective surfactant replacement therapy for the treatment of respiratory distress syndrome. Because of concerns and difficulties associated with animal-derived surfactants, recent investigations have focused on the creation of synthetic analogues of the LS proteins. However, creating an accurate mimic of SP-C that retains its biophysical surface activity is extraordinarily challenging given the lipopeptide's extreme hydrophobicity and propensity to misfold and aggregate. One successful approach that overcomes these difficulties is the use of poly-N-substituted glycines, or peptoids, to mimic SP-C. To develop a non-natural, bioactive mimic of SP-C and to investigate the effects of side chain chemistry and length of the helical hydrophobic region, we synthesized, purified, and performed in vitro testing of two classes of peptoid SP-C mimics: those having a rigid alpha-chiral aromatic helix and those having a biomimetic alpha-chiral aliphatic helix. The length of the two classes of mimics was also systematically altered. Circular dichroism spectroscopy gave evidence that all of the peptoid-based mimics studied here emulated SP-C's secondary structure, forming stable helical structures in solution. Langmuir-Wilhelmy surface balance, fluorescence microscopy, and pulsating bubble surfactometry experiments provide evidence that the aromatic-based SP-C peptoid mimics, in conjunction with a synthetic lipid mixture, have superior surface activity and biomimetic film morphology in comparison to the aliphatic-based mimics and that there is an increase in surface activity corresponding to increasing helical length.

  13. Autoantibodies against Cytochrome P450 Side-Chain Cleavage Enzyme in Dogs (Canis lupus familiaris) Affected with Hypoadrenocorticism (Addison's Disease).

    Science.gov (United States)

    Boag, Alisdair M; Christie, Michael R; McLaughlin, Kerry A; Syme, Harriet M; Graham, Peter; Catchpole, Brian

    2015-01-01

    Canine hypoadrenocorticism likely arises from immune-mediated destruction of adrenocortical tissue, leading to glucocorticoid and mineralocorticoid deficiency. In humans with autoimmune Addison's disease (AAD) or autoimmune polyendocrine syndrome (APS), circulating autoantibodies have been demonstrated against enzymes associated with adrenal steroid synthesis. The current study investigates autoantibodies against steroid synthesis enzymes in dogs with spontaneous hypoadrenocorticism. Coding regions of canine CYP21A2 (21-hydroxylase; 21-OH), CYP17A1 (17-hydroxylase; 17-OH), CYP11A1 (P450 side-chain cleavage enzyme; P450scc) and HSD3B2 (3β hydroxysteroid dehydrogenase; 3βHSD) were amplified, cloned and expressed as 35S-methionine radiolabelled recombinant protein. In a pilot study, serum samples from 20 dogs with hypoadrenocorticism and four unaffected control dogs were screened by radio-immunoprecipitation assay. There was no evidence of reactivity against 21-OH, 17-OH or 3βHSD, but five dogs with hypoadrenocorticism showed immunoreactivity to P450scc compared with controls. Serum samples were subsequently obtained from 213 dogs diagnosed with hypoadrenocorticism and 110 dogs from a hospital control population. Thirty control dogs were randomly selected to establish a threshold for antibody positivity (mean + 3 × standard deviation). Dogs with hypoadrenocorticism were more likely to be P450scc autoantibody positive than hospital controls (24% vs. 1.2%, respectively; p = 0.0016). Sex was significantly associated with the presence of P450scc autoantibodies in the case population, with 30% of females testing positive compared with 17% of males (p = 0.037). Significant associations with breed (p = 0.015) and DLA-type (DQA1*006:01 allele; p = 0.017) were also found. This cross-sectional study indicates that P450scc autoantibodies are present in a proportion of dogs affected with hypoadrenocorticism.

  14. Autoantibodies against Cytochrome P450 Side-Chain Cleavage Enzyme in Dogs (Canis lupus familiaris Affected with Hypoadrenocorticism (Addison's Disease.

    Directory of Open Access Journals (Sweden)

    Alisdair M Boag

    Full Text Available Canine hypoadrenocorticism likely arises from immune-mediated destruction of adrenocortical tissue, leading to glucocorticoid and mineralocorticoid deficiency. In humans with autoimmune Addison's disease (AAD or autoimmune polyendocrine syndrome (APS, circulating autoantibodies have been demonstrated against enzymes associated with adrenal steroid synthesis. The current study investigates autoantibodies against steroid synthesis enzymes in dogs with spontaneous hypoadrenocorticism. Coding regions of canine CYP21A2 (21-hydroxylase; 21-OH, CYP17A1 (17-hydroxylase; 17-OH, CYP11A1 (P450 side-chain cleavage enzyme; P450scc and HSD3B2 (3β hydroxysteroid dehydrogenase; 3βHSD were amplified, cloned and expressed as 35S-methionine radiolabelled recombinant protein. In a pilot study, serum samples from 20 dogs with hypoadrenocorticism and four unaffected control dogs were screened by radio-immunoprecipitation assay. There was no evidence of reactivity against 21-OH, 17-OH or 3βHSD, but five dogs with hypoadrenocorticism showed immunoreactivity to P450scc compared with controls. Serum samples were subsequently obtained from 213 dogs diagnosed with hypoadrenocorticism and 110 dogs from a hospital control population. Thirty control dogs were randomly selected to establish a threshold for antibody positivity (mean + 3 × standard deviation. Dogs with hypoadrenocorticism were more likely to be P450scc autoantibody positive than hospital controls (24% vs. 1.2%, respectively; p = 0.0016. Sex was significantly associated with the presence of P450scc autoantibodies in the case population, with 30% of females testing positive compared with 17% of males (p = 0.037. Significant associations with breed (p = 0.015 and DLA-type (DQA1*006:01 allele; p = 0.017 were also found. This cross-sectional study indicates that P450scc autoantibodies are present in a proportion of dogs affected with hypoadrenocorticism.

  15. Quasi-elastic neutron scattering study of a re-entrant side-chain liquid-crystal polyacrylate

    Science.gov (United States)

    Benguigui, L.; Noirez, L.; Kahn, R.; Keller, P.; Lambert, M.; Cohen de Lara, E.

    1991-04-01

    We present a first investigation of the dynamics of a side chain liquid crystal polyacrylate in the isotropic (I), nematic (N), smectic A (SA), and re-entrant nematic (NRe) phases by means of quasi-elastic neutron scattering. The motion or/and the mobility of the mesogen protons decreases as soon as the temperature decreases after the isotropic-nematic transition. The I-N and SA-NRe transitions corrspond to a jump in the curve of the Elastic Incoherent Structure Factor (ratio: elastic scattering/ total scattering) versus temperature, on the other hand the transition N-SA occurs without any change of slope. We conclude that the local order is very similar in the nematic and the smectic A phases. Nous présentons une première étude dynamique par diffusion quasi-élastique des neutrons, d'un échantillon de polyacrylate mésomorphe en peigne dans chacune des phases : isotrope, nématique, smectique et nématique rentrante. On montre que le mouvement et/ou la mobilité des protons du mésogène se restreint à mesure que la température diminue après la transition isotrope-nématique. Contrairement à la transition N-SA, les transitions I-N et SA-NRe correspondent à une discontinuité dans la courbe du Facteur de Structure Incohérent Elastique (rapport : intensité élastique/intensité totale) en fonction de la température ; l'ordre local semble donc très proche pour les phases nématique et smectique.

  16. Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification.

    Science.gov (United States)

    Eudes, Aymerick; George, Anthe; Mukerjee, Purba; Kim, Jin S; Pollet, Brigitte; Benke, Peter I; Yang, Fan; Mitra, Prajakta; Sun, Lan; Cetinkol, Ozgül P; Chabout, Salem; Mouille, Grégory; Soubigou-Taconnat, Ludivine; Balzergue, Sandrine; Singh, Seema; Holmes, Bradley M; Mukhopadhyay, Aindrila; Keasling, Jay D; Simmons, Blake A; Lapierre, Catherine; Ralph, John; Loqué, Dominique

    2012-06-01

    Lignocellulosic biomass is utilized as a renewable feedstock in various agro-industrial activities. Lignin is an aromatic, hydrophobic and mildly branched polymer integrally associated with polysaccharides within the biomass, which negatively affects their extraction and hydrolysis during industrial processing. Engineering the monomer composition of lignins offers an attractive option towards new lignins with reduced recalcitrance. The presented work describes a new strategy developed in Arabidopsis for the overproduction of rare lignin monomers to reduce lignin polymerization degree (DP). Biosynthesis of these 'DP reducers' is achieved by expressing a bacterial hydroxycinnamoyl-CoA hydratase-lyase (HCHL) in lignifying tissues of Arabidopsis inflorescence stems. HCHL cleaves the propanoid side-chain of hydroxycinnamoyl-CoA lignin precursors to produce the corresponding hydroxybenzaldehydes so that plant stems expressing HCHL accumulate in their cell wall higher amounts of hydroxybenzaldehyde and hydroxybenzoate derivatives. Engineered plants with intermediate HCHL activity levels show no reduction in total lignin, sugar content or biomass yield compared with wild-type plants. However, cell wall characterization of extract-free stems by thioacidolysis and by 2D-NMR revealed an increased amount of unusual C₆C₁ lignin monomers most likely linked with lignin as end-groups. Moreover the analysis of lignin isolated from these plants using size-exclusion chromatography revealed a reduced molecular weight. Furthermore, these engineered lines show saccharification improvement of pretreated stem cell walls. Therefore, we conclude that enhancing the biosynthesis and incorporation of C₆C₁ monomers ('DP reducers') into lignin polymers represents a promising strategy to reduce lignin DP and to decrease cell wall recalcitrance to enzymatic hydrolysis. © 2012 The Authors. Plant Biotechnology Journal © 2012 Society for Experimental Biology, Association of Applied

  17. SYNTHESIS, CHARACTERIZATION, AND CHEMOSENSING APPLICATION OF POLY(METHYL METHACRYLATE-CO-HYDROXYETHYL METHACRYLATE WITH DANSYL SIDE GROUP

    Directory of Open Access Journals (Sweden)

    Erdinç DOĞANCI

    2016-10-01

    Full Text Available A novel dansyl side-functional polymer (P2 was prepared and employed as the metal cation sensing chemical probe. The synthesis of P2 was performed via free radical polymerization and esterification reactions in a two-step reaction sequence. P2 showed characteristic UV-vis and fluorescence emission bands for the dansyl unit. The fluorescence emission intensity of P2 gradually decreased as the concentrations of the added metal ions were increased. The highest quenching efficiencies (QE were observed for Pb2+ (84.56% and Co2+ (83.69%. Besides, the responses of P2 to the addition of Pb2+ cation were quite linear up to 50 equivalent. The presence of Cd2+, Hg2+, Mn2+, and Zn2+ cations did not pose significant interferences. Thus, P2 is a potential candidate for the fluorescence chemical sensor for Pb2+ cation.

  18. Linear side chains in benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-c] pyrrole-4,6-dione polymers direct self-assembly and solar cell performance

    KAUST Repository

    Cabanetos, Clement; El Labban, Abdulrahman; Bartelt, Jonathan A.; Douglas, Jessica D.; Mateker, William R.; Frechet, Jean; McGehee, Michael D.; Beaujuge, Pierre

    2013-01-01

    role that linear side-chain substituents play in poly(benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers for bulk heterojunction (BHJ) solar cell applications. We show that replacing branched side chains by linear ones

  19. Phenylpropanoid 2,3-dioxygenase involved in the cleavage of the ferulic acid side chain to form vanillin and glyoxylic acid in Vanilla planifolia.

    Science.gov (United States)

    Negishi, Osamu; Negishi, Yukiko

    2017-09-01

    Enzyme catalyzing the cleavage of the phenylpropanoid side chain was partially purified by ion exchange and gel filtration column chromatography after (NH 4 ) 2 SO 4 precipitation. Enzyme activities were dependent on the concentration of dithiothreitol (DTT) or glutathione (GSH) and activated by addition of 0.5 mM Fe 2+ . Enzyme activity for ferulic acid was as high as for 4-coumaric acid in the presence of GSH, suggesting that GSH acts as an endogenous reductant in vanillin biosynthesis. Analyses of the enzymatic reaction products with quantitative NMR (qNMR) indicated that an amount of glyoxylic acid (GA) proportional to vanillin was released from ferulic acid by the enzymatic reaction. These results suggest that phenylpropanoid 2,3-dioxygenase is involved in the cleavage of the ferulic acid side chain to form vanillin and GA in Vanilla planifolia.

  20. The probability distribution of side-chain conformations in [Leu] and [Met]enkephalin determines the potency and selectivity to mu and delta opiate receptors

    DEFF Research Database (Denmark)

    Nielsen, Bjørn Gilbert; Jensen, Morten Østergaard; Bohr, Henrik

    2003-01-01

    The structure of enkephalin, a small neuropeptide with five amino acids, has been simulated on computers using molecular dynamics. Such simulations exhibit a few stable conformations, which also have been identified experimentally. The simulations provide the possibility to perform cluster analysis...... in the space defined by potentially pharmacophoric measures such as dihedral angles, side-chain orientation, etc. By analyzing the statistics of the resulting clusters, the probability distribution of the side-chain conformations may be determined. These probabilities allow us to predict the selectivity...... of [Leu]enkephalin and [Met]enkephalin to the known mu- and delta-type opiate receptors to which they bind as agonists. Other plausible consequences of these probability distributions are discussed in relation to the way in which they may influence the dynamics of the synapse....

  1. Effects of side-chain and electron exchange correlation on the band structure of perylene diimide liquid crystals: a density functional study.

    Science.gov (United States)

    Arantes, J T; Lima, M P; Fazzio, A; Xiang, H; Wei, Su-Huai; Dalpian, G M

    2009-04-23

    The structural and electronic properties of perylene diimide liquid crystal PPEEB are studied using ab initio methods based on the density functional theory (DFT). Using available experimental crystallographic data as a guide, we propose a detailed structural model for the packing of solid PPEEB. We find that due to the localized nature of the band edge wave function, theoretical approaches beyond the standard method, such as hybrid functional (PBE0), are required to correctly characterize the band structure of this material. Moreover, unlike previous assumptions, we observe the formation of hydrogen bonds between the side chains of different molecules, which leads to a dispersion of the energy levels. This result indicates that the side chains of the molecular crystal not only are responsible for its structural conformation but also can be used for tuning the electronic and optical properties of these materials.

  2. Synthesis of novel vitamin K derivatives with alkylated phenyl groups introduced at the ω-terminal side chain and evaluation of their neural differentiation activities.

    Science.gov (United States)

    Sakane, Rie; Kimura, Kimito; Hirota, Yoshihisa; Ishizawa, Michiyasu; Takagi, Yuta; Wada, Akimori; Kuwahara, Shigefumi; Makishima, Makoto; Suhara, Yoshitomo

    2017-11-01

    Vitamin K is an essential cofactor of γ-glutamylcarboxylase as related to blood coagulation and bone formation. Menaquinone-4, one of the vitamin K homologues, is biosynthesized in the body and has various biological activities such as being a ligand for steroid and xenobiotic receptors, protection of neuronal cells from oxidative stress, and so on. From this background, we focused on the role of menaquinone in the differentiation activity of progenitor cells into neuronal cells and we synthesized novel vitamin K derivatives with modification of the ω-terminal side chain. We report here new vitamin K analogues, which introduced an alkylated phenyl group at the ω-terminal side chain. These compounds exhibited potent differentiation activity as compared to control. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  3. Stereospecific assignment of the NH2 resonances from the primary amides of asparagine and glutamine side chains in isotopically labeled proteins

    International Nuclear Information System (INIS)

    McIntosh, Lawrence P.; Brun, Emmanuel; Kay, Lewis E.

    1997-01-01

    An HMQC-based pulse scheme is presented for the stereospecific assignment of asparagine and glutamine side-chain amide protons. The approach makes use of the recently developed quantitative-J correlation spectroscopy [Bax, A. et al. (1994) Methods Enzymol., 239,79-105] to distinguish the E and Z primary amide protons and, as such, eliminates the need for assignments derived from more time-consuming and potentially ambiguous NOE methods. An application of this method to a uniformly 15N,13C-labeled cellulose-binding domain is presented. When used in combination with a NOESY-HSQC experiment, the predominant χ2 dihedral angles of two asparagine side chains in this protein can also be defined

  4. Side-chain amino-acid-based pH-responsive self-assembled block copolymers for drug delivery and gene transfer.

    Science.gov (United States)

    Kumar, Sonu; Acharya, Rituparna; Chatterji, Urmi; De, Priyadarsi

    2013-12-10

    Developing safe and effective nanocarriers for multitype of delivery system is advantageous for several kinds of successful biomedicinal therapy with the same carrier. In the present study, we have designed amino acid biomolecules derived hybrid block copolymers which can act as a promising vehicle for both drug delivery and gene transfer. Two representative natural chiral amino acid-containing (l-phenylalanine and l-alanine) vinyl monomers were polymerized via reversible addition-fragmentation chain transfer (RAFT) process in the presence of monomethoxy poly(ethylene glycol) based macro-chain transfer agents (mPEGn-CTA) for the synthesis of well-defined side-chain amino-acid-based amphiphilic block copolymers, monomethoxy poly(ethylene glycol)-b-poly(Boc-amino acid methacryloyloxyethyl ester) (mPEGn-b-P(Boc-AA-EMA)). The self-assembled micellar aggregation of these amphiphilic block copolymers were studied by fluorescence spectroscopy, atomic force microscopy (AFM) and scanning electron microscopy (SEM). Potential applications of these hybrid polymers as drug carrier have been demonstrated in vitro by encapsulation of nile red dye or doxorubicin drug into the core of the micellar nanoaggregates. Deprotection of side-chain Boc- groups in the amphiphilic block copolymers subsequently transformed them into double hydrophilic pH-responsive cationic block copolymers having primary amino groups in the side-chain terminal. The DNA binding ability of these cationic block copolymers were further investigated by using agarose gel retardation assay and AFM. The in vitro cytotoxicity assay demonstrated their biocompatible nature and these polymers can serve as "smart" materials for promising bioapplications.

  5. Diketopyrrolopyrrole-Based Conjugated Polymer Entailing Triethylene Glycols as Side Chains with High Thin-Film Charge Mobility without Post-Treatments

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Si-Fen [Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 P. R. China; University of Chinese Academy of Sciences, Beijing 100049 P. R. China; Liu, Zi-Tong [Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 P. R. China; Cai, Zheng-Xu [Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 P. R. China; Dyson, Matthew J. [Department of Materials and Centre for Plastic Electronics, Imperial College London, London SW72AZ UK; Stingelin, Natalie [Department of Materials and Centre for Plastic Electronics, Imperial College London, London SW72AZ UK; Chen, Wei [Materials Science Division, Argonne National Laboratory, 9700 Cass Avenue Lemont IL 60439 USA; Institute for Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue Chicago IL 60637 USA; Ju, Hua-Jun [Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 P. R. China; Zhang, Guan-Xin [Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 P. R. China; Zhang, De-Qing [Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 P. R. China; University of Chinese Academy of Sciences, Beijing 100049 P. R. China

    2017-04-18

    Side chain engineering of conjugated donor-acceptor polymers is a new way to manipulate their optoelectronic properties. Two new diketopyrrolopyrrole (DPP)-terthiophene-based conjugated polymers PDPP3T-1 and PDPP3T-2, with both hydrophilic triethylene glycol (TEG) and hydrophobic alkyl chains, are reported. It is demonstrated that the incorporation of TEG chains has a significant effect on the interchain packing and thin-film morphology with noticeable effect on charge transport. Polymer chains of PDPP3T-1 in which TEG chains are uniformly distributed can self-assemble spontaneously into a more ordered thin film. As a result, the thin film of PDPP3T-1 exhibits high saturated hole mobility up to 2.6 cm(2) V-1 s(-1) without any post-treatment. This is superior to those of PDPP3T with just alkyl chains and PDPP3T-2. Moreover, the respective field effect transistors made of PDPP3T-1 can be utilized for sensing ethanol vapor with high sensitivity (down to 100 ppb) and good selectivity.

  6. Side-chain tunability of furan-containing low-band-gap polymers provides control of structural order in efficient solar cells

    KAUST Repository

    Yiu, Alan T.; Beaujuge, Pierre; Lee, Olivia P.; Woo, Claire; Toney, Michael F.; Frechet, Jean

    2012-01-01

    The solution-processability of conjugated polymers in organic solvents has classically been achieved by modulating the size and branching of alkyl substituents appended to the backbone. However, these substituents impact structural order and charge transport properties in thin-film devices. As a result, a trade-off must be found between material solubility and insulating alkyl content. It was recently shown that the substitution of furan for thiophene in the backbone of the polymer PDPP2FT significantly improves polymer solubility, allowing for the use of shorter branched side chains while maintaining high device efficiency. In this report, we use PDPP2FT to demonstrate that linear alkyl side chains can be used to promote thin-film nanostructural order. In particular, linear side chains are shown to shorten π-π stacking distances between backbones and increase the correlation lengths of both π-π stacking and lamellar spacing, leading to a substantial increase in the efficiency of bulk heterojunction solar cells. © 2011 American Chemical Society.

  7. Side-chain tunability of furan-containing low-band-gap polymers provides control of structural order in efficient solar cells

    KAUST Repository

    Yiu, Alan T.

    2012-02-01

    The solution-processability of conjugated polymers in organic solvents has classically been achieved by modulating the size and branching of alkyl substituents appended to the backbone. However, these substituents impact structural order and charge transport properties in thin-film devices. As a result, a trade-off must be found between material solubility and insulating alkyl content. It was recently shown that the substitution of furan for thiophene in the backbone of the polymer PDPP2FT significantly improves polymer solubility, allowing for the use of shorter branched side chains while maintaining high device efficiency. In this report, we use PDPP2FT to demonstrate that linear alkyl side chains can be used to promote thin-film nanostructural order. In particular, linear side chains are shown to shorten π-π stacking distances between backbones and increase the correlation lengths of both π-π stacking and lamellar spacing, leading to a substantial increase in the efficiency of bulk heterojunction solar cells. © 2011 American Chemical Society.

  8. Effect of the Side Chains and Anode Material on Thermal Stability and Performance of Bulk-Heterojunction Solar Cells Using DPP(TBFu2 Derivatives as Donor Materials

    Directory of Open Access Journals (Sweden)

    Alexander Kovalenko

    2015-01-01

    Full Text Available An optimized fabrication of bulk-heterojunction solar cells (BHJ SCs based on previously reported diketopyrrolopyrrole donor, ethyl-hexylated DPP(TBFu2, as well as two new DPP(TBFu2 derivatives with ethyl-hexyl acetate and diethyl acetal solubilizing side-chains and PC60BM as an acceptor is demonstrated. Slow gradual annealing of the solar cell causing the effective donor-acceptor reorganization, and as a result higher power conversion efficiency (PCE, is described. By replacing a hole transporting layer PEDOT:PSS with MoO3 we obtained higher PCE values as well as higher thermal stability of the anode contact interface. DPP(TBFu2 derivative containing ethyl-hexyl acetate solubilizing side-chains possessed the best as-cast self-assembly and high crystallinity. However, the presence of ethyl-hexyl acetate and diethyl acetal electrophilic side-chains stabilizes HOMO energy of isolated DPP(TBFu2 donors with respect to the ethyl-hexylated one, according to cyclic voltammetry.

  9. Enhanced performance and durability of low catalyst loading PEM water electrolyser based on a short-side chain perfluorosulfonic ionomer

    International Nuclear Information System (INIS)

    Siracusano, Stefania; Baglio, Vincenzo; Van Dijk, Nicholas; Merlo, Luca; Aricò, Antonino Salvatore

    2017-01-01

    Graphical abstract: Tripling current density (>3 A·cm"−"2) with respect to the state of the art of commercial PEM electrolyser can be achieved also in the presence of a significant reduction, about 4-fold, of the total noble metal loading (0.5 mg·cm"−"2) while achieving high efficiency (>80%) and proper durability. - Highlights: • Current density >3 A·cm"−"2 is achieved in electrolysis cells with efficiency >80%. • A 4-fold reduction of noble metal loading is demonstrated in electrolysis cells. • Degradation rate <5 μV/h is achieved in a 1000 h durability test at 1 A·cm"−"2. • Degradation associated to a change in Lewis acidity characteristics is observed. - Abstract: Water electrolysis supplied by renewable energy is the foremost technology for producing “green” hydrogen for fuel cell vehicles. In addition, the ability to rapidly follow an intermittent load makes electrolysis an ideal solution for grid-balancing caused by differences in supply and demand for energy generation and consumption. Membrane-electrode assemblies (MEAs) designed for polymer electrolyte membrane (PEM) water electrolysis, based on a novel short-side chain (SSC) perfluorosulfonic acid (PFSA) membrane, Aquivion®, with various cathode and anode noble metal loadings, were investigated in terms of both performance and durability. Utilizing a nanosized Ir_0_._7Ru_0_._3O_x solid solution anode catalyst and a supported Pt/C cathode catalyst, in combination with the Aquivion® membrane, gave excellent electrolysis performances exceeding 3.2 A·cm"−"2 at 1.8 V terminal cell voltage (∼80% efficiency) at 90 °C in the presence of a total catalyst loading of 1.6 mg⋅cm"−"2. A very small loss of efficiency, corresponding to 30 mV voltage increase, was recorded at 3 A⋅cm"−"2 using a total noble metal catalyst loading of less than 0.5 mg·cm"−"2 (compared to the industry standard of 2 mg·cm"−"2). Steady-state durability tests, carried out for 1000 h at 1 A

  10. Pronounced Side Chain Effects in Triple Bond-Conjugated Polymers Containing Naphthalene Diimides for n-Channel Organic Field-Effect Transistors

    KAUST Repository

    Nam, Sungho

    2018-03-23

    Three triple bond-conjugated naphthalene diimide (NDI) copolymers, poly{[N,N′-bis(2-R1)-naphthalene-1,4,5,8-bis(dicarboximide)-2,6-diyl]-alt-[(2,5-bis(2-R2)-1,4-phenylene)bis(ethyn-2,1-diyl)]} (PNDIR1-R2), were synthesized via Sonogashira coupling polymerization with varying alkyl side chains at the nitrogen atoms of the imide ring and 2,5-positions of the 1,4-diethynylbenzene moiety. Considering their identical polymer backbone structures, the side chains were found to have a strong influence on the surface morphology/nanostructure, thus playing a critical role in charge-transporting properties of the three NDI-based copolymers. Among the polymers, the one with an octyldodecyl (OD) chain at the nitrogen atoms of imide ring and a hexadecyloxy (HO) chain at the 2,5-positions of 1,4-diethynylbenzene, P(NDIOD-HO), exhibited the highest electron mobility of 0.016 cm2 V–1 s–1, as compared to NDI-based copolymers with an ethylhexyl chain at the 2,5-positions of 1,4-diethynylbenzene. The enhanced charge mobility in the P(NDIOD-HO) layers is attributed to the well-aligned nano-fiber-like surface morphology and highly ordered packing structure with a dominant edge-on orientation, thus enabling efficient in-plane charge transport. Our results on the molecular structure–charge transport property relationship in these materials may provide an insight into novel design of n-type conjugated polymers for applications in the organic electronics of the future.

  11. On the turn-inducing properties of asparagine: the structuring role of the amide side chain, from isolated model peptides to crystallized proteins.

    Science.gov (United States)

    Habka, S; Sohn, W Y; Vaquero-Vara, V; Géléoc, M; Tardivel, B; Brenner, V; Gloaguen, E; Mons, M

    2018-01-31

    Asparagine (Asn) is a powerful turn-inducer residue, with a large propensity to occupy the second position in the central region of β-turns of proteins. The present work aims at investigating the role of a local anchoring between the Asn side chain and the main chain in this remarkable property. For this purpose, the H-bonding patterns of an asparagine residue in an isolated protein chain fragment forming a γ- or a β-turn have been determined using IR/UV double resonance gas phase spectroscopy on laser-desorbed, jet-cooled short models in conjunction with relevant quantum chemistry calculations. These gas phase data provide evidence for an original double anchoring linking the Asn primary amide side chain (SC), which adopts a gauche+ rotameric form, to its main chain (MC) local environment. From both IR spectroscopic evidence (H-bond induced red shifts) and quantum chemistry, Asn SC is found to behave as a stronger H-bond acceptor than donor, resulting in stronger MC→SC H-bonds than SC→MC ones. These gas phase structural data, relevant to a hydrophobic environment, have been used as a reference to assess the anchoring taking place in high resolution crystallized proteins of the Protein Data Bank. This approach reveals that, when the SC adopts a gauche+ orientation, the stronger MC→SC bonds are preserved in many cases whereas the SC→MC bonds are always disrupted, in qualitative agreement with the gas phase ranking of these interactions. Most interestingly, when Asn occupies the second position of central part of a β-turn (i.e., the very turn-inducer position), the MC→SC H-bonds are also disrupted and replaced by a water-mediated SC to MC anchoring. Owing to the specific features of the hydrated Asn side chain, we propose that it could be a turn precursor structure, able to facilitate turn formation in the early events of the folding process.

  12. On the interaction of the morphological structure and the LC behaviour of LC side chain block copolymers

    NARCIS (Netherlands)

    Fischer, H.R.; Poser, S.; Arnold, M.

    1995-01-01

    The interaction between morphological structure and phase behaviour of a LC side group block copolymer has been investigated using DSC, TEM and small angle X-ray diffraction. All samples of Polystyrene-block-2-(3-cholesteryloxycarbonyloxy)ethyl methacrylate (PS-b-PChEMA) show a phase separation

  13. On the interaction of the morphological structure and the LC behaviour of LC side chain block copolymers

    NARCIS (Netherlands)

    Fischer, H.R.; Arnold, M.

    1995-01-01

    The interaction between morphological structure and phase behaviour of a group of LC side group block copolymers have been investigated using DSC, TEM and small angle X-ray diffraction. Generally, phase separation between the two blocks was observed. It was found that in the case of those samples,

  14. [Variation of long-chain 3-hydroxyacyl-CoA dehydrogenase DNA methylation in placenta of different preeclampsia-like mouse models].

    Science.gov (United States)

    Han, Yiwei; Yang, Zi; Ding, Xiaoyan; Yu, Huan; Yi, Yanhong

    2015-10-01

    By detecting the variation of long-chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD) DNA methylation in preeclampsia-like mouse models generated by different ways, to explore the roles of multifactor and multiple pathways in preeclampsia pathogenesis on molecular basis. Established preeclampsia-like mouse models in different ways and divided into groups as follows: (1) Nw-nitro-L-arginine-methyl ester (L-NAME) group: wild-type pregnant mouse received subcutaneous injection of L-NAME; (2) lipopolysaccharide (LPS) group: wild-type pregnant mouse received intraperitoneal injection of LPS; (3) apolipoprotein C-III (ApoC3) group: ApoC3 transgenic pregnant mouse with dysregulated lipid metabolism received subcutaneous injection of L-NAME; (4) β2 glycoprotein I (β-2GPI) group: wild-type pregnant mouse received subcutaneous injection of β-2GPI. According to the first injection time (on day 3, 11, 16 respectively), the L-NAME, LPS and ApoC3 groups were further subdivided into: pre-implantation (PI) experimental stage, early gestation (EG) experimental stage, and late gestation (LG) experimental stage. β-2GPI group was only injected before implantation. LCHAD gene methylation levels in placental were detected in different experimental stage. Normal saline control groups were set within wild-type and ApoC3 transgenic pregnant mice simultaneously. (1) CG sites in LCHAD DNA: 45 CG sites were detected in the range of 728 bp before LCHAD gene transcription start site, the 5, 12, 13, 14, 15, 16, 19, 24, 25, 27, 28, 29, 30, 31, 32, 34, 35, 43 CG sites were complex sites which contained two or more CG sequences, others were single site which contained one CG sequence. The 3, 5, 6, 11, 13, 14, 18, 28 sites in L-NAME, LPS, ApoC3 and β-2GPI groups showed different high levels of methylation; the 16, 25, 31, 42, 44 sites showed different low levels of methylation; other 32 sites were unmethylated. (2) Comparison of LCHAD gene methylation between different groups: the methylation levels

  15. Acidic-basic properties of three alanine-based peptides containing acidic and basic side chains: comparison between theory and experiment.

    Science.gov (United States)

    Makowska, Joanna; Bagińska, Katarzyna; Liwo, Adam; Chmurzyński, Lech; Scheraga, Harold A

    2008-01-01

    The purpose of this work was to evaluate the effect of the nature of the ionizable end groups, and the solvent, on their acid-base properties in alanine-based peptides. Hence, the acid-base properties of three alanine-based peptides: Ac-KK-(A)(7)-KK-NH(2) (KAK), Ac-OO-(A)(7)-DD-NH(2) (OAD), Ac-KK-(A)(7)-EE-NH(2) (KAE), where A, D, E, K, and O denote alanine, aspartic acid, glutamic acid, lysine, and ornithine, respectively, were determined in water and in methanol by potentiometry. With the availability of these data, the ability of two theoretical methods to simulate pH-metric titration of those peptides was assessed: (i) the electrostatically driven Monte Carlo method with the ECEPP/3 force field and the Poisson-Boltzmann approach to compute solvation energy (EDMC/PB/pH), and (ii) the molecular dynamics method with the AMBER force field and the Generalized Born model (MD/GB/pH). For OAD and KAE, pK(a1) and pK(a2) correspond to the acidic side chains. For all three compounds in both solvents, the pK(a1) value is remarkably lower than the pK(a) of a compound modeling the respective isolated side chain, which can be explained by the influence of the electrostatic field from positively charged ornithine or lysine side chains. The experimental titration curves are reproduced well by the MD/GB/pH approach, the agreement being better if restraints derived from NMR measurements are incorporated in the conformational search. Poorer agreement is achieved by the EDMC/PB/pH method.

  16. Solvent dielectric effect and side chain mutation on the structural stability of Burkholderia cepacia lipase active site: a quantum mechanical/molecular mechanics study.

    Science.gov (United States)

    Tahan, A; Monajjemi, M

    2011-12-01

    Quantum mechanical and molecular dynamics methods were used to analyze the structure and stability of neutral and zwitterionic configurations of the extracted active site sequence from a Burkholderia cepacia lipase, histidyl-seryl-glutamin (His86-Ser87-Gln88) and its mutated form, histidyl-cysteyl-glutamin (His86-Cys87-Gln88) in vacuum and different solvents. The effects of solvent dielectric constant, explicit and implicit water molecules and side chain mutation on the structure and stability of this sequence in both neutral and zwitterionic forms are represented. The quantum mechanics computations represent that the relative stability of zwitterionic and neutral configurations depends on the solvent structure and its dielectric constant. Therefore, in vacuum and the considered non-polar solvents, the neutral form of the interested sequences is more stable than the zwitterionic form, while their zwitterionic form is more stable than the neutral form in the aqueous solution and the investigated polar solvents in most cases. However, on the potential energy surfaces calculated, there is a barrier to proton transfer from the positively charged ammonium group to the negatively charged carboxylat group or from the ammonium group to the adjacent carbonyl oxygen and or from side chain oxygen and sulfur to negatively charged carboxylat group. Molecular dynamics simulations (MD) were also performed by using periodic boundary conditions for the zwitterionic configuration of the hydrated molecules in a box of water molecules. The obtained results demonstrated that the presence of explicit water molecules provides the more compact structures of the studied molecules. These simulations also indicated that side chain mutation and replacement of sulfur with oxygen leads to reduction of molecular flexibility and packing.

  17. Chemoenzymatic synthesis of statine side chain building blocks and application in the total synthesis of the cholesterol-lowering compound solistatin.

    Science.gov (United States)

    Rieder, Oliver; Wolberg, Michael; Foegen, Silke E; Müller, Michael

    2017-09-20

    The synthesis and enzymatic reduction of several 6-substituted dioxohexanoates are presented. Two-step syntheses of tert-butyl 6-bromo-3,5-dioxohexanoate and the corresponding 6-hydroxy compound have been achieved in 89% and 59% yield, respectively. Regio- and enantioselective reduction of these diketones and of the 6-chloro derivative with alcohol dehydrogenase from Lactobacillus brevis (LBADH) gave the (5S)-5-hydroxy-3-oxo products with enantiomeric excesses of 91%, 98.4%, and >99.5%, respectively. Chain elongation of the reduction products by one carbon via cyanide addition, and by more than one carbon by Julia-Kocienski olefination, gave access to well-established statine side-chain building blocks. Application in the synthesis of the cholesterol-lowering natural compound solistatin is given. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. New theories for smectic and nematic liquid-crystal polymers: Backbone LCPs [liquid crystalline polymers] and their mixtures and side-chain LCPs

    International Nuclear Information System (INIS)

    Dowell, F.

    1987-01-01

    A summary of predictions and explanations from statistical-physics theories for both backbone and side-chain liquid crystalline polymers (LCPs) and for mixtures with backbone LCPs are presented. Trends in the thermodynamic and molecular ordering properties have been calculated as a function of pressure, density, temperature, and molecule chemical structures (including degree of polymerization and the following properties of the chemical structures of the repeat units: lengths and shapes, intra-chain rotation energies, dipole moments, site-site polarizabilities and Lennard-Jones potentials, etc.) in nematic and multiple smectic-A LC phases and in the isotropic liquid phase. The theoretical results are found to be in good agreement with existing experimental data. These theories can also be applied to combined LCPs. Since these theories have no ad hoc or arbitrarily adjustable parameters, these theories can be used to design new LCPs and new solvents as well as to predict and explain properties. 27 refs., 4 tabs

  19. Study of methyl bromide reactivity with human and mouse hemoglobin

    African Journals Online (AJOL)

    A study has been carried out on in-vitro reactivity of human and mouse hemoglobin spectrophotometrically at physiological pH, using different protein to reagent ratios. Hemoglobin side chains were modified with different concentrations of methyl bromide on agro-soil fumigant. To ascertain if the site of alkylation was the ...

  20. Influence of Side Chain Position on the Electrical Properties of Organic Solar Cells Based on Dithienylbenzothiadiazole-alt-phenylene Conjugated Polymers

    DEFF Research Database (Denmark)

    Livi, Francesco; Zawacka, Natalia Klaudia; Angmo, Dechan

    2015-01-01

    backbone for polymer solar cells. All the polymers were roll slot die coated under ambient conditions on flexible ITO-free plastic substrates to give inverted polymer solar cell devices with an upscaled active area of 1 cm2. The best characteristics were found for the polymer carrying alkoxy side chains...... showed excellent performance under constant illumination and high temperature (exhibiting stable photovoltaic properties even after 670 h under conditions similar to ISOS-L-2 lifetime protocol). This makes P7 a good candidate for further upscaling and device optimization. The photovoltaic performance...

  1. Side chain requirements for affinity and specificity in D5, an HIV-1 antibody derived from the VH1-69 germline segment.

    Science.gov (United States)

    Stewart, Alex; Harrison, Joseph S; Regula, Lauren K; Lai, Jonathan R

    2013-04-08

    Analysis of factors contributing to high affinity antibody-protein interactions provides insight into natural antibody evolution, and guides the design of antibodies with new or enhanced function. We previously studied the interaction between antibody D5 and its target, a designed protein based on HIV-1 gp41 known as 5-Helix, as a model system [Da Silva, G. F.; Harrison, J. S.; Lai, J. R., Biochemistry, 2010, 49, 5464-5472]. Antibody D5 represents an interesting case study because it is derived from the VH1-69 germline segment; this germline segment is characterized by a hydrophobic second heavy chain complementarity determining region (HCDR2) that constitutes the major functional paratope in D5 and several antibodies derived from the same progenitor. Here we explore side chain requirements for affinity and specificity in D5 using phage display. Two D5-based libraries were prepared that contained diversity in all three light chain complementarity determining regions (LCDRs 1-3), and in the third HCDR (HCDR3). The first library allowed residues to vary among a restricted set of six amino acids (Tyr/Ala/Asp/Ser/His/Pro; D5-Lib-I). The second library was designed based on a survey of existing VH1-69 antibody structures (D5-Lib-II). Both libraries were subjected to multiple rounds of selection against 5-Helix, and individual clones characterized. We found that selectants from D5-Lib-I generally had moderate affinity and specificity, while many clones from D5-Lib-II exhibited D5-like properties. Additional analysis of the D5-Lib-II functional population revealed position-specific biases for particular amino acids, many that differed from the identity of those side chains in D5. Together these results suggest that there is some permissiveness for alternative side chains in the LCDRs and HCDR3 of D5, but that replacement with a minimal set of residues is not tolerated in this scaffold for 5-Helix recognition. This work provides novel information about this high

  2. Blocking of proteolytic processing and deletion of glycosaminoglycan side chain of mouse DMP1 by substituting critical amino acid residues.

    Science.gov (United States)

    Peng, Tao; Huang, Bingzhen; Sun, Yao; Lu, Yongbo; Bonewald, Lynda; Chen, Shuo; Butler, William T; Feng, Jerry Q; D'Souza, Rena N; Qin, Chunlin

    2009-01-01

    Dentin matrix protein 1 (DMP1) is present in the extracellular matrix (ECM) of dentin and bone as processed NH(2)- and COOH-terminal fragments, resulting from proteolytic cleavage at the NH(2) termini of 4 aspartic acid residues during rat DMP1 processing. One cleavage site residue, Asp(181) (corresponding to Asp(197) of mouse DMP1), and its flanking region are highly conserved across species. We speculate that cleavage at the NH(2) terminus of Asp(197) of mouse DMP1 represents an initial, first-step scission in the whole cascade of proteolytic processing. To test if Asp(197) is critical for initiating the proteolytic processing of mouse DMP1, we substituted Asp(197) with Ala(197) by mutating the corresponding nucleotides of mouse cDNA that encode this amino acid residue. This mutant DMP1 cDNA was cloned into a pcDNA3.1 vector. Data from transfection experiments indicated that this single substitution blocked the proteolytic processing of mouse DMP1 in HEK-293 cells, indicating that cleavage at the NH(2) terminus of Asp(197) is essential for exposing other cleavage sites for the conversion of DMP1 to its fragments. The NH(2)-terminal fragment of DMP1 occurs as a proteoglycan form (DMP1-PG) that contains a glycosaminoglycan (GAG) chain. Previously, we showed that a GAG chain is linked to Ser(74) in rat DMP1 (Ser(89) in mouse DMP1). To confirm that mouse DMP1-PG possesses a single GAG chain attached to Ser(89), we substituted Ser(89) by Gly(89). Data from transfection analysis indicated that this substitution completely prevented formation of the GAG-containing form, confirming that DMP1-PG contains a single GAG chain attached to Ser(89) in mouse DMP1. Copyright 2008 S. Karger AG, Basel.

  3. Highly crystalline films of PCPDTBT with branched side chains by solvent vapor crystallization: influence on opto-electronic properties.

    Science.gov (United States)

    Fischer, Florian S U; Trefz, Daniel; Back, Justus; Kayunkid, Navaphun; Tornow, Benjamin; Albrecht, Steve; Yager, Kevin G; Singh, Gurpreet; Karim, Alamgir; Neher, Dieter; Brinkmann, Martin; Ludwigs, Sabine

    2015-02-18

    PCPDTBT, a marginally crystallizable polymer, is crystallized into a new crystal structure using solvent-vapor annealing. Highly ordered areas with three different polymer-chain orientations are identified using TEM/ED, GIWAXS, and polarized Raman spectroscopy. The optical and structural properties differ significantly from films prepared by standard device preparation protocols. Bilayer solar cells, however, show similar performance. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Allelic Dropout During Polymerase Chain Reaction due to G-Quadruplex Structures and DNA Methylation Is Widespread at Imprinted Human Loci

    Directory of Open Access Journals (Sweden)

    Aaron J. Stevens

    2017-03-01

    Full Text Available Loss of one allele during polymerase chain reaction (PCR amplification of DNA, known as allelic dropout, can be caused by a variety of mechanisms. Allelic dropout during PCR may have profound implications for molecular diagnostic and research procedures that depend on PCR and assume biallelic amplification has occurred. Complete allelic dropout due to the combined effects of cytosine methylation and G-quadruplex formation was previously described for a differentially methylated region of the human imprinted gene, MEST. We now demonstrate that this parent-of-origin specific allelic dropout can potentially occur at several other genomic regions that display genomic imprinting and have propensity for G-quadruplex formation, including AIM1, BLCAP, DNMT1, PLAGL1, KCNQ1, and GRB10. These findings demonstrate that systematic allelic dropout during PCR is a general phenomenon for regions of the genome where differential allelic methylation and G-quadruplex motifs coincide, and suggest that great care must be taken to ensure biallelic amplification is occurring in such situations.

  5. Allelic Dropout During Polymerase Chain Reaction due to G-Quadruplex Structures and DNA Methylation Is Widespread at Imprinted Human Loci.

    Science.gov (United States)

    Stevens, Aaron J; Taylor, Millie G; Pearce, Frederick Grant; Kennedy, Martin A

    2017-03-10

    Loss of one allele during polymerase chain reaction (PCR) amplification of DNA, known as allelic dropout, can be caused by a variety of mechanisms. Allelic dropout during PCR may have profound implications for molecular diagnostic and research procedures that depend on PCR and assume biallelic amplification has occurred. Complete allelic dropout due to the combined effects of cytosine methylation and G-quadruplex formation was previously described for a differentially methylated region of the human imprinted gene, MEST We now demonstrate that this parent-of-origin specific allelic dropout can potentially occur at several other genomic regions that display genomic imprinting and have propensity for G-quadruplex formation, including AIM1 , BLCAP , DNMT1 , PLAGL1 , KCNQ1 , and GRB10 These findings demonstrate that systematic allelic dropout during PCR is a general phenomenon for regions of the genome where differential allelic methylation and G-quadruplex motifs coincide, and suggest that great care must be taken to ensure biallelic amplification is occurring in such situations. Copyright © 2017 Stevens et al.

  6. Beta-scission of alkoxyl radicals on peptides and proteins can give rise to backbone cleavage and loss of side-chains

    International Nuclear Information System (INIS)

    Headlam, H.A.; Davies, M.J.; Mortimer, A.; Easton, C.J.

    2000-01-01

    Full text: Exposure of proteins to radicals in the presence of O 2 brings about multiple changes including side-chain oxidation, backbone fragmentation, cross-linking, unfolding, changes in hydrophobicity and conformation, altered susceptibility to proteolytic enzymes and formation of new reactive groups (e.g. hydroperoxides and 3,4-dihydroxyphenylalanine). All of these processes can result in loss of structural or enzymatic activity. The mechanisms that give rise to backbone cleavage are only partly understood. Whilst it is known that direct hydrogen atom abstraction at a-carbon sites gives backbone cleavages it has also been proposed that initial attack at side-chain sites might also give rise to backbone cleavage. In this study we have examined whether initial attack at the β- (C-3) position can give rise to α-carbon radicals (and hence backbone cleavage) via the formation, and subsequent β- scission, of C-3 alkoxyl radicals. This process has been observed previously with protected amino acids in organic solvents (J. Chem. Soc. Perkin Trans. 2, 1997, 503-507) but the occurrence of such reactions with proteins in aqueous solution has not been explored. Alkoxyl radicals were generated at the C-3 position of a variety of protected amino acids and small peptides by two methods: metal-ion catalysed decomposition of hydroperoxides formed as a result of γ-radiolysis in the presence of O 2 , and UV photolysis of nitrate esters. In most cases radicals have been detected by EPR spectroscopy using nitroso and nitrone spin traps, which can be assigned by comparison with literature data to α-carbon radicals; in some case assignments were confirmed by the generation of the putative species by other routes. With Ala peptide hydroperoxides and nitrate esters, and MNP as the spin trap, the major radical detected in each case has been assigned to the adduct of an α-carbon radical with partial structure - NH- . CH-C(O) - consistent with the rapid occurrence of the above

  7. Partial molar volumes of proteins: amino acid side-chain contributions derived from the partial molar volumes of some tripeptides over the temperature range 10-90 degrees C.

    Science.gov (United States)

    Häckel, M; Hinz, H J; Hedwig, G R

    1999-11-15

    The partial molar volumes of tripeptides of sequence glycyl-X-glycine, where X is one of the amino acids alanine, leucine, threonine, glutamine, phenylalanine, histidine, cysteine, proline, glutamic acid, and arginine, have been determined in aqueous solution over the temperature range 10-90 degrees C using differential scanning densitometry . These data, together with those reported previously, have been used to derive the partial molar volumes of the side-chains of all 20 amino acids. The side-chain volumes are critically compared with literature values derived using partial molar volumes for alternative model compounds. The new amino acid side-chain volumes, along with that for the backbone glycyl group, were used to calculate the partial specific volumes of several proteins in aqueous solution. The results obtained are compared with those observed experimentally. The new side-chain volumes have also been used to re-determine residue volume changes upon protein folding.

  8. Introduction of a tryptophan side chain into subsite +1 enhances transglycosylation activity of a GH-18 chitinase from Arabidopsis thaliana, AtChiC

    DEFF Research Database (Denmark)

    Umemoto, Naoyuki; Ohnuma, Takayuki; Mizuhara, Mamiko

    2013-01-01

    A tryptophan side chain was introduced into subsite +1 of family GH-18 (class V) chitinases from Nicotiana tabacum and Arabidopsis thaliana (NtChiV and AtChiC, respectively) by the mutation of a glycine residue to tryptophan (G74W-NtChiV and G75W-AtChiC). The specific activity toward glycol chitin...... of the two mutant enzymes was 70-71% of that of the wild type. Using chitin oligosaccharides, (GlcNAc)(n) (n = 4, 5 and 6), as the substrates, we found the transglycosylation reaction to be significantly enhanced in G74W-NtChiV and G75W-AtChiC when compared with the corresponding wild-type enzymes....... The introduced tryptophan side chain might protect the oxazolinium ion intermediate from attack by a nucleophilic water molecule. The enhancement of transglycosylation activity was much more distinct in G75W-AtChiC than in G74W-NtChiV. Nuclear magnetic resonance titration experiments using the inactive double...

  9. Succinimide Formation from an NGR-Containing Cyclic Peptide: Computational Evidence for Catalytic Roles of Phosphate Buffer and the Arginine Side Chain

    Directory of Open Access Journals (Sweden)

    Ryota Kirikoshi

    2017-02-01

    Full Text Available The Asn-Gly-Arg (NGR motif and its deamidation product isoAsp-Gly-Arg (isoDGR have recently attracted considerable attention as tumor-targeting ligands. Because an NGR-containing peptide and the corresponding isoDGR-containing peptide target different receptors, the spontaneous NGR deamidation can be used in dual targeting strategies. It is well known that the Asn deamidation proceeds via a succinimide derivative. In the present study, we computationally investigated the mechanism of succinimide formation from a cyclic peptide, c[CH2CO-NGRC]-NH2, which has recently been shown to undergo rapid deamidation in a phosphate buffer. An H2PO4− ion was explicitly included in the calculations. We employed the density functional theory using the B3LYP functional. While geometry optimizations were performed in the gas phase, hydration Gibbs energies were calculated by the SM8 (solvation model 8 continuum model. We have found a pathway leading to the five-membered ring tetrahedral intermediate in which both the H2PO4− ion and the Arg side chain act as catalyst. This intermediate, once protonated at the NH2 group on the five-membered ring, was shown to easily undergo NH3 elimination leading to the succinimide formation. This study is the first to propose a possible catalytic role for the Arg side chain in the NGR deamidation.

  10. Evidence for side-chain π-delocalization in a planar substituted benzene: an experimental and theoretical charge density study on 2,5-dimethoxybenzaldehyde thiosemicarbazone.

    Science.gov (United States)

    Farrugia, Louis J; Khalaji, Aliakbar Dehno

    2011-11-17

    The charge density in 2,5-dimethoxybenzaldehyde thiosemicarbazone (1) has been studied experimentally using Mo-K(α) X-ray diffraction at 100 K, and by theory using DFT calculations at the B3LYP/6-311++G(2d,2p) level. The quantum theory of atoms in molecules (QTAIM) was used to investigate the extent of π-delocalization in the thioamide side-chain, which is virtually coplanar with the benzene ring. The experimental and theoretical ellipticity profiles along the bond paths were in excellent agreement, and showed that some of the formal single bonds in the side-chain have significant π-bond character. This view was supported by the magnitudes of the topological bond orders and by the delocalization indices δ(Ω(A), Ω(B)). An orbital decomposition of δ(Ω(A), Ω(B)) demonstrated that there was significant π-character in all the interchain non-H chemical bonds. On the other hand, the source function referenced at the interchain bond critical points could not provide any evidence for π-delocalization, showing instead only limited σ-delocalization between nearest neighbors. Overall, the topological evidence and the atomic graphs of the oxygen atoms did not provide convincing evidence for π-delocalization involving the methoxy substituents.

  11. Synthesis and evaluation of new long alkyl side chain acetamide, isoxazolidine and isoxazoline derivatives as corrosion inhibitors

    International Nuclear Information System (INIS)

    Yildirim, A.; Cetin, M.

    2008-01-01

    2-(Alkylsulfanyl)-N-(pyridin-2-yl) acetamide derivatives were synthesized via amidation reaction of acyl chlorides bearing S atom in the long chain with 2-aminopyridine. Derivatives of isoxazolidine and isoxazoline were synthesized through 1,3-dipolar cycloaddition reactions with three different long chain alkenes containing O or S as hetero atoms and C,N-diphenyl nitrone or benzonitrile-N-oxide, respectively. Synthesized compounds were characterized with their FT-IR, 1 H NMR spectra and then their physical properties and corrosion prevention efficiencies were investigated. All compounds were tested with steel coupons in acidic medium by gravimetric method, and also some of them were tested with steel stripe in paraffin based mineral oil medium via standard method. Acidic test was done with a medium concentration of 2 M HCl for 20 h at room temperature. Mineral oil was used and the test in this medium was done at 60 deg. C constant temperature but varying time from 42 to 63 h. The best inhibition was generally obtained at 50 ppm inhibitor concentration in the acidic medium. All tested inhibitors except two of them in oil medium also showed promising inhibition efficiencies

  12. Thioether-Bearing Hyperbranched Polyether Polyols with Methionine-Like Side-Chains: A Versatile Platform for Orthogonal Functionalization.

    Science.gov (United States)

    Seiwert, Jan; Herzberger, Jana; Leibig, Daniel; Frey, Holger

    2017-01-01

    The synthesis of thioether-bearing hyperbranched polyether polyols based on an AB/AB 2 type copolymerization (cyclic latent monomers) is introduced. The polymers are prepared by anionic ring-opening multibranching copolymerization of glycidol and 2-(methylthio)ethyl glycidyl ether (MTEGE), which is conveniently accessible in a single etherification step. Slow monomer addition provides control over molecular weights. Moderate dispersities (Đ = 1.48-1.85) are obtained, given the hyperbranched structure. In situ 1 H NMR copolymerization kinetics reveal reactivity ratios of r G = 3.7 and r MTEGE = 0.27. Using slow monomer addition, copolymer composition can be systematically varied, allowing for the adjustment of the hydroxyl/thioether ratio, the degree of branching (DB = 0.36-0.48), thermal properties, and cloud point temperatures in aqueous solution in the range of 29-75 °C. Thioether oxidation to sulfoxides enables to tailor the copolymers' solubility profile. Use of these copolymers as a versatile, multifunctional platform for orthogonal modification is highlighted. The methyl sulfide groups can be selectively alkoxylated, using propylene oxide, allyl glycidyl ether, or furfuryl glycidyl ether, resulting in functional hyperbranched polyelectrolytes. Reaction of the alcohol groups with benzyl isocyanate demonstrates successful orthogonal functionalization. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Roles of head group architecture and side chain length on colorimetric response of polydiacetylene vesicles to temperature, ethanol and pH.

    Science.gov (United States)

    Charoenthai, Nipaphat; Pattanatornchai, Thanutpon; Wacharasindhu, Sumrit; Sukwattanasinitt, Mongkol; Traiphol, Rakchart

    2011-08-15

    In this contribution, we report the relationship between molecular structures of polydiacetylene (PDA) vesicles, fabricated by using three monomers, 10,12-tricosadiynoic acid (TCDA), 10,12-pentacosadiynoic acid (PCDA) and N-(2-aminoethyl)pentacosa-10,12-diynamide (AEPCDA), and their color-transition behaviors. The modification of side chain length and head group of the PDA vesicles strongly affects the colorimetric response to temperature, ethanol and pH. A shorter side chain of poly(TCDA) yields weaker inter- and intra-chain dispersion interactions in the bilayers compared to the system of poly(PCDA), which in turn results in a faster color transition upon exposure to all stimuli. A change of head group in poly(AEPCDA) slightly reduces the transition temperature. Interestingly, the colorimetric response of poly(AEPCDA) vesicles to the addition of ethanol is found to occur in a two-step fashion while the response of poly(PCDA) vesicles takes place in a one-step process. The amount of ethanol required for inducing complete color-transition of poly(AEPCDA) vesicles is also much higher, about 87% v/v. The increase of pH to ~9 and ~10 causes a color-transition of poly(TCDA) and poly(PCDA) vesicles, respectively. The poly(AEPCDA) vesicles, on the other hand, change color upon decreasing pH to ~0. The colorimetric response also occurs in a multi-step fashion. These discrepancies are attributed to the architecture of surface layers of poly(AEPCDA), constituting amine and amide groups separated by ethyl linkers. Copyright © 2011 Elsevier Inc. All rights reserved.

  14. Oxidative cleavage of the octyl side chain of 1-(3,4-dichlorobenzyl)-5-octylbiguanide (OPB-2045) in rat and dog liver preparations.

    Science.gov (United States)

    Umehara, K; Kudo, S; Hirao, Y; Morita, S; Uchida, M; Odomi, M; Miyamoto, G

    2000-08-01

    The metabolism of 1-(3,4-dichlorobenzyl)-5-octylbiguanide (OPB-2045), a new potent biguanide antiseptic, was investigated using rat and dog liver preparations to elucidate the mechanism of OPB-2045 metabolite formation, in which the octyl side chain is reduced to four, five, or six carbon atoms. Chemical structures of metabolites were characterized by 1H NMR, fast atom bombardment/mass spectrometry, and liquid chromatography/electrospray ionization-tandem mass spectrometry. Three main metabolites were observed during incubation of OPB-2045 with rat liver S9: 2-octanol (M-1), 3-octanol (M-2), and 4-octanol (M-3). In the incubation of OPB-2045 with dog liver S9, eight metabolites were observed, seven of which being M-1, M-2, M-3, 2-octanone (M-4), threo-2,3-octandiol (M-5), erythro-2,3-octandiol (M-6), and 1,2-octandiol (M-7). M-5 and M-6 were further biotransformed to a ketol derivative and C-C bond cleavage metabolite (hexanoic acid derivative), an in vivo end product, in the incubation with dog liver microsomes. The reactions required NADPH as a cofactor and were significantly inhibited by the various inhibitors of cytochrome P450 (i.e., CO, n-octylamine, SKF 525-A, metyrapone, and alpha-naphthoflavone). The results indicate that the degraded products of OPB-2045 are produced by C-C bond cleavage after monohydroxylation, dihydroxylation, and ketol formation at the site of the octyl side chain with possible involvement of cytochrome P450 systems. This aliphatic C-C bond cleavage by sequential oxidative reactions may play an important role in the metabolism of other drugs or endogenous compounds that possess aliphatic chains.

  15. Alkyl side chain on the 1-methylimidazolium ring of countercation modulating thermal and magnetic properties of metal-dithiolene complexes

    Science.gov (United States)

    Duan, Hai-Bao; Yu, Shan-Shan; Cai, Ying; Zhang, Hui

    2015-05-01

    Two low-dimensional ion-pair compounds [1,5-bis(1-methylimidazolium)pentane][Ni(mnt)2]2 (1) and [1,9-bis(1-methylimidazolium)nonane][Ni(mnt)2]2 (2) (mnt2- = maleonitriledithiolate) were designed and synthesized. The cations and anions formed mixed column along the crystallographic a-axis direction in the crystal of 1·0.5DMF. Two compounds display different thermal and magnetic behaviors. Multi-step solid to solid state phase transition was observed for 1 by DSC. 1 exhibits weak paramagnetism over the temperature range of 2-400 K and 2 shows spin gap in the low-temperature phase. Thus by changing of the alky chain length of the counter-cation allows the modulation thermal and magnetic behaviors for such system.

  16. A novel α-galactosidase from Fusarium oxysporum and its application in determining the structure of the gum arabic side chain.

    Science.gov (United States)

    Maruta, Akiho; Yamane, Mirei; Matsubara, Midori; Suzuki, Shiho; Nakazawa, Masami; Ueda, Mitsuhiro; Sakamoto, Tatsuji

    2017-08-01

    We previously reported that Fusarium oxysporum 12S produces two bifunctional proteins, FoAP1 and FoAP2, with α-d-galactopyranosidase (GPase) and β-l-arabinopyranosidase (APase) activities. The aim of this paper was to purify a third GPase, FoGP1, from culture supernatant of F. oxysporum 12S, to characterize it, and to determine its mode of action towards gum arabic. A cDNA encoding FoGP1 was cloned and the protein was overexpressed in Escherichia coli. Module sequence analysis revealed the presence of a GH27 domain in FoGP1. The recombinant enzyme (rFoGP1) showed a GPase/APase activity ratio of 330, which was quite different from that of FoAP1 (1.7) and FoAP2 (0.2). Among the natural substrates tested, rFoGP1 showed the highest activity towards gum arabic. In contrast to other well-characterized GPases, rFoGP1 released a small amount of galactose from α-galactosyl oligosaccharides such as raffinose and exhibited no activity toward galactomannans, which are highly substituted with α-galactosyl side chains. This indicated that FoGP1 is an unusual type of GPase. rFoGP1 released 30% of the total galactose from gum arabic, suggesting the existence of a large number of α-galactosyl residues at the non-reducing ends of gum arabic side chains. Together, rFoGP1 and α-l-arabinofuranosidase released four times more arabinose than α-l-arabinofuranosidase acting alone. This suggested that a large number of α-l-arabinofuranosyl residues is capped by α-galactosyl residues. 1 H NMR experiments revealed that rFoGP1 hydrolyzed the α-1,3-galactosidic linkage within the side chain structure of [α-d-Galp-(1→3)-α-l-Araf-(1→] in gum arabic. In conclusion, rFoGP1 is highly active toward α-1,3-galactosyl linkages but negligibly or not active toward α-1,6-galactosyl linkages. The novel FoGP1 might be used to modify the physical properties of gum arabic, which is an industrially important polysaccharide used as an emulsion stabilizer and coating agent. Copyright © 2017

  17. Effects of Odd–Even Side Chain Length of Alkyl-Substituted Diphenylbithiophenes on First Monolayer Thin Film Packing Structure

    KAUST Repository

    Akkerman, Hylke B.

    2013-07-31

    Because of their preferential two-dimensional layer-by-layer growth in thin films, 5,5′bis(4-alkylphenyl)-2,2′-bithiophenes (P2TPs) are model compounds for studying the effects of systematic chemical structure variations on thin-film structure and morphology, which in turn, impact the charge transport in organic field-effect transistors. For the first time, we observed, by grazing incidence X-ray diffraction (GIXD), a strong change in molecular tilt angle in a monolayer of P2TP, depending on whether the alkyl chain on the P2TP molecules was of odd or even length. The monolayers were deposited on densely packed ultrasmooth self-assembled alkane silane modified SiO2 surfaces. Our work shows that a subtle change in molecular structure can have a significant impact on the molecular packing structure in thin film, which in turn, will have a strong impact on charge transport of organic semiconductors. This was verified by quantum-chemical calculations that predict a corresponding odd-even effect in the strength of the intermolecular electronic coupling. © 2013 American Chemical Society.

  18. Effects of Odd–Even Side Chain Length of Alkyl-Substituted Diphenylbithiophenes on First Monolayer Thin Film Packing Structure

    KAUST Repository

    Akkerman, Hylke B.; Mannsfeld, Stefan C. B.; Kaushik, Ananth P.; Verploegen, Eric; Burnier, Luc; Zoombelt, Arjan P.; Saathoff, Jonathan D.; Hong, Sanghyun; Atahan-Evrenk, Sule; Liu, Xueliang; Aspuru-Guzik, Alá n; Toney, Michael F.; Clancy, Paulette; Bao, Zhenan

    2013-01-01

    Because of their preferential two-dimensional layer-by-layer growth in thin films, 5,5′bis(4-alkylphenyl)-2,2′-bithiophenes (P2TPs) are model compounds for studying the effects of systematic chemical structure variations on thin-film structure and morphology, which in turn, impact the charge transport in organic field-effect transistors. For the first time, we observed, by grazing incidence X-ray diffraction (GIXD), a strong change in molecular tilt angle in a monolayer of P2TP, depending on whether the alkyl chain on the P2TP molecules was of odd or even length. The monolayers were deposited on densely packed ultrasmooth self-assembled alkane silane modified SiO2 surfaces. Our work shows that a subtle change in molecular structure can have a significant impact on the molecular packing structure in thin film, which in turn, will have a strong impact on charge transport of organic semiconductors. This was verified by quantum-chemical calculations that predict a corresponding odd-even effect in the strength of the intermolecular electronic coupling. © 2013 American Chemical Society.

  19. Circulating N-Linked Glycoprotein Side-Chain Biomarker, Rosuvastatin Therapy, and Incident Cardiovascular Disease: An Analysis From the JUPITER Trial.

    Science.gov (United States)

    Akinkuolie, Akintunde O; Glynn, Robert J; Padmanabhan, Latha; Ridker, Paul M; Mora, Samia

    2016-07-13

    GlycA, a novel protein glycan biomarker of N-acetyl side chains of acute-phase proteins, was recently associated with incident cardiovascular disease (CVD) in healthy women. Whether GlycA predicts CVD events in the setting of statin therapy in men and women without CVD but with evidence of chronic inflammation is unknown. In the Justfication for the Use of Statins in Prevention: an Intervention Trial Evaluating Rosuvastatin (JUPITER) trial (NCT00239681), participants with low-density lipoprotein cholesterol 0.20). In the JUPITER trial, increased levels of GlycA were associated with an increased risk of CVD events independent of traditional risk factors and hsCRP. URL: http://www.clinicaltrials.gov. Unique identifier: NCT00239681. © 2016 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

  20. Characterizing hydrophobicity of amino acid side chains in a protein environment via measuring contact angle of a water nanodroplet on planar peptide network.

    Science.gov (United States)

    Zhu, Chongqin; Gao, Yurui; Li, Hui; Meng, Sheng; Li, Lei; Francisco, Joseph S; Zeng, Xiao Cheng

    2016-11-15

    Hydrophobicity of macroscopic planar surface is conventionally characterized by the contact angle of water droplets. However, this engineering measurement cannot be directly extended to surfaces of proteins, due to the nanometer scale of amino acids and inherent nonplanar structures. To measure the hydrophobicity of side chains of proteins quantitatively, numerous parameters were developed to characterize behavior of hydrophobic solvation. However, consistency among these parameters is not always apparent. Herein, we demonstrate an alternative way of characterizing hydrophobicity of amino acid side chains in a protein environment by constructing a monolayer of amino acids (i.e., artificial planar peptide network) according to the primary and the β-sheet secondary structures of protein so that the conventional engineering measurement of the contact angle of a water droplet can be brought to bear. Using molecular dynamics simulations, contact angles θ of a water nanodroplet on the planar peptide network, together with excess chemical potentials of purely repulsive methane-sized Weeks-Chandler-Andersen solute, are computed. All of the 20 types of amino acids and the corresponding planar peptide networks are studied. Expectedly, all of the planar peptide networks with nonpolar amino acids are hydrophobic due to θ [Formula: see text] 90°, whereas all of the planar peptide networks of the polar and charged amino acids are hydrophilic due to θ [Formula: see text] 90°. Planar peptide networks of the charged amino acids exhibit complete-wetting behavior due to θ [Formula: see text] 0°. This computational approach for characterization of hydrophobicity can be extended to artificial planar networks of other soft matter.

  1. Functionalized PHB granules provide the basis for the efficient side-chain cleavage of cholesterol and analogs in recombinant Bacillus megaterium.

    Science.gov (United States)

    Gerber, Adrian; Kleser, Michael; Biedendieck, Rebekka; Bernhardt, Rita; Hannemann, Frank

    2015-07-29

    Cholesterol, the precursor of all steroid hormones, is the most abundant steroid in vertebrates and exhibits highly hydrophobic properties, rendering it a difficult substrate for aqueous microbial biotransformations. In the present study, we developed a Bacillus megaterium based whole-cell system that allows the side-chain cleavage of this sterol and investigated the underlying physiological basis of the biocatalysis. CYP11A1, the side-chain cleaving cytochrome P450, was recombinantly expressed in the Gram-positive soil bacterium B. megaterium combined with the required electron transfer proteins. By applying a mixture of 2-hydroxypropyl-β-cyclodextrin and Quillaja saponin as solubilizing agents, the zoosterols cholesterol and 7-dehydrocholesterol, as well as the phytosterol β-sitosterol could be efficiently converted to pregnenolone or 7-dehydropregnenolone. Fluorescence-microscopic analysis revealed that cholesterol accumulates in the carbon and energy storage-serving poly(3-hydroxybutyrate) (PHB) bodies and that the membrane proteins CYP11A1 and its redox partner adrenodoxin reductase (AdR) are likewise localized to their surrounding phospholipid/protein monolayer. The capacity to store cholesterol was absent in a mutant strain devoid of the PHB-producing polymerase subunit PhaC, resulting in a drastically decreased cholesterol conversion rate, while no effect on the expression of the recombinant proteins could be observed. We established a whole-cell system based on B. megaterium, which enables the conversion of the steroid hormone precursor cholesterol to pregnenolone in substantial quantities. We demonstrate that the microorganism's PHB granules, aggregates of bioplastic coated with a protein/phospholipid monolayer, are crucial for the high conversion rate by serving as substrate storage. This microbial system opens the way for an industrial conversion of the abundantly available cholesterol to any type of steroid hormones, which represent one of the

  2. Hybrid bulk heterojunction solar cells based on poly(3-hexylthiophene) and ZnO nanoparticles modified by side-chain functional polythiophenes

    International Nuclear Information System (INIS)

    Li, Fan; Du, Yanhui; Chen, Yiwang

    2012-01-01

    We report the investigation of the hybrid bulk heterojunction solar cells based on the blend of poly(3-hexylthiophene) (P3HT) and ZnO nanoparticles modified by side-chain thiol functional poly(3-thiophenehexanethiol) (P3HT-SH). Grafting of P3HT-SH onto ZnO nanoparticles can promote the dispersion of ZnO nanoparticles within P3HT matrix and facilitate electron injection process into ZnO nanoparticles, resulting in a more efficient photoinduced charge transfer than that in simple physical mixture of P3HT and non-modified ZnO nanoparticles (P3HT/ZnO). Furthermore, the performance of hybrid photovoltaic device based on P3HT/P3HT-SH-modified ZnO blend exhibits an improved device efficiency compared with P3HT/ZnO even before thermal treatment. After being annealed at 80 °C, the P3HT/P3HT-SH-modified ZnO device shows the power conversion efficiency as high as 0.68%, with the short-circuit current density of 1.89 mA/cm 2 , the open-circuit voltage of 0.599 V and a fill factor of 60.5% under AM 1.5 G illumination with 100 mW/cm 2 light intensity. - Highlights: ► Hybrid solar cells based on poly(3-hexylthiophene) and modified ZnO nanoparticles ► ZnO nanoparticles modified by side-chain functional polythiophenes ► Uniform dispersion and intimate contact between polymers and nanoparticles ► Efficient charge transfer leading to the improvement of device efficiency

  3. Activity of 3-Ketosteroid 9α-Hydroxylase (KshAB) Indicates Cholesterol Side Chain and Ring Degradation Occur Simultaneously in Mycobacterium tuberculosis*

    Science.gov (United States)

    Capyk, Jenna K.; Casabon, Israël; Gruninger, Robert; Strynadka, Natalie C.; Eltis, Lindsay D.

    2011-01-01

    Mycobacterium tuberculosis (Mtb), a significant global pathogen, contains a cholesterol catabolic pathway. Although the precise role of cholesterol catabolism in Mtb remains unclear, the Rieske monooxygenase in this pathway, 3-ketosteroid 9α-hydroxylase (KshAB), has been identified as a virulence factor. To investigate the physiological substrate of KshAB, a rhodococcal acyl-CoA synthetase was used to produce the coenzyme A thioesters of two cholesterol derivatives: 3-oxo-23,24-bisnorchol-4-en-22-oic acid (forming 4-BNC-CoA) and 3-oxo-23,24-bisnorchola-1,4-dien-22-oic acid (forming 1,4-BNC-CoA). The apparent specificity constant (kcat/Km) of KshAB for the CoA thioester substrates was 20–30 times that for the corresponding 17-keto compounds previously proposed as physiological substrates. The apparent KmO2 was 90 ± 10 μm in the presence of 1,4-BNC-CoA, consistent with the value for two other cholesterol catabolic oxygenases. The Δ1 ketosteroid dehydrogenase KstD acted with KshAB to cleave steroid ring B with a specific activity eight times greater for a CoA thioester than the corresponding ketone. Finally, modeling 1,4-BNC-CoA into the KshA crystal structure suggested that the CoA moiety binds in a pocket at the mouth of the active site channel and could contribute to substrate specificity. These results indicate that the physiological substrates of KshAB are CoA thioester intermediates of cholesterol side chain degradation and that side chain and ring degradation occur concurrently in Mtb. This finding has implications for steroid metabolites potentially released by the pathogen during infection and for the design of inhibitors for cholesterol-degrading enzymes. The methodologies and rhodococcal enzymes used to generate thioesters will facilitate the further study of cholesterol catabolism. PMID:21987574

  4. A novel branched side-chain-type sulfonated polyimide membrane with flexible sulfoalkyl pendants and trifluoromethyl groups for vanadium redox flow batteries

    Science.gov (United States)

    Li, Jinchao; Liu, Suqin; He, Zhen; Zhou, Zhi

    2017-04-01

    A novel branched side-chain-type sulfonated polyimide (6F-s-bSPI) membrane with accessible branching agents of melamine, hydrophobic trifluoromethyl groups (sbnd CF3), and flexible sulfoalkyl pendants is prepared by a high-temperature polycondensation and post-sulfonation method for use in vanadium redox flow batteries (VRFBs). The chemical structure of the 6F-s-bSPI membrane is confirmed by ATR-FTIR and 1H NMR spectra. The physico-chemical properties of the as-prepared 6F-s-bSPI membrane are systematically investigated and found to be strongly related to the specially designed structure. The 6F-s-bSPI membrane offers a reduced cost and possesses a significantly lowered vanadium ion permeability (1.18 × 10-7 cm2 min-1) compared to the linear SPI (2.25 × 10-7 cm2 min-1) and commercial Nafion 115 (1.36 × 10-6 cm2 min-1) membranes, prolonging the self-discharge duration of the VRFBs. In addition, the VRFB assembled with a 6F-s-bSPI membrane shows higher coulombic (98.3%-99.7%) and energy efficiencies (88.4%-66.12%) than that with a SPI or Nafion 115 membrane under current densities ranging from 20 to 100 mA cm-2. Moreover, the VRFB with a 6F-s-bSPI membrane delivers a stable cycling performance over 100 cycles with no decline in coulombic and energy efficiencies. These results show that the branched side-chain-type structure is a promising design to prepare excellent proton conductive membranes.

  5. Composition of the epicuticular waxes coating the adaxial side of Phyllostachys aurea leaves: Identification of very-long-chain primary amides.

    Science.gov (United States)

    Racovita, Radu C; Jetter, Reinhard

    2016-10-01

    The present study presents comprehensive chemical analyses of cuticular wax mixtures of the bamboo Phyllostachys aurea. The epicuticular and intracuticular waxes were sampled selectively from the adaxial side of leaves on young and old plants and investigated by gas chromatography-mass spectrometry and flame ionization detection. The epi- and intracuticular layers on young and old leaves had wax loads ranging from 1.7 μg/cm(2) to 1.9 μg/cm(2). Typical very-long-chain aliphatic wax constituents were found with characteristic chain length patterns, including alkyl esters (primarily C48), alkanes (primarily C29), fatty acids (primarily C28 and C16), primary alcohols (primarily C28) and aldehydes (primarily C30). Alicyclic wax components were identified as tocopherols and triterpenoids, including substantial amounts of triterpenoid esters. Alkyl esters, alkanes, fatty acids and aldehydes were found in greater amounts in the epicuticular layer, while primary alcohols and most terpenoids accumulated more in the intracuticular wax. Alkyl esters occurred as mixtures of metamers, combining C20 alcohol with various acids into shorter ester homologs (C36C40), and a wide range of alcohols with C22 and C24 acids into longer esters (C42C52). Primary amides were identified, with a characteristic chain length profile peaking at C30. The amides were present exclusively in the epicuticular layer and thus at or near the surface, where they may affect plant-herbivore or plant-pathogen interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Reduction of Line Edge Roughness of Polystyrene-block-Poly(methyl methacrylate) Copolymer Nanopatterns By Introducing Hydrogen Bonding at the Junction Point of Two Block Chains.

    Science.gov (United States)

    Lee, Kyu Seong; Lee, Jaeyong; Kwak, Jongheon; Moon, Hong Chul; Kim, Jin Kon

    2017-09-20

    To apply well-defined block copolymer nanopatterns to next-generation lithography or high-density storage devices, small line edge roughness (LER) of nanopatterns should be realized. Although polystyrene-block-poly(methyl methacrylate) copolymer (PS-b-PMMA) has been widely used to fabricate nanopatterns because of easy perpendicular orientation of the block copolymer nanodomains and effective removal of PMMA block by dry etching, the fabricated nanopatterns show poorer line edge roughness (LER) due to relatively small Flory-Huggins interaction parameter (χ) between PS and PMMA chains. Here, we synthesized PS-b-PMMA with urea (U) and N-(4-aminomethyl-benzyl)-4-hydroxymethyl-benzamide (BA) moieties at junction of PS and PMMA chains (PS-U-BA-PMMA) to improve the LER. The U-BA moieties serves as favorable interaction (hydrogen bonding) sites. The LER of PS line patterns obtained from PS-U-BA-PMMA was reduced ∼25% compared with that obtained from neat PS-b-PMMA without BA and U moieties. This is attributed to narrower interfacial width induced by hydrogen bonding between two blocks, which is confirmed by small-angle X-ray scattering. This result implies that the introduction of hydrogen bonding into block copolymer interfaces offers an opportunity to fabricate well-defined nanopatterns with improved LER by block copolymer self-assembly, which could be a promising alternative to next-generation extreme ultraviolet lithography.

  7. A chemical approach for site-specific identification of NMR signals from protein side-chain NH{sub 3}{sup +} groups forming intermolecular ion pairs in protein–nucleic acid complexes

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Kurtis M. [University of Texas Health Science Center at Houston, Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine (United States); Nguyen, Dan; Esadze, Alexandre; Zandrashvili, Levani [University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (United States); Gorenstein, David G. [University of Texas Health Science Center at Houston, Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine (United States); Iwahara, Junji, E-mail: juiwahar@utmb.edu, E-mail: j.iwahara@utmb.edu [University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (United States)

    2015-05-15

    Protein–nucleic acid interactions involve intermolecular ion pairs of protein side-chain and DNA or RNA phosphate groups. Using three protein–DNA complexes, we demonstrate that site-specific oxygen-to-sulfur substitution in phosphate groups allows for identification of NMR signals from the protein side-chain NH{sub 3}{sup +} groups forming the intermolecular ion pairs. A characteristic change in their {sup 1}H and {sup 15}N resonances upon this modification (i.e., substitution of phosphate to phosphorodithioate) can represent a signature of an intermolecular ion pair. Hydrogen-bond scalar coupling between protein side-chain {sup 15}N and DNA phosphorodithiaote {sup 31}P nuclei provides direct confirmation of the intermolecular ion pair. The same approach is likely applicable to protein–RNA complexes as well.

  8. A chemical approach for site-specific identification of NMR signals from protein side-chain NH3+ groups forming intermolecular ion pairs in protein–nucleic acid complexes

    International Nuclear Information System (INIS)

    Anderson, Kurtis M.; Nguyen, Dan; Esadze, Alexandre; Zandrashvili, Levani; Gorenstein, David G.; Iwahara, Junji

    2015-01-01

    Protein–nucleic acid interactions involve intermolecular ion pairs of protein side-chain and DNA or RNA phosphate groups. Using three protein–DNA complexes, we demonstrate that site-specific oxygen-to-sulfur substitution in phosphate groups allows for identification of NMR signals from the protein side-chain NH 3 + groups forming the intermolecular ion pairs. A characteristic change in their 1 H and 15 N resonances upon this modification (i.e., substitution of phosphate to phosphorodithioate) can represent a signature of an intermolecular ion pair. Hydrogen-bond scalar coupling between protein side-chain 15 N and DNA phosphorodithiaote 31 P nuclei provides direct confirmation of the intermolecular ion pair. The same approach is likely applicable to protein–RNA complexes as well

  9. Insertion of molecular oxygen into a palladium(II) methyl bond: a radical chain mechanism involving palladium(III) intermediates.

    Science.gov (United States)

    Boisvert, Luc; Denney, Melanie C; Hanson, Susan Kloek; Goldberg, Karen I

    2009-11-04

    The reaction of (bipy)PdMe(2) (1) (bipy = 2,2'-bipyridine) with molecular oxygen results in the formation of the palladium(II) methylperoxide complex (bipy)PdMe(OOMe) (2). The identity of the product 2 has been confirmed by independent synthesis. Results of kinetic studies of this unprecedented oxygen insertion reaction into a palladium alkyl bond support the involvement of a radical chain mechanism. Reproducible rates, attained in the presence of the radical initiator 2,2'-azobis(2-methylpropionitrile) (AIBN), reveal that the reaction is overall first-order (one-half-order in both [1] and [AIBN], and zero-order in [O(2)]). The unusual rate law (half-order in [1]) implies that the reaction proceeds by a mechanism that differs significantly from those for organic autoxidations and for the recently reported examples of insertion of O(2) into Pd(II) hydride bonds. The mechanism for the autoxidation of 1 is more closely related to that found for the autoxidation of main group and early transition metal alkyl complexes. Notably, the chain propagation is proposed to proceed via a stepwise associative homolytic substitution at the Pd center of 1 with formation of a pentacoordinate Pd(III) intermediate.

  10. Activity of 3-ketosteroid 9α-hydroxylase (KshAB) indicates cholesterol side chain and ring degradation occur simultaneously in Mycobacterium tuberculosis.

    Science.gov (United States)

    Capyk, Jenna K; Casabon, Israël; Gruninger, Robert; Strynadka, Natalie C; Eltis, Lindsay D

    2011-11-25

    Mycobacterium tuberculosis (Mtb), a significant global pathogen, contains a cholesterol catabolic pathway. Although the precise role of cholesterol catabolism in Mtb remains unclear, the Rieske monooxygenase in this pathway, 3-ketosteroid 9α-hydroxylase (KshAB), has been identified as a virulence factor. To investigate the physiological substrate of KshAB, a rhodococcal acyl-CoA synthetase was used to produce the coenzyme A thioesters of two cholesterol derivatives: 3-oxo-23,24-bisnorchol-4-en-22-oic acid (forming 4-BNC-CoA) and 3-oxo-23,24-bisnorchola-1,4-dien-22-oic acid (forming 1,4-BNC-CoA). The apparent specificity constant (k(cat)/K(m)) of KshAB for the CoA thioester substrates was 20-30 times that for the corresponding 17-keto compounds previously proposed as physiological substrates. The apparent K(m)(O(2)) was 90 ± 10 μM in the presence of 1,4-BNC-CoA, consistent with the value for two other cholesterol catabolic oxygenases. The Δ(1) ketosteroid dehydrogenase KstD acted with KshAB to cleave steroid ring B with a specific activity eight times greater for a CoA thioester than the corresponding ketone. Finally, modeling 1,4-BNC-CoA into the KshA crystal structure suggested that the CoA moiety binds in a pocket at the mouth of the active site channel and could contribute to substrate specificity. These results indicate that the physiological substrates of KshAB are CoA thioester intermediates of cholesterol side chain degradation and that side chain and ring degradation occur concurrently in Mtb. This finding has implications for steroid metabolites potentially released by the pathogen during infection and for the design of inhibitors for cholesterol-degrading enzymes. The methodologies and rhodococcal enzymes used to generate thioesters will facilitate the further study of cholesterol catabolism.

  11. Catalyst-Directed Diastereoselective Isomerization of Allylic Alcohols for the Stereoselective Construction of C(20) in Steroid Side Chains: Scope and Topological Diversification.

    Science.gov (United States)

    Li, Houhua; Mazet, Clément

    2015-08-26

    The stereoselective construction of C20 in steroidal derivatives by a highly diastereoselective Ir-catalyzed isomerization of primary allylic alcohols is reported. A key aspect of this strategy is a straightforward access to geometrically pure steroidal enol tosylate and enol triflate intermediates for subsequent high yielding stereoretentive Negishi cross-coupling reactions to allow structural diversity to be introduced. A range of allylic alcohols participates in the diastereoselective isomerization under the optimized reaction conditions. Electron-rich and electron-poor aryl or heteroaryl substituents are particularly well-tolerated, and the stereospecific nature of the reaction provides indifferently access to the natural C20-(R) and unnatural C20-(S) configurations. Alkyl containing substrates are more challenging as they affect regioselectivity of iridium-hydride insertion. A rationale for the high diastereoselectivities observed is proposed for aryl containing precursors. The scope of our method is further highlighted through topological diversification in the side chain and within the polycyclic domain of advanced and complex steroidal architectures. These findings have the potential to greatly simplify access to epimeric structural analogues of important steroid scaffolds for applications in biological, pharmaceutical, and medical sciences.

  12. Influence of the strength of the smectic order on the backbone anisotropy of side-chain liquid crystal polymers as revealed by SANS

    Science.gov (United States)

    Noirez, L.; Keller, P.; Cotton, J. P.

    1992-06-01

    It is proposed that the strength of the smectic order determines the backbone anisotropy of side-chain liquid crystal polymers. Here this strength increases with the length of the alkyl terminal group of the mesogens. Two liquid crystal polymethacrylates differing only by the mesogenic tails —OCH3 and —OC4H9 are considered. The backbone anisotropy of these polymers is measured by small angle neutron scattering (SANS) whereas the smectic order is evaluated from the intensity of the 001 Bragg peak. Il est proposé que la qualité de l'ordre smectique détermine l'anisotropie du squelette de polymères mésomorphes en peigne confinés dans les lamelles. Ici l'ordre smectique est augmenté en allongeant le groupe alkyl terminal des mésogènes. Nous étudions deux polyméthacrylates cristal liquide qui ne différent que par leurs groupes terminaux : —OCH3 et —OC4H9. L'anisotropie du squellete est mesurée par diffusion de neutrons aux petits angles tandis que l'ordre smectique est évalué à l'aide de l'intensité du pic de Bragg 001.

  13. Photoinduced electron transfer involving eosin-tryptophan conjugates. Long-lived radical pair states for systems incorporating aromatic amino acid side chains

    Energy Technology Data Exchange (ETDEWEB)

    Jones, G. II; Farahat, C.W.; Oh, C. (Boston Univ., MA (United States))

    1994-07-14

    The electron-transfer photochemistry of the covalent derivatives of the dye eosin, in which the xanthene dye is covalently attached to the amino acid L-tryptophan via the thiohydantoin derivative, the tryptophan dipeptide, and an ethyl ester derivative, has been investigated. The singlet excited state of the dye is significantly quenched on attachment of the aromatic amino acid residue. Dye triplet states are also intercepted through intramolecular interaction of excited dye and amino acid pendants. Flash photolysis experiments verify that this interaction involves electron transfer from the indole side chains of tryptophan. Rate constants for electron transfer are discussed in terms of the distance relationships for the eosin chromophore and aromatic redox sites on peptide derivatives, the pathway for [sigma]-[pi] through-bond interaction between redox sites, and the multiplicity and state of protonation for electron-transfer intermediates. Selected electron-transfer photoreactions were studied under conditions of binding of the peptide derivatives in a high molecular weight, water-soluble, globular polymer, poly(vinyl-2-pyrrolidinone). 28 refs., 4 figs., 1 tab.

  14. Amino Acid Functionalization of Doped Single-Walled Carbon Nanotubes: Effects of Dopants and Side Chains as Well as Zwitterionic Stabilizations.

    Science.gov (United States)

    Jiang, Lisha; Zhu, Chang; Fu, Yujie; Yang, Gang

    2017-04-06

    Functionalization of single-walled carbon nanotubes (SWCNTs) is necessitated in a number of conditions such as drug delivery, and here amino acid functionalization of SWCNTs is conducted within the framework of density functional theory. Functionalization efficiencies of Gly are largely determined by dopants, as a combined effect of atomic radius, electronic configuration, and distortion to SWCNTs. Different functionalization sites in Gly have divergent interaction strengths with M/SWCNTs that decline as O b > N > O a , and this trend seems almost independent of the identity of metallic dopants. B/SWCNT behaves distinctly and prefers to the N site. Dopants affect principally interaction strengths, while amino acids regulate significantly both functionalization configurations and interaction energies. Then focus is given to stabilization of zwitterionic amino acids due to enhanced interactions with the widely used zwitterionic drugs. All metallic dopants render zwitterionic Gly to be the most stable, and side chains in amino acids rather than dopants in M/SWCNTs cause more pronounced effects to zwitterionic stabilizations. Charge transfers between amino acids and M/SWCNTs are closely associated with zwitterionic stabilization effects, and different charge transfer mechanisms between M/SWCNTs and metal ions are interpreted. Thus, this work provides a comprehensive understanding of amino acid functionalization of M/SWCNTs.

  15. Fluorescence spectroscopic study of the aggregation behavior of non-cross-linked and cross-linked poly(alkylmethyldiallylammonium bromides) having decyl, octyl, and hexyl side chains in aqueous solution

    NARCIS (Netherlands)

    Wang, G.J; Engberts, J.B.F.N.

    1996-01-01

    The conformational state of a series of non-cross-linked and cross-linked poly(alkylmethyldiallylammonium bromides) bearing decyl, octyl, and hexyl side chains ((CL)-CopolC1-10, (CL)-CopolC1-8, and (CL)-CopolC1-6, respectively) in aqueous solutions were investigated by fluorescence spectroscopy

  16. Mechanism of radiation-induced degradation of poly(methyl methacrylate)

    International Nuclear Information System (INIS)

    Ichikawa, Tsuneki; Oyama, Ken-ichi; Yoshida, Hiroshi

    1995-01-01

    ESR and gel permeation chromatographic measurements of poly(methyl methacrylate) γ-irradiated between 77 K and 300 K have been carried out to elucidate the mechanism of radiation-induced degradation of the polymer. It is revealed that the scission of the main chain is not taken place immediately after the absorption of radiation energy but is induced by the intramolecular radical conversion of the side-chain -COOCH 2 radical to the tertiary -CH 2 -C(CH 3 )- radical followed by the main-chain β-scission of the latter radical. The degradation is not taken place below 190 K, because the side-chain radical starts to convert only above 190 K. The residual monomer in the polymer reacts with the side-chain radical below 190 K to generate the stable propagating-type radical, so that the degradation is suppressed even after warming the polymer to the ambient temperature. (author)

  17. Testosterone stimulates progesterone production and STAR, P450 cholesterol side-chain cleavage and LH receptor mRNAs expression in hen (Gallus domesticus) granulosa cells.

    Science.gov (United States)

    Rangel, P L; Rodríguez, A; Rojas, S; Sharp, P J; Gutierrez, C G

    2009-12-01

    The chicken ovary is organized into a hierarchy of yellow yolky follicles that ovulate on successive days. Active or passive immunization of laying hens against testosterone blocks ovulation without affecting follicle development. Testosterone may play a role in pre-ovulatory follicle maturation by stimulating granulosa progesterone production. We assessed whether this stimulus is dose-related and depends on the maturity of the donor follicle, and if it does so by stimulating granulosa cell STAR, P450 cholesterol side-chain cleavage (P450scc), and LH receptor (LHCGR) mRNAs expression. Progesterone production by granulosa cells from F1, F3, and F4 follicles, cultured for 3 h without testosterone was greater in cells collected 11-14 h than 1-4 h after ovulation. These differences in progesterone production were less pronounced after granulosa cells had been cultured for 24 h. Culture of granulosa cells for 3 or 24 h with testosterone (1-100 ng/ml) stimulated progesterone production in cells collected from F4, F3, or F1 follicles 1-4, or 11-14 h after ovulation. Testosterone (0-4000 ng/ml) alone or in combination with LH (0-100 ng/ml) increased progesterone production by F1 granulosa cells, collected 1-4 and 11-14 h after ovulation and cultured for 3 h. Finally, testosterone (10 or 100 ng/ml) increased STAR, P450scc, and LHCGR mRNAs, when added to 3 h cultures of F1 granulosa cells. In conclusion, testosterone stimulates granulosa cell progesterone production in hen pre-ovulatory hierarchical follicles irrespective of maturational state, acting alone or additively with LH. We propose that testosterone promotes granulosa cell maturation to facilitate the pre-ovulatory release of LH.

  18. Sensitivity improvement for correlations involving arginine side-chain Nε/Hε resonances in multi-dimensional NMR experiments using broadband 15N 180o pulses

    International Nuclear Information System (INIS)

    Iwahara, Junji; Clore, G. Marius

    2006-01-01

    Due to practical limitations in available 15 N rf field strength, imperfections in 15 N 180 o pulses arising from off-resonance effects can result in significant sensitivity loss, even if the chemical shift offset is relatively small. Indeed, in multi-dimensional NMR experiments optimized for protein backbone amide groups, cross-peaks arising from the Arg guanidino 15 Nε (∼85 ppm) are highly attenuated by the presence of multiple INEPT transfer steps. To improve the sensitivity for correlations involving Arg Nε-Hε groups, we have incorporated 15 N broadband 180 deg. pulses into 3D 15 N-separated NOE-HSQC and HNCACB experiments. Two 15 N-WURST pulses incorporated at the INEPT transfer steps of the 3D 15 N-separated NOE-HSQC pulse sequence resulted in a ∼1.5-fold increase in sensitivity for the Arg Nε-Hε signals at 800 MHz. For the 3D HNCACB experiment, five 15 N Abramovich-Vega pulses were incorporated for broadband inversion and refocusing, and the sensitivity of Arg 1 Hε- 15 Nε- 13 Cγ/ 13 Cδ correlation peaks was enhanced by a factor of ∼1.7 at 500 MHz. These experiments eliminate the necessity for additional experiments to assign Arg 1 Hε and 15 Nε resonances. In addition, the increased sensitivity afforded for the detection of NOE cross-peaks involving correlations with the 15 Nε/ 1 Hε of Arg in 3D 15 N-separated NOE experiments should prove to be very useful for structural analysis of interactions involving Arg side-chains

  19. Absence of arabinan in the side chains of the pectic polysaccharides strongly associated with cell walls of Nicotiana plumbaginifolia non-organogenic callus with loosely attached constituent cells.

    Science.gov (United States)

    Iwai, H; Ishii, T; Satoh, S

    2001-10-01

    When leaf disks from haploid plants of Nicotiana plumbaginifolia Viv. were transformed with T-DNA and cultured on shoot-inducing medium, nonorganogenic callus. designated nolac (for non-organogenic callus with loosely attached cells), appeared on approximately 7% of leaf disks. In contrast, normal callus was generated on T-DNA-transformed leaf disks from diploid plants and on non-transformed leaf disks from haploid and diploid plants. Transmission electron microscopy revealed that the middle lamellae and the cell walls of one line of mutant callus (nolac-H14) were barely stained by ruthenium red. even after demethylesterification with NaOH, whereas the entire cell wall and the middle lamella were strongly stained in normal callus. In cultures of nolac-H14 callus, the level of sugar components of pectic polysaccharides in the hemicellulose fraction was reduced and that in the culture medium was elevated, as compared with cultures of normal callus. These results indicate that pectic polysaccharides are not retained in the cell walls and middle lamellae of nolac-H14 callus. In nolac-H14, the ratio of arabinose to galactose was low in the pectic polysaccharides purified from all cell wall fractions and from the medium, in particular, in the hemicellulose fractions. The low levels of arabinofuranosyl (T-Araf, 5-Araf, 2,5-Araf, and 3,5-Araf) residues in the pectic polysaccharides of the hemicellulosic fraction of nolac-H,14 indicated that no neutral-sugar side chains, composed mainly of linear arabinan. were present in nolac-H14. Arabinose-rich pectins. which are strongly associated with cellulose-hemicellulose complexes, might play an important role in intercellular attachment in the architecture of the cell wall.

  20. Critical role in CXCR4 signaling and internalization of the polypeptide main chain in the amino terminus of SDF-1α probed by novel N-methylated synthetically and modularly modified chemokine analogues.

    Science.gov (United States)

    Dong, Chang-Zhi; Tian, Shaomin; Choi, Won-Tak; Kumar, Santhosh; Liu, Dongxiang; Xu, Yan; Han, Xiaofeng; Huang, Ziwei; An, Jing

    2012-07-31

    The replication of human immunodeficiency virus type 1 (HIV-1) can be profoundly inhibited by the natural ligands of two major HIV-1 coreceptors, CXCR4 and CCR5. Stromal cell-derived factor-1α (SDF-1α) is a natural ligand of CXCR4. We have recently developed a synthetic biology approach of using synthetically and modularly modified (SMM)-chemokines to dissect various aspects of the structure-function relationship of chemokines and their receptors. Here, we used this approach to design novel SMM-SDF-1α analogues containing unnatural N-methylated residues in the amino terminus to investigate whether the polypeptide main chain amide bonds in the N-terminus of SDF-1α play a role in SDF-1α signaling via CXCR4 and/or receptor internalization. The results show that SDF-1α analogues with a modified N-methylated main chain at position 2, 3, or 5 retain significant CXCR4 binding and yet completely lose signaling activities. Furthermore, a representative N-methylated analogue has been shown to be incapable of causing CXCR4 internalization. These results suggest that the ability of SDF-1α to activate CXCR4 signaling and internalization is dependent upon the main chain amide bonds in the N-terminus of SDF-1α. This study demonstrates the feasibility and value of applying a synthetic biology approach to chemically engineer natural proteins and peptide ligands as probes of important biological functions that are not addressed by other biological techniques.

  1. Associations of maternal long-chain polyunsaturated fatty acids, methyl mercury, and infant development in the Seychelles Child Development Nutrition Study.

    Science.gov (United States)

    Strain, J J; Davidson, Philip W; Bonham, Maxine P; Duffy, Emeir M; Stokes-Riner, Abbie; Thurston, Sally W; Wallace, Julie M W; Robson, Paula J; Shamlaye, Conrad F; Georger, Lesley A; Sloane-Reeves, Jean; Cernichiari, Elsa; Canfield, Richard L; Cox, Christopher; Huang, Li Shan; Janciuras, Joanne; Myers, Gary J; Clarkson, Thomas W

    2008-09-01

    Fish consumption during gestation can provide the fetus with long-chain polyunsaturated fatty acids (LCPUFA) and other nutrients essential for growth and development of the brain. However, fish consumption also exposes the fetus to the neurotoxicant, methyl mercury (MeHg). We studied the association between these fetal exposures and early child development in the Seychelles Child Development Nutrition Study (SCDNS). Specifically, we examined a priori models of Omega-3 and Omega-6 LCPUFA measures in maternal serum to test the hypothesis that these LCPUFA families before or after adjusting for prenatal MeHg exposure would reveal associations with child development assessed by the BSID-II at ages 9 and 30 months. There were 229 children with complete outcome and covariate data available for analysis. At 9 months, the PDI was positively associated with total Omega-3 LCPUFA and negatively associated with the ratio of Omega-6/Omega-3 LCPUFA. These associations were stronger in models adjusted for prenatal MeHg exposure. Secondary models suggested that the MeHg effect at 9 months varied by the ratio of Omega-6/Omega-3 LCPUFA. There were no significant associations between LCPUFA measures and the PDI at 30 months. There were significant adverse associations, however, between prenatal MeHg and the 30-month PDI when the LCPUFA measures were included in the regression analysis. The BSID-II mental developmental index (MDI) was not associated with any exposure variable. These data support the potential importance to child development of prenatal availability of Omega-3 LCPUFA present in fish and of LCPUFA in the overall diet. Furthermore, they indicate that the beneficial effects of LCPUFA can obscure the determination of adverse effects of prenatal MeHg exposure in longitudinal observational studies.

  2. Property Enhancement Effects of Side-Chain-Type Naphthalene-Based Sulfonated Poly(arylene ether ketone) on Nafion Composite Membranes for Direct Methanol Fuel Cells.

    Science.gov (United States)

    Wang, Baolong; Hong, Lihua; Li, Yunfeng; Zhao, Liang; Zhao, Chengji; Na, Hui

    2017-09-20

    Nafion/SNPAEK-x composite membranes were prepared by blending raw Nafion and synthesized side-chain-type naphthalene-based sulfonated poly(arylene ether ketone) with a sulfonation degree of 1.35 (SNPAEK-1.35). The incorporation of SNPAEK-1.35 polymer with ion exchange capacity (IEC) of 2.01 mequiv·g -1 into a Nafion matrix has the property enhancement effects, such as increasing IECs, improving proton conductivity, enhancing mechanical properties, reducing methanol crossover, and improving single cell performance of Nafion. Morphology studies show that Nafion/SNPAEK-x composite membranes exhibit a well-defined microphase separation structure depending on the contents of SNPAEK-1.35 polymer. Among them, Nafion/SNPAEK-7.5% with a bicontinuous morphology exhibits the best comprehensive properties. For example, it shows the highest proton conductivities of 0.092 S cm -1 at 25 °C and 0.163 S cm -1 at 80 °C, which are higher than those of recast Nafion with 0.073 S cm -1 at 25 °C and 0.133 S cm -1 at 80 °C, respectively. Nafion/SNPAEK-5.0% and Nafion/SNPAEK-7.5% membranes display an open circuit voltage of 0.77 V and a maximum power density of 47 mW cm -2 at 80 °C, which are much higher than those of recast Nafion of 0.63 V and 24 mW cm -2 under the same conditions. Nafion/SNPAEK-5.0% membrane also has comparable tensile strength (12.7 MPa) to recast Nafion (13.7 MPa), and higher Young's modulus (330 MPa) than that of recast Nafion (240 MPa). By combining their high proton conductivities, comparable mechanical properties, and good single cell performance, Nafion/SNPAEK-x composite membranes have the potential to be polymer electrolyte materials for direct methanol fuel cell applications.

  3. Nano-Mole Scale Side-Chain Signal Assignment by 1H-Detected Protein Solid-State NMR by Ultra-Fast Magic-Angle Spinning and Stereo-Array Isotope Labeling

    KAUST Repository

    Wang, Songlin

    2015-04-09

    We present a general approach in 1H-detected 13C solid-state NMR (SSNMR) for side-chain signal assignments of 10-50 nmol quantities of proteins using a combination of a high magnetic field, ultra-fast magic-angle spinning (MAS) at ~80 kHz, and stereo-array-isotope-labeled (SAIL) proteins [Kainosho M. et al., Nature 440, 52–57, 2006]. First, we demonstrate that 1H indirect detection improves the sensitivity and resolution of 13C SSNMR of SAIL proteins for side-chain assignments in the ultra-fast MAS condition. 1H-detected SSNMR was performed for micro-crystalline ubiquitin (~55 nmol or ~0.5mg) that was SAIL-labeled at seven isoleucine (Ile) residues. Sensitivity was dramatically improved by 1H-detected 2D 1H/13C SSNMR by factors of 5.4-9.7 and 2.1-5.0, respectively, over 13C-detected 2D 1H/13C SSNMR and 1D 13C CPMAS, demonstrating that 2D 1H-detected SSNMR offers not only additional resolution but also sensitivity advantage over 1D 13C detection for the first time. High 1H resolution for the SAIL-labeled side-chain residues offered reasonable resolution even in the 2D data. A 1H-detected 3D 13C/13C/1H experiment on SAIL-ubiquitin provided nearly complete 1H and 13C assignments for seven Ile residues only within ~2.5 h. The results demonstrate the feasibility of side-chain signal assignment in this approach for as little as 10 nmol of a protein sample within ~3 days. The approach is likely applicable to a variety of proteins of biological interest without any requirements of highly efficient protein expression systems.

  4. Nano-Mole Scale Side-Chain Signal Assignment by 1H-Detected Protein Solid-State NMR by Ultra-Fast Magic-Angle Spinning and Stereo-Array Isotope Labeling

    KAUST Repository

    Wang, Songlin; Parthasarathy, Sudhakar; Nishiyama, Yusuke; Endo, Yuki; Nemoto, Takahiro; Yamauchi, Kazuo; Asakura, Tetsuo; Takeda, Mitsuhiro; Terauchi, Tsutomu; Kainosho, Masatsune; Ishii, Yoshitaka

    2015-01-01

    We present a general approach in 1H-detected 13C solid-state NMR (SSNMR) for side-chain signal assignments of 10-50 nmol quantities of proteins using a combination of a high magnetic field, ultra-fast magic-angle spinning (MAS) at ~80 kHz, and stereo-array-isotope-labeled (SAIL) proteins [Kainosho M. et al., Nature 440, 52–57, 2006]. First, we demonstrate that 1H indirect detection improves the sensitivity and resolution of 13C SSNMR of SAIL proteins for side-chain assignments in the ultra-fast MAS condition. 1H-detected SSNMR was performed for micro-crystalline ubiquitin (~55 nmol or ~0.5mg) that was SAIL-labeled at seven isoleucine (Ile) residues. Sensitivity was dramatically improved by 1H-detected 2D 1H/13C SSNMR by factors of 5.4-9.7 and 2.1-5.0, respectively, over 13C-detected 2D 1H/13C SSNMR and 1D 13C CPMAS, demonstrating that 2D 1H-detected SSNMR offers not only additional resolution but also sensitivity advantage over 1D 13C detection for the first time. High 1H resolution for the SAIL-labeled side-chain residues offered reasonable resolution even in the 2D data. A 1H-detected 3D 13C/13C/1H experiment on SAIL-ubiquitin provided nearly complete 1H and 13C assignments for seven Ile residues only within ~2.5 h. The results demonstrate the feasibility of side-chain signal assignment in this approach for as little as 10 nmol of a protein sample within ~3 days. The approach is likely applicable to a variety of proteins of biological interest without any requirements of highly efficient protein expression systems.

  5. Synthesis and photophysical and electroluminescent properties of poly(1,4-phenylene–ethynylene)-alt-poly(1,4-phenylene–vinylene)s with various dissymmetric substitution of alkoxy side chains

    Czech Academy of Sciences Publication Activity Database

    Bouguerra, N.; Růžička, Aleš; Ulbricht, C.; Enengl, C.; Enengl, S.; Pokorná, Veronika; Výprachtický, Drahomír; Tordin, E.; Aitout, R.; Cimrová, Věra; Egbe, D. A. M.

    2016-01-01

    Roč. 49, č. 2 (2016), s. 455-464 ISSN 0024-9297 R&D Projects: GA ČR(CZ) GA13-26542S; GA ČR(CZ) GAP106/12/0827 Institutional support: RVO:61389013 Keywords : poly(1,4-phenylene-ethynylene)-alt-poly(1,4-phenylene-vinylene)s * dissymmetric side chains * synthesis Subject RIV: CD - Macromolecular Chemistry Impact factor: 5.835, year: 2016

  6. Binding cooperativity between a ligand carbonyl group and a hydrophobic side chain can be enhanced by additional H-bonds in a distance dependent manner: A case study with thrombin inhibitors.

    Science.gov (United States)

    Said, Ahmed M; Hangauer, David G

    2015-01-01

    One of the underappreciated non-covalent binding factors, which can significantly affect ligand-protein binding affinity, is the cooperativity between ligand functional groups. Using four different series of thrombin inhibitors, we reveal a strong positive cooperativity between an H-bond accepting carbonyl functionality and the adjacent P3 hydrophobic side chain. Adding an H-bond donating amine adjacent to the P3 hydrophobic side chain further increases this positive cooperativity thereby improving the Ki by as much as 546-fold. In contrast, adding an amidine multiple H-bond/salt bridge group in the distal S1 pocket does not affect this cooperativity. An analysis of the crystallographic B-factors of the ligand groups inside the binding site indicates that the strong cooperativity is mainly due to a significant mutual reduction in the residual mobility of the hydrophobic side chain and the H-bonding functionalities that is absent when the separation distance is large. This type of cooperativity is important to encode in binding affinity prediction software, and to consider in SAR studies. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  7. Linear side chains in benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-c] pyrrole-4,6-dione polymers direct self-assembly and solar cell performance

    KAUST Repository

    Cabanetos, Clement

    2013-03-27

    While varying the size and branching of solubilizing side chains in π-conjugated polymers impacts their self-assembling properties in thin-film devices, these structural changes remain difficult to anticipate. This report emphasizes the determining role that linear side-chain substituents play in poly(benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers for bulk heterojunction (BHJ) solar cell applications. We show that replacing branched side chains by linear ones in the BDT motifs induces a critical change in polymer self-assembly and backbone orientation in thin films that correlates with a dramatic drop in solar cell efficiency. In contrast, we show that for polymers with branched alkyl-substituted BDT motifs, controlling the number of aliphatic carbons in the linear N-alkyl-substituted TPD motifs is a major contributor to improved material performance. With this approach, PBDTTPD polymers were found to reach power conversion efficiencies of 8.5% and open-circuit voltages of 0.97 V in BHJ devices with PC71BM, making PBDTTPD one of the best polymer donors for use in the high-band-gap cell of tandem solar cells. © 2013 American Chemical Society.

  8. Investigation of antidepressant-like and anxiolytic-like actions and cognitive and motor side effects of four N-methyl-D-aspartate receptor antagonists in mice

    DEFF Research Database (Denmark)

    Refsgaard, Louise Konradsen; Pickering, Darryl S; Andreasen T., Jesper

    2017-01-01

    antagonists. MK-801, ketamine, S-ketamine, RO 25-6981 and the positive control, citalopram, were tested for antidepressant-like and anxiolytic-like effects in mice using the forced-swim test, the elevated zero maze and the novelty-induced hypophagia test. Side effects were assessed using a locomotor activity...... test, the modified Y-maze and the rotarod test. All compounds increased swim distance in the forced-swim test. In the elevated zero maze, the GluN2B subtype-selective RO 25-6981 affected none of the measured parameters, whereas all other compounds showed anxiolytic-like effects. In the novelty......-induced hypophagia test, citalopram and MK-801 showed anxiogenic-like action. All NMDAR antagonists induced hyperactivity. The high doses of ketamine and MK-801 impaired performance in the modified Y-maze test, whereas S-ketamine and RO 25-6891 showed no effects in this test. Only MK-801 impaired rotarod performance...

  9. Reorientation of the Methyl Group in MAs(III) is the Rate-Limiting Step in the ArsM As(III) S-Adenosylmethionine Methyltransferase Reaction.

    Science.gov (United States)

    Packianathan, Charles; Li, Jiaojiao; Kandavelu, Palani; Sankaran, Banumathi; Rosen, Barry P

    2018-03-01

    The most common biotransformation of trivalent inorganic arsenic (As(III)) is methylation to mono-, di-, and trimethylated species. Methylation is catalyzed by As(III) S -adenosylmethionine (SAM) methyltransferase (termed ArsM in microbes and AS3MT in animals). Methylarsenite (MAs(III)) is both the product of the first methylation step and the substrate of the second methylation step. When the rate of the overall methylation reaction was determined with As(III) as the substrate, the first methylation step was rapid, whereas the second methylation step was slow. In contrast, when MAs(III) was used as the substrate, the rate of methylation was as fast as the first methylation step when As(III) was used as the substrate. These results indicate that there is a slow conformational change between the first and second methylation steps. The structure of CmArsM from the thermophilic alga Cyanidioschyzon merolae sp. 5508 was determined with bound MAs(III) at 2.27 Å resolution. The methyl group is facing the solvent, as would be expected when MAs(III) is bound as the substrate rather than facing the SAM-binding site, as would be expected for MAs(III) as a product. We propose that the rate-limiting step in arsenic methylation is slow reorientation of the methyl group from the SAM-binding site to the solvent, which is linked to the conformation of the side chain of a conserved residue Tyr70.

  10. (E-2-Methyl-6-{[(5-methylpyridin-2-ylimino]methyl}phenol

    Directory of Open Access Journals (Sweden)

    Md. Azharul Arafath

    2017-01-01

    Full Text Available In the title compound, C14H14N2O, the dihedral angle between the aromatic rings is 5.54 (9°. The conformation is reinforced by an intramolecular O—H...N hydrogen bond, which closes an S(6 ring. The pyridine N atom and methyl group lie to opposite sides of the molecule. In the crystal, the molecules are linked into a zigzag chain propagating in [0-11] by weak C—H...O hydrogen bonds.

  11. Side Effects

    Science.gov (United States)

    Side effects are problems that occur when cancer treatment affects healthy tissues or organs. Learn about side effects caused by cancer treatment. Know what signs and symptoms to call your doctor about. Learn about treatments for side effects.

  12. Pronounced Side Chain Effects in Triple Bond-Conjugated Polymers Containing Naphthalene Diimides for n-Channel Organic Field-Effect Transistors

    KAUST Repository

    Nam, Sungho; Hahm, Suk Gyu; Khim, Dongyoon; Kim, Hwajeong; Sajoto, Tissa; Ree, Moonhor; Marder, Seth R.; Anthopoulos, Thomas D.; Bradley, Donal D.C.; Kim, Youngkyoo

    2018-01-01

    on the surface morphology/nanostructure, thus playing a critical role in charge-transporting properties of the three NDI-based copolymers. Among the polymers, the one with an octyldodecyl (OD) chain at the nitrogen atoms of imide ring and a hexadecyloxy (HO

  13. Clinical Significance of IGFBP-3 Methylation in Patients with Early Stage Gastric Cancer

    Directory of Open Access Journals (Sweden)

    Seung Tae Kim

    2015-08-01

    Full Text Available BACKGROUND: IGFBP-3 is a multifunctional protein that inhibits growth and induces apoptosis of cancer cells. Hypermethylation of the promoter represses expression of the IGFBP-3 gene. We undertook this study to assess the impact of IGFBP-3 methylation on survival of early stage gastric cancer patients. METHODS: Of the 482 tissue samples from gastric cancer patients who underwent curative surgery, IGFBP-3 methylation was tested in 138 patients with stage IB/II gastric cancer. We also analyzed IGFBP-3 methylation in 26 gastric cancer cell lines. IGFBP-3 methylation was evaluated by methylation-specific polymerase chain reaction (MethyLight. Statistical analyses, all two-sided, were performed to investigate the prognostic effects of methylation status of the IGFBP-3 promoter on various clinical parameters. RESULTS: Hypermethylation of IGFBP-3 was observed in 26 (19% of the 138 stage IB/II gastric cancer patients. Clinicopathological factors such as age, Lauren classification, sex, tumor infiltration, lymph node metastasis, and histologic grade did not show a statistically significant association with the methylation status of the IGFBP-3 promoter. Patients with a hypermethylated IGFBP-3 promoter had similar 8-year disease-free survival compared with those without a hypermethylated IGFBP-3 promoter (73% vs 75%, P = .78. In subgroup analyses, females, but not males, seemed to have poorer prognosis for DFS and OS in the subset of patients with IGFBP-3 methylation as compared with those without IGFBP-3 methylation (8-year DFS: 55.6% vs 71.6%, P = .3694 and 8-year overall survival: 55.6% vs 68.4%, P = .491, respectively even with no statistical significance. CONCLUSIONS: The status of IGFBP-3 methylation as measured by methylation-specific polymerase chain reaction proposed the modest role for predicting survival in specific subgroups of patients with early-stage gastric cancer who undergo curative surgery. However, this needs further investigation.

  14. Studies on the O-polysaccharide of Escherichia albertii O2 characterized by non-stoichiometric O-acetylation and non-stoichiometric side-chain l-fucosylation.

    Science.gov (United States)

    Naumenko, Olesya I; Zheng, Han; Xiong, Yanwen; Senchenkova, Sof'ya N; Wang, Hong; Shashkov, Alexander S; Li, Qun; Wang, Jianping; Knirel, Yuriy A

    2018-05-22

    An O-polysaccharide was isolated from the lipopolysaccharide of Escherichia albertii O2 and studied by chemical methods and 1D and 2D 1 H and 13 C NMR spectroscopy. The following structure of the O-polysaccharide was established: . The O-polysaccharide is characterized by masked regularity owing to a non-stoichiometric O-acetylation of an l-fucose residue in the main chain and a non-stoichiometric side-chain l-fucosylation of a β-GlcNAc residue. A regular linear polysaccharide was obtained by sequential Smith degradation and alkaline O-deacetylation of the O-polysaccharide. The content of the O-antigen gene cluster of E. albertii O2 was found to be essentially consistent with the O-polysaccharide structure established. Copyright © 2018 Elsevier Ltd. All rights reserved.

  15. Structure activity correlations in the inhibition of brain synaptosomal 3H-norepinephrine uptake by phenethylamine analogs. The role of α-alkyl side chain and methoxyl ring substitutions

    International Nuclear Information System (INIS)

    Makriyannis, A.; Bowerman, D.; Sze, P.Y.; Fournier, D.; Jong, A.P. de

    1982-01-01

    α-Ethylphenethylamine proved to be a weaker inhibitor of rat brain synaptosomal [ 3 H]norepinephrine ([ 3 H]NE) uptake than amphetamine, while 2-amino-tetralin and 2-amino-1,2-dihydronaphtalene, compounds in which the α-side chain ethyl group is tied to the aromatic ring have a similar inhibiting potency as amphetamine. Hallucinogenic polymethoxy substituted phenethylamine analogs have very low inhibitory potencies indicating that inhibition of NE-reuptake in brain noradrenergic neurons is not associated with the drug-induced hallucinogenic syndrome. (Auth.)

  16. Property-based design and synthesis of new chloroquine hybrids via simple incorporation of 2-imino-thiazolidine-4-one or 1h-pyrrol-2, 5-dione fragments on the 4-amino-7-chloroquinoline side chain

    International Nuclear Information System (INIS)

    Rojas, Fernando A.; Kouznetsov, Vladimir V.

    2011-01-01

    In the present work, the syntheses of new 4-amino-7-chloroquinoline N-derivatives were performed by selective modification of the side chain amino group of N-(7-chloroquinoline-4-yl) alkyldiamines, basis framework of chloroquine (CQ) drug through the incorporation of heterocyclic 2-imino-thiazolidine-4-one and 1 H-pyrrol-2,5-dione systems. These potential activity modulators were selected thanks to their characteristic properties, and evaluated by virtual screening employing the OSIRIS and Molinspirations platforms. Designed and synthesized quinolinic derivatives could increase the antimalarial activity of CQ analogues without affecting the lipophilicity as described in literature, suggesting them as candidates for further biological assessments. (author)

  17. Property-based design and synthesis of new chloroquine hybrids via simple incorporation of 2-imino-thiazolidine-4-one or 1h-pyrrol-2, 5-dione fragments on the 4-amino-7-chloroquinoline side chain

    Energy Technology Data Exchange (ETDEWEB)

    Rojas, Fernando A; Kouznetsov, Vladimir V., E-mail: kouznet@uis.edu.co [Laboratorio de Quimica Organica y Biomolecular, Escuela de Quimica, Universidad Industrial de Santander, Bucaramanga (Colombia)

    2011-09-15

    In the present work, the syntheses of new 4-amino-7-chloroquinoline N-derivatives were performed by selective modification of the side chain amino group of N-(7-chloroquinoline-4-yl) alkyldiamines, basis framework of chloroquine (CQ) drug through the incorporation of heterocyclic 2-imino-thiazolidine-4-one and {sup 1}H-pyrrol-2,5-dione systems. These potential activity modulators were selected thanks to their characteristic properties, and evaluated by virtual screening employing the OSIRIS and Molinspirations platforms. Designed and synthesized quinolinic derivatives could increase the antimalarial activity of CQ analogues without affecting the lipophilicity as described in literature, suggesting them as candidates for further biological assessments. (author)

  18. Chemical Kinetic Influences of Alkyl Chain Structure on the High Pressure and Temperature Oxidation of a Representative Unsaturated Biodiesel: Methyl Nonenoate.

    Science.gov (United States)

    Fridlyand, Aleksandr; Goldsborough, S Scott; Brezinsky, Kenneth

    2015-07-16

    The high pressure and temperature oxidation of methyl trans-2-nonenoate, methyl trans-3-nonenoate, 1-octene, and trans-2-octene are investigated experimentally to probe the influence of the double bond position on the chemical kinetics of long esters and alkenes. Single pulse shock tube experiments are performed in the ranges p = 3.8-6.2 MPa and T = 850-1500 K, with an average reaction time of 2 ms. Gas chromatographic measurements indicate increased reactivity for trans-2-octene compared to 1-octene, whereas both methyl nonenoate isomers have reactivities similar to that of 1-octene. A difference in the yield of stable intermediates is observed for the octenes when compared to the methyl nonenoates. Chemical kinetic models are developed with the aid of the Reaction Mechanism Generator to interpret the experimental results. The models are created using two different base chemistry submodels to investigate the influence of the foundational chemistry (i.e., C0-C4), whereas Monte Carlo simulations are performed to examine the quality of agreement with the experimental results. Significant uncertainties are found in the chemistry of unsaturated esters with the double bonds located close to the ester groups. This work highlights the importance of the foundational chemistry in predictive chemical kinetics of biodiesel combustion at engine relevant conditions.

  19. Methylobacterium extorquens AM1 produces a novel type of acyl-homoserine lactone with a double unsaturated side chain under methylotrophic growth conditions.

    Science.gov (United States)

    Nieto Penalver, Carlos G; Morin, Danièle; Cantet, Franck; Saurel, Olivier; Milon, Alain; Vorholt, Julia A

    2006-01-23

    Acyl-homoserine lactones (acyl-HSLs) have emerged as important regulatory molecules for many gram-negative bacteria. We have found that Methylobacterium extorquens AM1, a member of the pink-pigmented facultative methylotrophs commonly present on plant surfaces, produces several acyl-HSLs depending upon the carbon source. A novel HSL was discovered with a double unsaturated carbon chain (N-(tetradecenoyl)) (C14:2) and characterized by MS and proton NMR. This long-chain acyl-HSL is synthesized by MlaI that also directs synthesis of C14:1-HSL. The Alphaproteobacterium also produces N-hexanoyl-HSL (C6-HSL) and N-octanoyl-HSL (C8-HSL) via MsaI.

  20. Selectively deuterated liquid crystalline cyanoazobenzene side-chain polyesters. 3. Investigations of laser induced segmental mobility by Fourier transform infrared spectroscopy

    DEFF Research Database (Denmark)

    Kulinna, Christian; Hvilsted, Søren; Hendann, Claudia

    1998-01-01

    The laser-induced anisotropy in thin films of an extensive number of cyanoazobenzene sidechain liquid crystalline polytetradecanedioates, -dodecanedioates, and -adipates selectively deuterated at different positions have been investigated with polarized FTIR spectroscopy. The analysis of the segm......The laser-induced anisotropy in thin films of an extensive number of cyanoazobenzene sidechain liquid crystalline polytetradecanedioates, -dodecanedioates, and -adipates selectively deuterated at different positions have been investigated with polarized FTIR spectroscopy. The analysis...... of the segmental orientation based on dichroic ratios of characteristic absorption bands shows that, in polyesters with long main-chain spacing (tetradecanedioates and dodecanedioates), not only the light sensitive azo chromophore but also the main-chain methylene segment and to a smaller extent the flexible...

  1. Nuclear magnetic resonance studies of amino acids and proteins. Side-chain mobility of methionine in the crystalline amonio acid and in crystallne sperm whale (Physeter catodon) myoglobin

    International Nuclear Information System (INIS)

    Keniry, M.A.; Rothgeb, T.M.; Smith, R.L.; Gutowsky, H.S.; Oldfield, E.

    1983-01-01

    Deuterium ( 2 H) nuclear magnetic resonance (NMR) spectra and spin-lattice relaxation times (T 1 ) were obtained of L-[epsilon- 2 H 3 ]methionine, L-[epsilon- 2 H 3 ]methionine in a D,L lattice, and [S-methyl- 2 H 3 ]methionine in the crystalline solid state, as a function of temperature, in addition to obtaining 2 H T 1 and line-width results as a function of temperature on [epsilon- 2 H 3 ]methionine-labeled sperm whale (Physeter catodon) myoglobins by using the method of magnetic ordering. Also recorded were 13 C cross-polarization ''magic-angle'' sample-spinning NMR spectra of [epsilon- 13 C]methionine-labeled crystalline cyanoferrimyoglobin (at 37.7 MHz, corresponding to a magnetic field strength of 3.52 T) and of the same protein in aqueous solution

  2. O6-Methylguanine-DNA methyltransferase protein expression by immunohistochemistry in brain and non-brain systemic tumours: systematic review and meta-analysis of correlation with methylation-specific polymerase chain reaction

    International Nuclear Information System (INIS)

    Brell, Marta; Ibáñez, Javier; Tortosa, Avelina

    2011-01-01

    The DNA repair protein O 6 -Methylguanine-DNA methyltransferase (MGMT) confers resistance to alkylating agents. Several methods have been applied to its analysis, with methylation-specific polymerase chain reaction (MSP) the most commonly used for promoter methylation study, while immunohistochemistry (IHC) has become the most frequently used for the detection of MGMT protein expression. Agreement on the best and most reliable technique for evaluating MGMT status remains unsettled. The aim of this study was to perform a systematic review and meta-analysis of the correlation between IHC and MSP. A computer-aided search of MEDLINE (1950-October 2009), EBSCO (1966-October 2009) and EMBASE (1974-October 2009) was performed for relevant publications. Studies meeting inclusion criteria were those comparing MGMT protein expression by IHC with MGMT promoter methylation by MSP in the same cohort of patients. Methodological quality was assessed by using the QUADAS and STARD instruments. Previously published guidelines were followed for meta-analysis performance. Of 254 studies identified as eligible for full-text review, 52 (20.5%) met the inclusion criteria. The review showed that results of MGMT protein expression by IHC are not in close agreement with those obtained with MSP. Moreover, type of tumour (primary brain tumour vs others) was an independent covariate of accuracy estimates in the meta-regression analysis beyond the cut-off value. Protein expression assessed by IHC alone fails to reflect the promoter methylation status of MGMT. Thus, in attempts at clinical diagnosis the two methods seem to select different groups of patients and should not be used interchangeably

  3. O6-Methylguanine-DNA methyltransferase protein expression by immunohistochemistry in brain and non-brain systemic tumours: systematic review and meta-analysis of correlation with methylation-specific polymerase chain reaction

    Directory of Open Access Journals (Sweden)

    Ibáñez Javier

    2011-01-01

    Full Text Available Abstract Background The DNA repair protein O6-Methylguanine-DNA methyltransferase (MGMT confers resistance to alkylating agents. Several methods have been applied to its analysis, with methylation-specific polymerase chain reaction (MSP the most commonly used for promoter methylation study, while immunohistochemistry (IHC has become the most frequently used for the detection of MGMT protein expression. Agreement on the best and most reliable technique for evaluating MGMT status remains unsettled. The aim of this study was to perform a systematic review and meta-analysis of the correlation between IHC and MSP. Methods A computer-aided search of MEDLINE (1950-October 2009, EBSCO (1966-October 2009 and EMBASE (1974-October 2009 was performed for relevant publications. Studies meeting inclusion criteria were those comparing MGMT protein expression by IHC with MGMT promoter methylation by MSP in the same cohort of patients. Methodological quality was assessed by using the QUADAS and STARD instruments. Previously published guidelines were followed for meta-analysis performance. Results Of 254 studies identified as eligible for full-text review, 52 (20.5% met the inclusion criteria. The review showed that results of MGMT protein expression by IHC are not in close agreement with those obtained with MSP. Moreover, type of tumour (primary brain tumour vs others was an independent covariate of accuracy estimates in the meta-regression analysis beyond the cut-off value. Conclusions Protein expression assessed by IHC alone fails to reflect the promoter methylation status of MGMT. Thus, in attempts at clinical diagnosis the two methods seem to select different groups of patients and should not be used interchangeably.

  4. Density functional theory study of silodithiophene thiophenepyrrolopyrroledion-based small molecules: The effect of alkyl side chain length in electron donor materials

    Energy Technology Data Exchange (ETDEWEB)

    Seo, Dong Kyun; Yeo, Hak; Kwak, Kyung Won [Dept. of Chemistry, Chung-Ang University, Seoul (Korea, Republic of); Yoon, Young Woon; Kim, Bong Soo [Photo-electronic Hybrids Research Center, Korea Institute of Science and Technology, Seoul (Korea, Republic of); Lee, Kyung Koo [Dept. of Chemistry, Kunsan National University, Gunsan (Korea, Republic of)

    2015-02-15

    Push–pull small molecules are promising electron-donor materials for organic solar cells. Thus, precise prediction of their electronic structures is of paramount importance to control the optical and electrical properties of the solar cells. Various types of alkyl chains are usually introduced to increase solubility and modify the morphology of the resulting molecular films. Here, using density functional theory (DFT) and time-dependent DFT (TD-DFT), we report the precise effect of increasing the length of the alkyl chain on the electronic structure of an electron donor molecule 6,60-((4,4-dialkyl-4H-silolo[3,2-b:4,5-b′]-dithiophene-2,6-diyl) bis(thiophene-5,2-diyl))bis(2,5-alkyl-3-(thiophen-2-yl) -2,5-dihydropyrrolo[3,4-c]pyrrole-1,4-dione) (DTS1TDPP). Alkyl groups were attached to the bridging position (silicon atom) of the fused rings and nitrogen atom of the pyrrolopyrroledione groups. We demonstrate that the alkyl groups do not perturb the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels, π-delocalized backbone structure, and UV–Vis absorption spectrum when they are placed at the least steric effect positions.

  5. (1)H, (13)C, (15)N backbone and side-chain resonance assignment of Nostoc sp. C139A variant of the heme-nitric oxide/oxygen binding (H-NOX) domain.

    Science.gov (United States)

    Alexandropoulos, Ioannis I; Argyriou, Aikaterini I; Marousis, Kostas D; Topouzis, Stavros; Papapetropoulos, Andreas; Spyroulias, Georgios A

    2016-10-01

    The H-NOX (Heme-nitric oxide/oxygen binding) domain is conserved across eukaryotes and bacteria. In human soluble guanylyl cyclase (sGC) the H-NOX domain functions as a sensor for the gaseous signaling agent nitric oxide (NO). sGC contains the heme-binding H-NOX domain at its N-terminus, which regulates the catalytic site contained within the C-terminal end of the enzyme catalyzing the conversion of GTP (guanosine 5'-triphosphate) to GMP (guanylyl monophosphate). Here, we present the backbone and side-chain assignments of the (1)H, (13)C and (15)N resonances of the 183-residue H-NOX domain from Nostoc sp. through solution NMR.

  6. ¹H, ¹³C, and ¹⁵N backbone and side-chain chemical shift assignment of the toxin Doc in the unbound state.

    Science.gov (United States)

    De Gieter, Steven; Loris, Remy; van Nuland, Nico A J; Garcia-Pino, Abel

    2014-04-01

    Toxin-antitoxin (TA) modules in bacteria are involved in pathogenesis, antibiotic stress response, persister formation and programmed cell death. The toxin Doc, from the phd/doc module, blocks protein synthesis by targeting the translation machinery. Despite a large wealth of biophysical and biochemical data on the regulatory aspects of the operon transcription and role of Doc co-activator and co-repressor, little is still know on the molecular basis of Doc toxicity. Structural information about this toxin is only available for its inhibited state bound to the antitoxin Phd. Here we report the (1)H, (15)N and (13)C backbone and side chain chemical shift assignments of the toxin Doc from of bacteriophage P1 (the model protein from this family of TA modules) in its free state. The BMRB accession number is 18899.

  7. Reactivity of lignin with different composition of aromatic syringyl/guaiacyl structures and erythro/threo side chain structures in β-O-4 type during alkaline delignification: as a basis for the different degradability of hardwood and softwood lignin.

    Science.gov (United States)

    Shimizu, Satoko; Yokoyama, Tomoya; Akiyama, Takuya; Matsumoto, Yuji

    2012-07-04

    The reactivity of lignin during alkaline delignification was quantitatively investigated focusing on the effect of the structural differences between syringyl and guaiacyl aromatic nuclei and between erythro and threo in the side chain of β-O-4 type lignin substructure on the β-O-4 bond cleavage rate. It was known that the ratio of this reaction rate of the erythro to threo isomers of the dimeric β-O-4 type lignin model compound with two guaiacyl aromatic nuclei was ca. 4. However, the presence of a syringyl nucleus strongly influenced the rate, and the ratio of the syringyl type analogue was in the range between 2.7 and 8.0 depending on the reaction temperature. The effect of syringyl nucleus on the enhancement of the reaction rate appeared to be greater when the syringyl nucleus consists of the cleaving ether bond rather than being a member of the carbon framework.

  8. Side-chain dynamics of a detergent-solubilized membrane protein: Measurement of tryptophan and glutamine hydrogen-exchange rates in M13 coat protein by 1H NMR spectroscopy

    International Nuclear Information System (INIS)

    O'Neil, J.D.J.; Sykes, B.D.

    1989-01-01

    M13 coat protein is a small (50 amino acids) lipid-soluble protein that becomes an integral membrane protein during the infection stage of the life cycle of the M13 phage and is therefore used as a model membrane protein. To study side-chain dynamics in the protein, the authors have measured individual hydrogen-exchange rates for a primary amide in the side chain of glutamine-15 and for the indole amine of tryptophan-26. The protein was solubilized with the use of perdeuteriated sodium dodecyl sulfate (SDS), and hydrogen-exchange rates were measured by using 1 H nuclear magnetic resonance spectroscopy. The glutamine-15 syn proton exchanged at a rate identical with that in glutamine model peptides except that the pH corresponding to minimum exchange was elevated by about 1.5 pH units. The tryptophan-26 indole amine proton exchange was biphasic, suggesting that two populations of tryptophan-26 exist. It is suggested that the two populations may reflect protein dimerization or aggregation in the SDS micelles. The pH values of minimum exchange for tryptophan-26 in both environments were also elevated by 1.3-1.9 pH units. This phenomenon is reproduced when small tryptophan- and glutamine-containing hydrophobic peptides are dissolved in the presence of SDS micelles. The electrostatic nature of this phenomenon is proven by showing that the minimum pH for exchange can be reduced by dissolving the hydrophobic peptides in the positively charged detergent micelle dodecyltrimethylammonium bromide

  9. Comparing Demand Side Management approaches

    NARCIS (Netherlands)

    Molderink, Albert; Bakker, Vincent; Hurink, Johann L.; Smit, Gerardus Johannes Maria

    2012-01-01

    Due to increasing energy prices and the greenhouse effect, a more efficient energy supply is desirable, preferably based on renewable sources. To cope with the decrease of flexibility due to the introduction of renewables in production side of the supply chain, a more flexible consumer side is

  10. 2-Acetyl-amino-1,3,4,6-tetra-O-(tri-methyl-silyl)-2-de-oxy-α-d-gluco-pyran-ose.

    Science.gov (United States)

    Cheng, Zhao-Dong; Cui, Yan-Li; Mao, Jian-Wei

    2013-06-01

    The title compound, C20H47NO6Si4, was synthesized by per-O-tri-methyl-silylation of N-acetyl-d-glucosa-mine using chloro-tri-methyl-silane in the presence of hexa-methyl-disiloxane. The tri-methyl-silyl group and acetamido group are located on the same side of the pyran ring, showing an α-configuration glycoside. One of the tri-methyl-silyl groups is disordered over two orientations, with site-occupancy factors of 0.625 (9) and 0.375 (9). In the crystal, N-H⋯O hydrogen bonds link the mol-ecules into supra-molecular chains along the a-axis direction.

  11. Uniformity of Peptide Release Is Maintained by Methylation of Release Factors

    Directory of Open Access Journals (Sweden)

    William E. Pierson

    2016-09-01

    Full Text Available Termination of protein synthesis on the ribosome is catalyzed by release factors (RFs, which share a conserved glycine-glycine-glutamine (GGQ motif. The glutamine residue is methylated in vivo, but a mechanistic understanding of its contribution to hydrolysis is lacking. Here, we show that the modification, apart from increasing the overall rate of termination on all dipeptides, substantially increases the rate of peptide release on a subset of amino acids. In the presence of unmethylated RFs, we measure rates of hydrolysis that are exceptionally slow on proline and glycine residues and approximately two orders of magnitude faster in the presence of the methylated factors. Structures of 70S ribosomes bound to methylated RF1 and RF2 reveal that the glutamine side-chain methylation packs against 23S rRNA nucleotide 2451, stabilizing the GGQ motif and placing the side-chain amide of the glutamine toward tRNA. These data provide a framework for understanding how release factor modifications impact termination.

  12. Mutations blocking side chain assembly, polymerization, or transport of a Wzy-dependent Streptococcus pneumoniae capsule are lethal in the absence of suppressor mutations and can affect polymer transfer to the cell wall.

    Science.gov (United States)

    Xayarath, Bobbi; Yother, Janet

    2007-05-01

    Extracellular polysaccharides of many bacteria are synthesized by the Wzy polymerase-dependent mechanism, where long-chain polymers are assembled from undecaprenyl-phosphate-linked repeat units on the outer face of the cytoplasmic membrane. In gram-positive bacteria, Wzy-dependent capsules remain largely cell associated via membrane and peptidoglycan linkages. Like many Wzy-dependent capsules, the Streptococcus pneumoniae serotype 2 capsule is branched. In this study, we found that deletions of cps2K, cps2J, or cps2H, which encode a UDP-glucose dehydrogenase necessary for side chain synthesis, the putative Wzx transporter (flippase), and the putative Wzy polymerase, respectively, were obtained only in the presence of suppressor mutations. Most of the suppressor mutations were in cps2E, which encodes the initiating glycosyltransferase for capsule synthesis. The cps2K mutants containing the suppressor mutations produced low levels of high-molecular-weight polymer that was detected only in membrane fractions. cps2K-repaired mutants exhibited only modest increases in capsule production due to the effect of the secondary mutation, but capsule was detectable in both membrane and cell wall fractions. Lethality of the cps2K, cps2J, and cps2H mutations was likely due to sequestration of undecaprenyl-phosphate in the capsule pathway and either preclusion of its turnover for utilization in essential pathways or destabilization of the membrane due to an accumulation of lipid-linked intermediates. The results demonstrate that proper polymer assembly requires not only a functional transporter and polymerase but also complete repeat units. A central role for the initiating glycosyltransferase in controlling capsule synthesis is also suggested.

  13. Thermal Properties of Methyl Ester-Containing Poly(2-oxazolines

    Directory of Open Access Journals (Sweden)

    Petra J. M. Bouten

    2015-10-01

    Full Text Available This paper describes the synthesis and thermal properties in solution and bulk of poly(2-alkyl-oxazolines (PAOx containing a methyl ester side chain. Homopolymers of 2-methoxycarbonylethyl-2-oxazoline (MestOx and 2-methoxycarbonylpropyl-2-oxazoline (C3MestOx, as well as copolymers with 2-ethyl-2-oxazoline (EtOx and 2-n-propyl-2-oxazoline (nPropOx, with systematic variations in composition were prepared. The investigation of the solution properties of these polymers revealed that the cloud point temperatures (TCPs could be tuned in between 24 °C and 108 °C by variation of the PAOx composition. To the best of our knowledge, the TCPs of PMestOx and PC3MestOx are reported for the first time and they closely resemble the TCPs of PEtOx and PnPropOx, respectively, indicating similar hydrophilicity of the methyl ester and alkyl side chains. Furthermore, the thermal transitions and thermal stability of these polymers were investigated by DSC and TGA measurements, respectively, revealing amorphous polymers with glass transition temperatures between -1 °C and 54 °C that are thermally stable up to >300 °C.

  14. Chemical structure of chromium(III) crosslinked collagen-poly(methyl methacrylate) copolymers in radiation grafting

    International Nuclear Information System (INIS)

    Pietrucha, K.

    1991-01-01

    Upon γ-irradiation of aqueous emulsions of methyl methacrylate embedded into chrome tanned skin, the formation of graft copolymers is observed. The number-average molecular weight of the grafted poly(methyl methacrylate) side chains was in the range of 430000 (for a dose of 10 kGy) and practically independent of grafting degree. However, the number of branches per graft copolymer molecule increases from 0.3 to 0.8 when the degree of grafting increases from 32% to 88%. Similarly, the radiation yield, i.e. the number of branches formed per 100 eV of energy absorbed in the substrate polymer increases from 0.75 to 1.94. The value and meaning of molecular weight of graft copolymer is discussed along with the mechanism of polymer chain termination. (author) 14 refs.; 3 figs.; 4 tabs

  15. Melanocortin tetrapeptide Ac-His-DPhe-Arg-Trp-NH2 modified at the para position of the benzyl side chain (DPhe): importance for mouse melanocortin-3 receptor agonist versus antagonist activity.

    Science.gov (United States)

    Proneth, Bettina; Pogozheva, Irina D; Portillo, Federico P; Mosberg, Henry I; Haskell-Luevano, Carrie

    2008-09-25

    The melanocortin-3 and -4 receptors (MC3R, MC4R) have been implicated in energy homeostasis and obesity. Whereas the physiological role of the MC4R is extensively studied, little is known about the MC3R. One caveat is the limited availability of ligands that are selective for the MC3R. Previous studies identified Ac-His-DPhe(p-I)-Arg-Trp-NH 2, which possessed partial agonist/antagonist pharmacology at the mMC3R while retaining full nanomolar agonist pharmacology at the mMC4R. These data allowed for the hypothesis that the DPhe position in melanocortin tetrapeptides can be used to examine ligand side-chain determinants important for differentiation of mMC3R agonist versus antagonist activity. A series of 15 DPhe (7) modified Ac-His-DPhe (7)-Arg-Trp-NH 2 tetrapeptides has been synthesized and pharmacologically characterized. Most notable results include the identification of modifications that resulted in potent antagonists/partial agonists at the mMC3R and full, potent agonists at the mMC4R. These SAR studies provide experimental evidence that the molecular mechanism of antagonism at the mMC3R differentiates this subtype from the mMC4R.

  16. Improvement in the mechanical properties, proton conductivity, and methanol resistance of highly branched sulfonated poly(arylene ether)/graphene oxide grafted with flexible alkylsulfonated side chains nanocomposite membranes

    Science.gov (United States)

    Liu, Dong; Peng, Jinhua; Li, Zhuoyao; Liu, Bin; Wang, Lei

    2018-02-01

    Sulfonated polymer/graphene oxide (GO) nanocomposites exhibit excellent properties as proton exchange membranes. However, few investigations on highly branched sulfonated poly(arylene ether)s (HBSPE)/GO nanocomposites as proton exchange membranes are reported. In order to obtain HBSPE-based nanocomposite membranes with better dispersibility and properties, a novel GO containing flexible alkylsulfonated side chains (SGO) is designed and prepared for the first time in this work. The HBSPE/SGO nanocomposite membranes with excellent dispersibility are successfully prepared. The properties of these membranes, including the mechanical properties, ion-exchange capacity, water uptake, proton conductivity, and methanol resistance, are characterized. The nanocomposite membranes exhibit higher tensile strength (32.67 MPa), higher proton conductivity (0.39 S cm-1 at 80 °C) and lower methanol permeability (4.89 × 10-7 cm2 s-1) than the pristine membrane. The nanocomposite membranes also achieve a higher maximum power density (82.36 mW cm-2) than the pristine membrane (67.85 mW cm-2) in single-cell direct methanol fuel cell (DMFC) tests, demonstrating their considerable potential for applications in DMFCs.

  17. 2-Acetyl­amino-1,3,4,6-tetra-O-(tri­methyl­silyl)-2-de­oxy-α-d-gluco­pyran­ose

    Science.gov (United States)

    Cheng, Zhao-Dong; Cui, Yan-Li; Mao, Jian-Wei

    2013-01-01

    The title compound, C20H47NO6Si4, was synthesized by per-O-tri­methyl­silylation of N-acetyl-d-glucosa­mine using chloro­tri­methyl­silane in the presence of hexa­methyl­disiloxane. The tri­methyl­silyl group and acetamido group are located on the same side of the pyran ring, showing an α-configuration glycoside. One of the tri­methyl­silyl groups is disordered over two orientations, with site-occupancy factors of 0.625 (9) and 0.375 (9). In the crystal, N—H⋯O hydrogen bonds link the mol­ecules into supra­molecular chains along the a-axis direction. PMID:23795087

  18. Clinical Utility of promoter methylation of the tumor suppressor ...

    African Journals Online (AJOL)

    Aim: Aim is to examine the potential usefulness of blood based methylation specific polymerase chain reaction (MSP) of methylated DKK3 and RASSF1A genes in early detection of breast cancer. Method: Methylation status of DKK3 and RASSF1 was investigated in forty breast cancer patients, twenty fibroadenoma patients ...

  19. (¹⁵N ± ¹³C') edited (4, 3)D-H(CC)CONH TOCSY and (4, 3)D-NOESY HNCO experiments for unambiguous side chain and NOE assignments of proteins with high shift degeneracy.

    Science.gov (United States)

    Kumar, Dinesh; Arora, Ashish

    2011-11-01

    Well-resolved and unambiguous through-bond correlations and NOE data are crucial for high-quality protein structure determination by NMR. In this context, we present here (4, 3)D reduced dimensionality (RD) experiments: H(CC)CONH TOCSY and NOESY HNCO--which instead of (15)N shifts exploit the linear combination of (15)N(i) and (13)C'(i-1) shifts (where i is a residue number) to resolve the through-bond (1)H-(1)H correlations and through-space (1)H-(1)H NOEs. The strategy makes use of the fact that (15)N and (13)C' chemical shifts when combined linearly provide a dispersion which is better compared to those of the individual chemical shifts. The extended dispersion thus available in these experiments will help to obtain the unambiguous side chain and accurate NOE assignments especially for medium-sized alpha-helical or partially unstructured proteins [molecular weight (MW) between 12-15 kDa] as well as higher MW (between 15-25 kDa) folded proteins where spectral overlap renders inaccurate and ambiguous NOEs. Further, these reduced dimensionality experiments in combination with routinely used (15)N and (13)C' edited TOCSY and NOESY experiments will provide an alternative way for high-quality NMR structure determination of large unstable proteins (with very high shift degeneracy), which are not at all amenable to 4D NMR. The utility of these experiments has been demonstrated here using (13)C/(15)N labeled ubiquitin (76 aa) protein. Copyright © 2011 John Wiley & Sons, Ltd.

  20. Overexpression of the steroidogenic enzyme cytochrome P450 side chain cleavage in the ventral tegmental area increases 3α,5α-THP and reduces long-term operant ethanol self-administration.

    Science.gov (United States)

    Cook, Jason B; Werner, David F; Maldonado-Devincci, Antoniette M; Leonard, Maggie N; Fisher, Kristen R; O'Buckley, Todd K; Porcu, Patrizia; McCown, Thomas J; Besheer, Joyce; Hodge, Clyde W; Morrow, A Leslie

    2014-04-23

    Neuroactive steroids are endogenous neuromodulators capable of altering neuronal activity and behavior. In rodents, systemic administration of endogenous or synthetic neuroactive steroids reduces ethanol self-administration. We hypothesized this effect arises from actions within mesolimbic brain regions that we targeted by viral gene delivery. Cytochrome P450 side chain cleavage (P450scc) converts cholesterol to pregnenolone, the rate-limiting enzymatic reaction in neurosteroidogenesis. Therefore, we constructed a recombinant adeno-associated serotype 2 viral vector (rAAV2), which drives P450scc expression and neuroactive steroid synthesis. The P450scc-expressing vector (rAAV2-P450scc) or control GFP-expressing vector (rAAV2-GFP) were injected bilaterally into the ventral tegmental area (VTA) or nucleus accumbens (NAc) of alcohol preferring (P) rats trained to self-administer ethanol. P450scc overexpression in the VTA significantly reduced ethanol self-administration by 20% over the 3 week test period. P450scc overexpression in the NAc, however, did not alter ethanol self-administration. Locomotor activity was unaltered by vector administration to either region. P450scc overexpression produced a 36% increase in (3α,5α)-3-hydroxypregnan-20-one (3α,5α-THP, allopregnanolone)-positive cells in the VTA, but did not increase 3α,5α-THP immunoreactivity in NAc. These results suggest that P450scc overexpression and the resultant increase of 3α,5α-THP-positive cells in the VTA reduces ethanol reinforcement. 3α,5α-THP is localized to neurons in the VTA, including tyrosine hydroxylase neurons, but not astrocytes. Overall, the results demonstrate that using gene delivery to modulate neuroactive steroids shows promise for examining the neuronal mechanisms of moderate ethanol drinking, which could be extended to other behavioral paradigms and neuropsychiatric pathology.

  1. 1H NMR study of effects of synergistic anion and metal ion binding on pH titration of the histidinyl side-chain residues of the half-molecules of ovotransferrin

    International Nuclear Information System (INIS)

    Woodworth, R.C.; Butcher, N.D.; Brown, S.A.; Brown-Mason, A.

    1987-01-01

    Separation of ovotransferrin into C-terminal (OTf/2C) and N-terminal (OTf/2N) half-molecules has made possible the resolution of all expected histidinyl C(2)H resonances by proton nuclear magnetic resonance at 250 MHz. The chemical shift of many of the resonances decreases with increasing pH, allowing construction of titration curves, whereas a few resonances fail to titrate. On formation of the Ga/sup III/OTf/2(C 2 O 4 ) ternary complexes, two of the low-field C(2)H resonances in each half-molecule fail to titrate. This behavior implicates the imidazole groups giving rise to these resonances as ligands to the bound metal ion. A third C(2)H resonance in each half-molecule undergoes a marked reduction in pK'/sub a/ on formation of the ternary complex. The imidazole group displaying this resonance is implicated in a proton-relay scheme involved in binding the synergistic anion, oxalate, and a water of hydration on the bound metal ion. The titration curves for the various imidazole resonances have been fit to a four-parameter equation involving estimation of the pK'/sub a/, the limiting chemical shift values, and a Hill constant n. Hill constants of 1, which suggests positive cooperativity in the titration of this residue. The basis for this behavior cannot be rationalized at this time. 13 C NMR studies of [zeta- 13 C]Arg-OTf suggest the Arg side chains may not be intimately involved in formation of the ternary complex

  2. Sensitivity improvement for correlations involving arginine side-chain N{epsilon}/H{epsilon} resonances in multi-dimensional NMR experiments using broadband {sup 15}N 180{sup o} pulses

    Energy Technology Data Exchange (ETDEWEB)

    Iwahara, Junji; Clore, G. Marius [National Institutes of Health, Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Disease (United States)], E-mail: mariusc@intra.niddk.nih.gov

    2006-12-15

    Due to practical limitations in available {sup 15}N rf field strength, imperfections in {sup 15}N 180{sup o} pulses arising from off-resonance effects can result in significant sensitivity loss, even if the chemical shift offset is relatively small. Indeed, in multi-dimensional NMR experiments optimized for protein backbone amide groups, cross-peaks arising from the Arg guanidino {sup 15}N{epsilon} ({approx}85 ppm) are highly attenuated by the presence of multiple INEPT transfer steps. To improve the sensitivity for correlations involving Arg N{epsilon}-H{epsilon} groups, we have incorporated {sup 15}N broadband 180 deg. pulses into 3D {sup 15}N-separated NOE-HSQC and HNCACB experiments. Two {sup 15}N-WURST pulses incorporated at the INEPT transfer steps of the 3D {sup 15}N-separated NOE-HSQC pulse sequence resulted in a {approx}1.5-fold increase in sensitivity for the Arg N{epsilon}-H{epsilon} signals at 800 MHz. For the 3D HNCACB experiment, five {sup 15}N Abramovich-Vega pulses were incorporated for broadband inversion and refocusing, and the sensitivity of Arg{sup 1}H{epsilon}-{sup 15}N{epsilon}-{sup 13}C{gamma}/{sup 13}C{delta} correlation peaks was enhanced by a factor of {approx}1.7 at 500 MHz. These experiments eliminate the necessity for additional experiments to assign Arg {sup 1}H{epsilon} and {sup 15}N{epsilon} resonances. In addition, the increased sensitivity afforded for the detection of NOE cross-peaks involving correlations with the {sup 15}N{epsilon}/{sup 1}H{epsilon} of Arg in 3D {sup 15}N-separated NOE experiments should prove to be very useful for structural analysis of interactions involving Arg side-chains.

  3. In vitro evaluation of N-methyl amide tripeptidomimetics as substrates for the human intestinal di-/tri-peptide transporter hPEPT1

    DEFF Research Database (Denmark)

    Andersen, Rikke; Nielsen, Carsten Uhd; Begtrup, Mikael

    2006-01-01

    application of N-methyl amide bioisosteres as peptide bond replacements in tripeptides in order to decrease degradation by peptidases and yet retain affinity for and transport via hPEPT1. Seven structurally diverse N-methyl amide tripeptidomimetics were selected based on a principal component analysis...... of structural properties of 6859 N-methyl amide tripeptidomimetics. In vitro extracellular degradation of the selected tripeptidomimetics as well as affinity for and transepithelial transport via hPEPT1 were investigated in Caco-2 cells. Decreased apparent degradation was observed for all tripeptidomimetics...... to be substrates for hPEPT1 than tripeptidomimetics with charged side chains. The results of the present study indicate that the N-methyl amide peptide bond replacement approach for increasing bioavailability of tripeptidomimetic drug candidates is not generally applicable to all tripeptides. Nevertheless...

  4. Naturally occurring methyl salicylate glycosides.

    Science.gov (United States)

    Mao, Ping; Liu, Zizhen; Xie, Meng; Jiang, Rui; Liu, Weirui; Wang, Xiaohong; Meng, Shen; She, Gaimei

    2014-01-01

    As an important part of non steroids anti-inflammation drug (NSAIDs), salicylate has developed from natural substance salicylic acid to natrium salicylicum, to aspirin. Now, methyl salicylate glycoside, a new derivative of salicylic acid, is modified with a -COOH group integrated one methyl radical into formic ether, and a -OH linked with a monosaccharide, a disaccharide or a trisaccharide unit by glycosidic linkage. It has the similar pharmacological activities, anti-inflammatory, analgesic, antipyretic and antithrombotic as the previous salicylates' without resulting in serious side effects, particularly the gastrointestinal toxicity. Owing to the superiority of those significant bioactivities, methyl salicylate glycosides have became a hot research area in NSAIDs for several years. This paper compiles all 9 naturally occurring methyl salicylate glycosides, their distribution of the resource and pharmacological mechanism, which could contribute to the new drug discovery.

  5. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  6. Crystal structures of eight mono-methyl alkanes (C26–C32 via single-crystal and powder diffraction and DFT-D optimization

    Directory of Open Access Journals (Sweden)

    Lee Brooks

    2015-09-01

    Full Text Available The crystal structures of eight mono-methyl alkanes have been determined from single-crystal or high-resolution powder X-ray diffraction using synchrotron radiation. Mono-methyl alkanes can be found on the cuticles of insects and are believed to act as recognition pheromones in some social species, e.g. ants, wasps etc. The molecules were synthesized as pure S enantiomers and are (S-9-methylpentacosane, C26H54; (S-9-methylheptacosane and (S-11-methylheptacosane, C28H58; (S-7-methylnonacosane, (S-9-methylnonacosane, (S-11-methylnonacosane and (S-13-methylnonacosane, C30H62; and (S-9-methylhentriacontane, C32H66. All crystallize in space group P21. Depending on the position of the methyl group on the carbon chain, two packing schemes are observed, in which the molecules pack together hexagonally as linear rods with terminal and side methyl groups clustering to form distinct motifs. Carbon-chain torsion angles deviate by less than 10° from the fully extended conformation, but with one packing form showing greater curvature than the other near the position of the methyl side group. The crystal structures are optimized by dispersion-corrected DFT calculations, because of the difficulties in refining accurate structural parameters from powder diffraction data from relatively poorly crystalline materials.

  7. Thermoresponsive Poly(2-Oxazoline) Molecular Brushes by Living Ionic Polymerization: Modulation of the Cloud Point by Random and Block Copolymer Pendant Chains

    KAUST Repository

    Zhang, Ning

    2012-08-10

    Molecular brushes (MBs) of poly(2-oxazoline)s were prepared by living anionic polymerization of 2-isopropenyl-2-oxazoline to form the backbone and living cationic ring-opening polymerization of 2-n-propyl-2-oxazoline and 2-methyl-2-oxazoline to form random and block copolymers. Their aqueous solutions displayed a distinct thermoresponsive behavior as a function of the side-chain composition and sequence. The cloud point (CP) of MBs with random copolymer side chains is a linear function of the hydrophilic monomer content and can be modulated in a wide range. For MBs with block copolymer side chains, it was found that the block sequence had a strong and surprising effect on the CP. While MBs with a distal hydrophobic block had a CP at 70 °C, MBs with hydrophilic outer blocks already precipitated at 32 °C. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Involvement of adenosine monophosphate activated kinase in interleukin-6 regulation of steroidogenic acute regulatory protein and cholesterol side chain cleavage enzyme in the bovine zona fasciculata and zona reticularis.

    Science.gov (United States)

    De Silva, Matharage S I; Dayton, Adam W; Rhoten, Lance R; Mallett, John W; Reese, Jared C; Squires, Mathieu D; Dalley, Andrew P; Porter, James P; Judd, Allan M

    2018-06-01

    In bovine adrenal zona fasciculata (ZF) and NCI-H295R cells, interleukin-6 (IL-6) increases cortisol release, increases expression of steroidogenic acute regulatory protein (StAR), cholesterol side chain cleavage enzyme (P450scc), and steroidogenic factor 1 (SF-1) (increases steroidogenic proteins), and decreases the expression of adrenal hypoplasia congenita-like protein (DAX-1) (inhibits steroidogenic proteins). In contrast, IL-6 decreases bovine adrenal zona reticularis (ZR) androgen release, StAR, P450scc, and SF-1 expression, and increases DAX-1 expression. Adenosine monophosphate (AMP) activated kinase (AMPK) regulates steroidogenesis, but its role in IL-6 regulation of adrenal steroidogenesis is unknown. In the present study, an AMPK activator (AICAR) increased (P < 0.01) NCI-H295R StAR promoter activity, StAR and P450scc expression, and the phosphorylation of AMPK (PAMPK) and acetyl-CoA carboxylase (PACC) (indexes of AMPK activity). In ZR (decreased StAR, P450scc, SF-1, increased DAX-1) (P < 0.01) and ZF tissues (increased StAR, P450scc, SF-1, decreased DAX-1) (P < 0.01), AICAR modified StAR, P450scc, SF-1 and DAX-1 mRNAs/proteins similar to the effects of IL-6. The activity (increased PAMPK and PACC) (P < 0.01) of AMPK in the ZF and ZR was increased by AICAR and IL-6. In support of an AMPK role in IL-6 ZF and ZR effects, the AMPK inhibitor compound C blocked (P < 0.01) the effects of IL-6 on the expression of StAR, P450scc, SF-1, and DAX-1. Therefore, IL-6 modification of the expression of StAR and P450scc in the ZF and ZR may involve activation of AMPK and these changes may be related to changes in the expression of SF-1 and DAX-1. Copyright © 2018 Elsevier Inc. All rights reserved.

  9. Improved labeling strategy for 13C relaxation measurements of methyl groups in proteins

    International Nuclear Information System (INIS)

    Lee, Andrew L.; Urbauer, Jeffrey L.; Wand, A. Joshua

    1997-01-01

    Selective incorporation of 13 C into the methyl groups of protein side chains is described as a means for simplifying the measurement and interpretation of 13 C relaxation parameters.High incorporation (>90%) is accomplished by using pyruvate(3- 13 C, 99%) as the sole carbon source in the growth media for protein overexpression in E. coli. This improved labeling scheme increases the sensitivity of the relaxation experiments by approximately fivefold when compared to randomly fractionally 13 C-labeled protein, allowing high-quality measurements on relatively dilute (<1 mM)protein samples at a relatively low cost

  10. Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins

    Czech Academy of Sciences Publication Activity Database

    Berka, K.; Laskowski, R. A.; Hobza, P.; Vondrášek, Jiří

    2010-01-01

    Roč. 6, č. 7 (2010), s. 2191-2203 ISSN 1549-9618 R&D Projects: GA ČR GAP208/10/0725; GA MŠk LC512 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50520701 Keywords : protein structure * DFT method * force fields * interaction energy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.138, year: 2010

  11. methyl methacrylate

    Indian Academy of Sciences (India)

    Unknown

    1. Introduction. In recent times polymers are finding an important place ... Supply. Ferrite. Isolator. Movable. Short. Slide Screw. Tuner. Attenuator ... problems and thus yield real material parameters. The .... polymer chain at the amorphous or crystalline boundaries .... (Amsterdam: Elsevier Scientific Publishing Company).

  12. Biodegradation of diesel fuel by a microbial consortium in the presence of 1-alkoxymethyl-2-methyl-5-hydroxypyridinium chloride homologues

    DEFF Research Database (Denmark)

    Chrzanowski, L; Stasiewicz, M; Owsianiak, Mikolaj

    2009-01-01

    hypothesize that in the presence of diesel fuel low-water-soluble ionic liquids may become more toxic to hydrocarbon-degrading microorganisms. In this study the influence of 1-alkoxymethyl-2-methyl-5-hydroxypyridinium chloride homologues (side-chain length from C-3 to C-18) on biodegradation of diesel fuel...... by a bacterial consortium was investigated. Whereas test performed for the consortium cultivated on disodium succinate showed that toxicity of the investigated ionic liquids decreased with increase in side-chain length, only higher homologues (C-8-C-18) caused a decrease in diesel fuel biodegradation......, respectively. We conclude that in the presence of hydrocarbons acting as a solvent, the increased bioavailability of hydrophobic homologues is responsible for the decrease in biodegradation efficiency of diesel fuel....

  13. Synthesis of [5,6-13C2, 1-14C]olivetolic acid, methyl [1'-13C]olivetolate and [5,6-13C2, 1-14C]cannabigerolic acid

    International Nuclear Information System (INIS)

    Porwoll, J.P.; Leete, E.

    1985-01-01

    Potential advanced intermediates in the biosynthesis of delta 9 -tetrahydrocannabinol, the major psychoactive principle of marijuana, have been synthesized labeled with two contiguous 13 C atoms and 14 C. Methyl [5,6- 13 C 2 , 1- 14 C]olivetolate was prepared from lithium [ 13 C 2 ]acetylide and dimethyl [2- 14 C]malonate. Reaction with geranyl bromide afforded methyl [5,6- 13 C 2 , 1- 14 C]cannabigerolate, and hydrolysis of these methyl esters with lithium propyl mercaptide yielded the corresponding labeled acids. The 13 C- 13 C couplings observable in the 13 C NMR spectra of these 13 C-enriched compounds and their synthetic precursors are recorded. Methyl [1'- 14 C]olivetolate was prepared from 13 CO 2 to confirm assignments of the 13 C chemical shifts in the pentyl side chain of these compounds. (author)

  14. Reaction mechanism for radiation-induced degradation of poly(methyl methacrylate) as studied by ESR and ESE

    International Nuclear Information System (INIS)

    Yoshida, H.; Ichikawa, T.

    1991-01-01

    Reaction mechanism for the radiation-induced degradation of poly(methyl methacrylate) has been studied based on the ESR and electron spin echo observations of the free radicals in the polymer irradiated with γ-rays. It is indicated that the side-chain radical, -CH 2 -CCH 3 (COOC-radicalH 2 )-, is the precursor for the main-chain scission. This radical transforms into the propagating-type radical, a fingerprint of the main-chain scission, without loss of the total radical concentration. UV illumination converts the side-chain radical into the acyl-type radical, -CH 2 -CCH 3 (-C-radical=O)-, which thermally transforms into the propagating-type radical. The radical of the type, -CH 2 -C-radicalCH 3 -CH 2 -, is suggested as a common, immediate precursor for the main-chain scission with and without the UV illumination, though it has not been detected because of its short life-time. (author) 7 refs.; 2 figs

  15. Reply to the 'Comment on "Relating side chain organization of PNIPAm with its conformation in aqueous methanol"' by A. Pica and G. Graziano, Soft Matter, 2017, 13, DOI: 10.1039/C7SM01065F.

    Science.gov (United States)

    Mukherji, Debashish; Wagner, Manfred; Watson, Mark D; Winzen, Svenja; de Oliveira, Tiago E; Marques, Carlos M; Kremer, Kurt

    2017-11-01

    We have recently proposed preferential binding by a cosolvent as the mechanism for chain collapse under co-non-solvency. Here we summarise our earlier works and provide further evidence that alcohol preferentially binds to PNIPAm, forming cosolvent bridges, and thus drives the transition. We also clarify some of the common misconceptions evoked in this debate with Pica and Graziano (PG), reinforcing the arguments of our earlier reply-comment [Soft Matter, 2017, 13, 2292] and published works.

  16. Mutations Blocking Side Chain Assembly, Polymerization, or Transport of a Wzy-Dependent Streptococcus pneumoniae Capsule Are Lethal in the Absence of Suppressor Mutations and Can Affect Polymer Transfer to the Cell Wall▿

    OpenAIRE

    Xayarath, Bobbi; Yother, Janet

    2007-01-01

    Extracellular polysaccharides of many bacteria are synthesized by the Wzy polymerase-dependent mechanism, where long-chain polymers are assembled from undecaprenyl-phosphate-linked repeat units on the outer face of the cytoplasmic membrane. In gram-positive bacteria, Wzy-dependent capsules remain largely cell associated via membrane and peptidoglycan linkages. Like many Wzy-dependent capsules, the Streptococcus pneumoniae serotype 2 capsule is branched. In this study, we found that deletions ...

  17. Medications and Side Effects

    Science.gov (United States)

    ... to fully work. You might feel some side effects of your medication before your feel the benefits – ... as sleepiness, anxiety or headache) is a side effect or a symptom of your illness. Many side ...

  18. Specific labeling and assignment strategies of valine methyl groups for NMR studies of high molecular weight proteins

    Energy Technology Data Exchange (ETDEWEB)

    Mas, Guillaume; Crublet, Elodie [Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS) (France); Hamelin, Olivier [CNRS (France); Gans, Pierre; Boisbouvier, Jérôme, E-mail: jerome.boisbouvier@ibs.fr [Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS) (France)

    2013-09-28

    The specific protonation of valine and leucine methyl groups in proteins is typically achieved by overexpressing proteins in M9/D{sub 2}O medium supplemented with either labeled α-ketoisovalerate for the labeling of the four prochiral methyl groups or with 2-acetolactate for the stereospecific labeling of the valine and leucine side chains. However, when these labeling schemes are applied to large protein assemblies, significant overlap between the correlations of the valine and leucine methyl groups occurs, hampering the analysis of 2D methyl-TROSY spectra. Analysis of the leucine and valine biosynthesis pathways revealed that the incorporation of labeled precursors in the leucine pathway can be inhibited by the addition of exogenous l-leucine-d{sub 10}. We exploited this property to label stereospecifically the pro-R and pro-S methyl groups of valine with minimal scrambling to the leucine residues. This new labeling protocol was applied to the 468 kDa homododecameric peptidase TET2 to decrease the complexity of its NMR spectra. All of the pro-S valine methyl resonances of TET2 were assigned by combining mutagenesis with this innovative labeling approach. The assignments were transferred to the pro-R groups using an optimally labeled sample and a set of triple resonance experiments. This improved labeling scheme enables us to overcome the main limitation of overcrowding in the NMR spectra of prochiral methyl groups, which is a prerequisite for the site-specific measurement of the structural and dynamic parameters or for the study of interactions in very large protein assemblies.

  19. Falling chains

    OpenAIRE

    Wong, Chun Wa; Yasui, Kosuke

    2005-01-01

    The one-dimensional fall of a folded chain with one end suspended from a rigid support and a chain falling from a resting heap on a table is studied. Because their Lagrangians contain no explicit time dependence, the falling chains are conservative systems. Their equations of motion are shown to contain a term that enforces energy conservation when masses are transferred between subchains. We show that Cayley's 1857 energy nonconserving solution for a chain falling from a resting heap is inco...

  20. High CpG island methylation of p16 gene and loss of p16 protein

    Indian Academy of Sciences (India)

    Methylation-specific polymerase chain reaction (MSP) was employed to detect CpG island methylation in p16 promoter region andWestern blotting was used to detect p16 expression of all subjects. Real-time fluorescence quantitative polymerase chain reaction (FQ-PCR) was performed to test p16 mRNA expression.

  1. Comment on "Relating side chain organization of PNIPAm with its conformation in aqueous methanol" by D. Mukherji, M. Wagner, M. D. Watson, S. Winzen, T. E. de Oliveira, C. M. Marques and K. Kremer, Soft Matter, 2016, 12, 7995.

    Science.gov (United States)

    Pica, Andrea; Graziano, Giuseppe

    2017-11-01

    In a recent article, Kremer and co-workers have combined NMR measurements and very long, all-atom MD simulations to strengthen their original claim that PNIPAM cononsolvency in water-methanol solutions is driven by the ability of MeOH molecules to bridge different monomers far away along the polymeric chain. In this comment, the results presented by Kremer and co-workers are reviewed, analyzed, and questioned regarding their ability to provide support to the bridging mechanism. Here, some pieces of evidence are provided to show that: (1) the solvent-excluded volume effect plays always a fundamental role in polymer collapse; (2) PNIPAM cononsolvency is caused by the geometric-energetic frustration experienced by the polymer when it can interact with both water and methanol molecules at the same time.

  2. Sympathetic chain Schwannoma

    International Nuclear Information System (INIS)

    Al-Mashat, Faisal M.

    2009-01-01

    Schwannomas are rare, benign, slowly growing tumors arising from Schwann cells that line nerve sheaths. Schwannomas arising from the cervical sympathetic chain are extremely rare. Here, we report a case of a 70-year-old man who presented with only an asymptomatic neck mass. Physical examination revealed a left sided Horner syndrome and a neck mass with transmitted pulsation and anterior displacement of the carotid artery. Computed tomography (CT) showed a well-defined non-enhancing mass with vascular displacement. The nerve of origin of this encapsulated tumor was the sympathetic chain. The tumor was excised completely intact. The pathologic diagnosis was Schwannoma (Antoni type A and Antoni type B). The patient has been well and free of tumor recurrence for 14 months with persistence of asymptomatic left sided Horner syndrome. The clinical, radiological and pathological evaluations, therapy and postoperative complications of this tumor are discussed. (author)

  3. Conformationally constrained dipeptide surrogates with aromatic side-chains: synthesis of 4-aryl indolizidin-9-one amino acids by conjugate addition to a common alpha,omega-diaminoazelate enone intermediate.

    Science.gov (United States)

    Cluzeau, Jérôme; Lubell, William D

    2004-03-05

    Four methyl 9-oxo-8-(N-(Boc)-amino)-4-phenyl-1-azabicyclo[4.3.0]nonane carboxylates (11, 4-Ph-I(9)aa-OMe) were synthesized from (2S,8S,5E)-di-tert-butyl-4-oxo-5-ene-2,8-bis[N-(PhF)amino]azelate [(5E)-7, PhF = 9-(9-phenylfluorenyl)] via a seven-step process featuring a conjugate addition/reductive amination/lactam cyclization sequence. Various nucleophiles were used in the conjugate addition reactions on enone (5E)-7 as a general route for making alpha,omega-diaminoazelates possessing different substituents in good yield albeit low diastereoselectivity except in the case of aryl Grignard reagents (9/1 to 15/1 drs). 6-Phenylazelates (6S)-8d and (6R)-8d were separated by chromatography and diastereoselective precipitation and independently transformed into 4-Ph-I(9)aa-OMe. From (6S)-8d, (2S,4R,6R,8S)-4-Ph-I(9)aa-OMe 11 was prepared selectively in 51% yield. Reductive amination of (6R)-8d provided the desired pipecolates 9 along with desamino compound 10, which was minimized by performing the hydrogenation in the presence of ammonium acetate. Subsequent ester exchange, lactam cyclization, and amine protection provided three products (2R,4S,6S,8R)-, (2R,4S,6S,8S)-, and (2S,4S,6R,8S)-4-Ph-I(9)aa-OMe 11 in 10, 6, and 6% yields, respectively, from (6R)-8d. Ester hydrolysis of (2S,4R,6R,8S)-11 furnished 4-phenyl indolizidin-9-one N-(Boc)amino acid 3 as a novel constrained Ala-Phe dipeptide surrogate for studying conformation-activity relationships of biologically active peptides.

  4. Dissociation dynamics of methylal

    Energy Technology Data Exchange (ETDEWEB)

    Beaud, P; Frey, H -M; Gerber, T; Mischler, B; Radi, P P; Tzannis, A -P [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1999-08-01

    The dissociation of methylal is investigated using mass spectrometry, combined with a pyrolytic radical source and femtosecond pump probe experiments. Based on preliminary results two reaction paths of methylal dissociation are proposed and discussed. (author) 4 fig., 3 refs.

  5. Experimental vapor pressures (from 1 Pa to 100 kPa) of six saturated Fatty Acid Methyl Esters (FAMEs): Methyl hexanoate, methyl octanoate, methyl decanoate, methyl dodecanoate, methyl tetradecanoate and methyl hexadecanoate

    International Nuclear Information System (INIS)

    Sahraoui, Lakhdar; Khimeche, Kamel; Dahmani, Abdallah; Mokbel, Ilham; Jose, Jacques

    2016-01-01

    Highlight: • Vapor-liquid equilibria, Enthalpy of Vaporization, saturated Fatty Acid Methyl Ester. - Abstract: Vapor pressures of six saturated Fatty Acid Methyl Esters (FAMEs), methyl hexanoate (or methyl caproate), methyl octanoate (or methyl caprylate), Methyl decanoate (or methyl caprate), methyl dodecanoate (or methyl laurate), methyl tetradecanoate (or methyl myristate), and methyl hexadecanoate (or methyl palmitate) were measured from 1 Pa to 100 kPa and at temperature range between 262 and 453 K using a static apparatus. The experimental data (P-T) were compared with the available literature data.

  6. Methylation pattern of IFNG in periapical granulomas and radicular cysts.

    Science.gov (United States)

    Campos, Kelma; Gomes, Carolina Cavaliéri; de Fátima Correia-Silva, Jeane; Farias, Lucyana Conceição; Fonseca-Silva, Thiago; Bernardes, Vanessa Fátima; Pereira, Cláudia Maria; Gomez, Ricardo Santiago

    2013-04-01

    Interferon-γ plays an important role in the pathogenesis of periapical lesions, and the methylation of IFNG has been associated with transcriptional inactivation. The purpose of the present study was to investigate IFNG promoter methylation in association with gene transcription and protein levels in periapical granulomas and radicular cysts. Methylation-specific polymerase chain reaction was used to assess the DNA methylation pattern of the IFNG gene in 16 periapical granulomas and 13 radicular cyst samples. The transcription levels of IFNG mRNA were verified by quantitative real-time polymerase chain reaction, and protein expression was evaluated by immunohistochemistry. All the periapical lesion samples exhibited partial or total methylation of the IFNG gene. In addition, an increased methylation profile was found in radicular cysts compared with periapical granulomas. Increased IFNG mRNA expression was observed in the partially methylated periapical lesion samples relative to the samples that were completely methylated. The present study provides the first evidence of the possible impact of IFNG methylation on IFNG transcription in periapical lesions. Copyright © 2013 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  7. Side Effects (Management)

    Science.gov (United States)

    ... cancer care is relieving side effects, called symptom management, palliative care, or supportive care. It is important ... treat them. To learn about the symptoms and management of the long-term side effects of cancer ...

  8. Radiation Therapy Side Effects

    Science.gov (United States)

    Radiation therapy has side effects because it not only kills or slows the growth of cancer cells, it can also affect nearby healthy cells. Many people who get radiation therapy experience fatigue. Other side effects depend on the part of the body that is being treated. Learn more about possible side effects.

  9. Chain-modified radioiodinated fatty acids

    International Nuclear Information System (INIS)

    Otto, C.A.

    1987-01-01

    Several carbon chain manipulations have been studied in terms of their effects on myocardial activity levels and residence time. The manipulations examined included: chain length, chain branching, chain unsaturation, and carbon-iodine bond stabilization. It was found that chain length affects myocardial activity levels for both straight-chain alkyl acids and branched chain alkyl and aryl acids. Similar results have been reported for the straight-chain aryl acids. Generally, the longer chain lengths correlated with higher myocardial activity levels and longer residence times. This behavior is attributed to storage as triglycerides. Branched chain acids are designed to be anti-metabolites but only the aryl β-methyl acids possessed the expected time course of constant or very slowly decreasing activity levels. The alkyl β-methyl acids underwent rapid deiodination - a process apparently independent of β-oxidation. Inhibition of β-oxidation by incorporation of carbon-carbon double and triple bonds was studied. Deiodination of ω-iodo alkyl fatty acids prevented an assessment of suicide inhibition using an unsaturated alkynoic acid. Stabilization of the carbon-iodine bond by attachment of iodine to a vinylic or aryl carbon was studied. The low myocardial values and high blood values observed for an eleven carbon ω-iodo vinylic fatty acid were not encouraging but ω-iodo aryl fatty acids appear to avoid the problems of rapid deiodination. (Auth.)

  10. Development of Side Coupled Cavities

    International Nuclear Information System (INIS)

    Conto, J.M. de; Carretta, J.M.; Gomez-Martinez, Y.; Micoud, R.

    2008-01-01

    Side coupled Cavities are good candidates for proton accelerations in the 90-180 MeV range, as it has been first proposed for the CERN LINAC4 project. A side coupled Linac is made of a lump chain of resonant cavities, alternatively accelerating and coupling. A side coupled cavity has been designed in a CERN-LPSC collaboration to achieve LINAC4 requirements. After RF studies, a complete thermal study has been done, showing that 10-15% is the absolute maximum duty-cycle achievable by such a cavity. Error studies have been developed. They have shown that a tuning ring is mandatory and that a K equals 3% coupling factor is a good choice. A prototype has been built and each cell has been measured and tuned. A simple and accurate method has been used to get both the resonant frequency and the coupling factor, with a movable tuner and a linear fit. A similar method has been used to get the second order coupling factor. A large dispersion is observed on K. This is mainly due to the shape of the coupling apertures, which are very sensitive to mechanical errors. A future and realistic design must be very careful to guarantee a constant aperture (the important parameter is more the dispersion of k than its exact value). Finally, we analyse how to tune the cavity. This has to checked carefully and probably improved or corrected. Results are expected for mid-2008

  11. Single-sided NMR

    CERN Document Server

    Casanova, Federico; Blümich, Bernhard

    2011-01-01

    Single-Sided NMR describes the design of the first functioning single-sided tomograph, the related measurement methods, and a number of applications. One of the key advantages to this method is the speed at which the images are obtained.

  12. Whole-genome methylation caller designed for methyl- DNA ...

    African Journals Online (AJOL)

    etchie

    2013-02-20

    Feb 20, 2013 ... Our method uses a single-CpG-resolution, whole-genome methylation ... Key words: Methyl-DNA immunoprecipitation, next-generation sequencing, ...... methylation is prevalent in embryonic stem cells andmaybe mediated.

  13. CHAIN 2

    International Nuclear Information System (INIS)

    Bailey, D.

    1998-04-01

    The Second Processing Chain (CHAIN2) consists of a suite of ten programs which together provide a full local analysis of the bulk plasma physics within the JET Tokamak. In discussing these ten computational models this report is intended to fulfil two broad purposes. Firstly it is meant to be used as a reference source for any user of CHAIN2 data, and secondly it provides a basic User Manual sufficient to instruct anyone in running the CHAIN2 suite of codes. In the main report text each module is described in terms of its underlying physics and any associated assumptions or limitations, whilst deliberate emphasis is put on highlighting the physics and mathematics of the calculations required in deriving each individual datatype in the standard module PPF output. In fact each datatype of the CHAIN2 PPF output listed in Appendix D is cross referenced to the point in the main text where its evaluation is discussed. An effort is made not only to give the equation used to derive a particular data profile but also to explicitly define which external data sources are involved in the computational calculation

  14. Methylation pathways in schizophrenia

    International Nuclear Information System (INIS)

    Sargent, T.W. III.

    1982-01-01

    Research on the biochemical causes of human psychosis concentrates on investigating whether schizophremia is linked to abnormalities in the metabolism of methyl carbon groups in the body. The metabolism of C-14 labeled methyl groups in methionine is studied in animals, normal subjects and patient volunteers

  15. The effect of problems on supply chain wide efficiency

    Directory of Open Access Journals (Sweden)

    Micheline J. Naude

    2011-11-01

    This article reports on an exploratory empirical study to illustrate the effect of problems at one party in the supply chain on the whole supply chain. The study was done at automotive component manufacturers. To determine how problems at one place permeate through the whole supply chain, correlation testing was done between supply-side, internal operations, and distribution or customer-side problems. The study found that problems experienced at one place in the supply chain had a negative impact throughout the supply chain. Automotive supply chains should therefore be managed more as a system, taking into consideration the effect of decision making and actions at one part of the supply chain on other parts of the supply chain. There should be a supply chain wide co-operative effort to find solutions to inefficiencies at all places in the supply chain.

  16. SHORT COMMUNICATION Repellency property of long chain ...

    African Journals Online (AJOL)

    Repellency property of long chain aliphatic methyl ketones against Anopheles gambiae s.s ... tained from huge diversity of plant species are an important source of safe .... dry and then introduced with the hand covered by a glove in .... citronellal in repelling bees from basil (Oci- ... Journal of American Mosquito Control As-.

  17. Moving Segmentation Up the Supply-Chain: Supply Chain Segmentation and Artificial Neural Networks

    OpenAIRE

    Erevelles, Sunil; Fukawa, Nobuyuki

    2008-01-01

    This paper explained the concept of supply-side segmentation and transvectional alignment, and applies these concepts in the artificial neural network (ANN). To the best of our knowledge, no research has applied ANN in explaining the heterogeneity of both the supply-side and demand-side of a market in forming relational entity that consists of firms at all levels of the supply chain and the demand chain. The ANN offers a way of operationalizing the concept of supply-side segmentation. In toda...

  18. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)

    USER

    Due to the industrial facilities, heavy metal contents in environmental samples increase ... High performance liquid chromatography (HPLC) ... environmental waters by atomic absorption spectrometry (AAS) is very difficult due to the low.

  19. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)

    USER

    The presence of this lysine lowers the pKa of CysH3[125]β from the normal value for sulfhydryl groups (between 8 and 8.5) to .... However, DTNB has one disadvantage, it contains a disulfide bond, and the .... The pKa of the reacting sulfhydryl group varies between 5.9 and 6.4, with a mean value of. 6.1±0.2. (c) Assignment ...

  20. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)

    USER

    In the last decade, a large number of copper(II) complexes have been prepared and ... of glacial acetic acid, was added dropwise a solution of o-vanillin (6.16 g, 40.50 mmol) in 30 .... maximum indicates clearly antiferromagnetic interactions.

  1. Pendant triazole ring assisted mesogen containing side chain liquid ...

    Indian Academy of Sciences (India)

    Thermal stability of polymers was confirmed by thermogravimetric analysis. Mesomorphic property and phase transition temperature of polymers were ... group and investigated their mesomorphic property and their structure–property relationships. 2. Experimental. 2.1 Materials. Methanol, ethanol, phenol, THF, diethyl ether, ...

  2. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)

    USER

    was added the metal chloride or nitrate solution while stirring. The reaction mixture ... few drops of dilute ethanolic ammonium hydroxide to obtain the respective solid metal-ligand complex. ... indicating formation of thermally stable species.

  3. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)

    USER

    1Egerton University, Department of Chemistry, P.O. Box 536, Njoro, Kenya. 2Egerton ... War [13]. However, there is little data available about the chemical characterization of the essentials of the Ocimum .... Institute for Capacity Development).

  4. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)

    USER

    DETERMINATION OF THE MINOR AND TRACE ELEMENTS IN BIRINIWA'S TIN. PYRITE ... Lead and tin, the major elements, respectively, of the lead/zinc ore and tin ... In Africa, particularly in Nigeria, prior to the advent of modem cosmetics, ...

  5. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)

    USER

    GAS. Laitao Luo*, Zhonghua Gu, Jianjun Guo. Department of Chemistry, Nangchang University, Nangchang, 330047, Jiangxi, P.R. China. (Received June 4 ... KEY WORDS: Purification of exhaust gas, Pt Rh Pd/γ-Al2O3 catalyst, Transition metals .... An ideal d% will result in a useful improvement in catalyst effectiveness.

  6. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)

    USER

    2Department of Chemistry, University of Port Elizabeth, P.O. Box 1600, 6000 Port ... applications of rhenium radiopharmaceuticals in nuclear medicine[5, 6]. ... This report deals with the synthesis of complexes II, and their reactions with 2-.

  7. Microwave heating in peptide side chain modification via cysteine alkylation.

    Science.gov (United States)

    Calce, Enrica; De Luca, Stefania

    2016-09-01

    Microwave irradiation has been successfully applied to a selective synthetic procedure for introducing molecular substituents on peptides, providing a noticeable reduction of the reaction time and also an increased crude peptide purity for some compounds.

  8. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)

    USER

    above systems for environmental decontamination of organophosphates is discussed. ... and carbamates usually contain solvents such as petroleum distillates ... This kind of self-assembly, inherent to microemulsions, results in the .... applied to the soil depends largely on two of its properties: persistence and adsorption.

  9. Analysis of side chain rotational restrictions of membrane-embedded

    NARCIS (Netherlands)

    Strancar, J.; Kavalenka, A.A.; Ziherl, P.; Stopar, D.; Hemminga, M.A.

    2009-01-01

    Site-directed spin-labeling electron spin resonance (SDSL-ESR) is a promising tool for membrane protein structure determination. Here we propose a novel way to translate the local structural constraints gained by SDSL-ESR data into a low-resolution structure of a protein by simulating the

  10. Peptide Nucleic Acids Having Amino Acid Side Chains

    DEFF Research Database (Denmark)

    1998-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary DNA and RNA strands more strongly than the corresponding DNA or RNA strands, and exhibit increased sequence specificity and solubility. The peptide nucleic acids comprise ligands selected from a group consisting...

  11. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)

    USER

    aDepartment of Chemistry, Faculty of Science, University of Douala, P.O. Box 24157, Douala,. Cameroon. bLaboratoire de Chimie des Substances Naturelles, USM 0502 MNHN - UMR 5154 CNRS, 63 rue Buffon-75005 Paris, France. cDepartment of Organic Chemistry, Faculty of Science, University of Yaounde I, P.O. Box ...

  12. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)

    USER

    ORGANOSILICON CHEMISTRY I: CYCLOPROPANATION BY CARBENE OR. CARBENOID ... ammonium salt was highly hygroscopic. Related ... which stress the necessity of operating under anhydrous condition, due to rapid hydrolysis of.

  13. Methyl-Analyzer--whole genome DNA methylation profiling.

    Science.gov (United States)

    Xin, Yurong; Ge, Yongchao; Haghighi, Fatemeh G

    2011-08-15

    Methyl-Analyzer is a python package that analyzes genome-wide DNA methylation data produced by the Methyl-MAPS (methylation mapping analysis by paired-end sequencing) method. Methyl-MAPS is an enzymatic-based method that uses both methylation-sensitive and -dependent enzymes covering >80% of CpG dinucleotides within mammalian genomes. It combines enzymatic-based approaches with high-throughput next-generation sequencing technology to provide whole genome DNA methylation profiles. Methyl-Analyzer processes and integrates sequencing reads from methylated and unmethylated compartments and estimates CpG methylation probabilities at single base resolution. Methyl-Analyzer is available at http://github.com/epigenomics/methylmaps. Sample dataset is available for download at http://epigenomicspub.columbia.edu/methylanalyzer_data.html. fgh3@columbia.edu Supplementary data are available at Bioinformatics online.

  14. Side Effects: Sleep Problems

    Science.gov (United States)

    Sleep problems are a common side effect during cancer treatment. Learn how a polysomnogram can assess sleep problems. Learn about the benefits of managing sleep disorders in men and women with cancer.

  15. Side Effects: Fatigue

    Science.gov (United States)

    Fatigue is a common side effect of many cancer treatments such as chemotherapy, radiation therapy, immunotherapy, and surgery. Anemia and pain can also cause fatigue. Learn about symptoms and way to manage fatigue.

  16. Side Effects: Diarrhea

    Science.gov (United States)

    Diarrhea, a side effect of cancer treatment, may cause symptoms such as loose, watery stools. Diarrhea can lead to dehydration and malnutrition in cancer patients. Learn about ways to treat and manage diarrhea during cancer treatment.

  17. Side Effects: Appetite Loss

    Science.gov (United States)

    Cancer treatments may lower your appetite. Side effects such as nausea, fatigue, or mouth sores can also making eating difficult. Learn how to eat well to avoid losing weight or becoming dehydrated, so you stay strong during treatment.

  18. Side Effects: Pain

    Science.gov (United States)

    Controlling pain is an important part of your cancer treatment plan. Learn how to track levels of pain. Find out how pain, a side effect of cancer treatment, is treated using acupuncture, biofeedback, and physical therapy.

  19. Side Effects: Anemia

    Science.gov (United States)

    Anemia is a side effect of cancer treatments, including chemotherapy and radiation therapy. It can make women and men feel fatigued, dizzy, and short of breath. Learn how to manage fatigue caused by anemia during cancer treatment.

  20. Side core lifter

    Energy Technology Data Exchange (ETDEWEB)

    Edelman, Ya A

    1982-01-01

    A side core lifter is proposed which contains a housing with guide slits and a removable core lifter with side projections on the support section connected to the core receiver. In order to preserve the structure of the rock in the core sample by means of guaranteeing rectilinear movement of the core lifter in the rock, the support and core receiver sections are hinged. The device is equipped with a spring for angular shift in the core-reception part.

  1. Heavy Chain Diseases

    Science.gov (United States)

    ... of heavy chain produced: Alpha Gamma Mu Alpha Heavy Chain Disease Alpha heavy chain disease (IgA heavy ... the disease or lead to a remission. Gamma Heavy Chain Disease Gamma heavy chain disease (IgG heavy ...

  2. [Psychoanalysis and Side Effect].

    Science.gov (United States)

    Shirahase, Joichiro

    2015-01-01

    A study of psychoanalysis from the perspective of side effects reveals that its history was a succession of measures to deal with its own side effects. This, however, does not merely suggest that, as a treatment method, psychoanalysis is incomplete and weak: rather, its history is a record of the growth and development of psychoanalysis that discovered therapeutic significance from phenomena that were initially regarded as side effects, made use of these discoveries, and elaborated them as a treatment method. The approach of research seen during the course of these developments is linked to the basic therapeutic approach of psychoanalysis. A therapist therefore does not draw conclusions about a patient's words and behaviors from a single aspect, but continues to make efforts to actively discover a variety of meanings and values from them, and to make the patient's life richer and more productive. This therapeutic approach is undoubtedly one of the unique aspects of psychoanalysis. I discuss the issue of psychoanalysis and side effects with the aim of clarifying this unique characteristic of psychoanalysis. The phenomenon called resistance inevitably emerges during the process of psychoanalytic treatment. Resistance can not only obstruct the progress of therapy; it also carries the risk of causing a variety of disadvantages to the patient. It can therefore be seen as an adverse effect. However, if we re-examine this phenomenon from the perspective of transference, we find that resistance is in fact a crucial tool in psychoanalysis, and included in its main effect, rather than a side effect. From the perspective of minimizing the character of resistance as a side effect and maximizing its character as a main effect, I have reviewed logical organization, dynamic evaluation, the structuring of treatment, the therapist's attitudes, and the training of therapists. I conclude by stating that psychoanalysis has aspects that do not match the perspective known as a side

  3. High temperature initiator-free RAFT polymerization of methyl methacrylate in a microwave reactor

    NARCIS (Netherlands)

    Paulus, R.M.; Becer, C.R.; Hoogenboom, R.; Schubert, U.S.

    2009-01-01

    The reversible additionfragmentation chain transfer (RAFT) polymerization of methyl methacrylate (MMA) was investigated under microwave irradiation. At first, a comparison was made between microwave and thermal heating for the RAFT polymerization of MMA with azobis(isobutyronitrile) (AIBN) as

  4. The synthesis of chlorophyll-a biosynthetic precursors and methyl substituted iron porphyrins

    International Nuclear Information System (INIS)

    Matera, K.M.

    1988-01-01

    The biosynthetic intermediates were incubated in a plant system. The activity levels calculated show that magnesium 6-acrylate porphyrins and one of the magnesium 6-β-hydroxypropionate porphyrins are not intermediates. In addition, plant systems incubated with 18 O 2 were found to synthesize magnesium 2,4-divinyl pheoporphyrin-a 5 incorporated with 18 O at the 9-carbonyl oxygen. Mass spectroscopy confirmed the presence of the oxygen label, thus eliminating one of two hypothesized pathways to chlorophyll-a. An overall description is given of iron porphyrins and iron porphyrin containing proteins. The function of the propionic side chains of the heme prosthetic group during electron transport reactions will be investigated. The synthesis of a series of iron(III) hexamethyl porphyrins with increasingly longer substituents in the remaining two peripheral positions of the porphyrin is described. Models for NMR studies of iron chlorin containing enzymes are discussed. Iron(III) pyropheophorbide-a and methyl pyropheophorbide-a were synthesized in addition to 5-CD 3 , 10-CD 2 iron(III) pyropheophorbide-a and methyl pyropheophorbide-a. Together, these pyropheophorbides were used to assign NMR resonances and ultimately provide a model for other iron chlorins. The synthesis of nickel(II) anhydro-mesorhodoporphyrin from zinc(III) anhydromesorhodochlorin is described; this nickel porphyrin was used as a standard for ring current calculations of reduced nickel analogs of anhydromesorhodoporphyrin

  5. Working the Dark Side

    DEFF Research Database (Denmark)

    Bjering, Jens Christian Borrebye

    A few days after the terror attacks of 9/11, then Vice President Dick Cheney appeared on television with a call for “working the dark side.” While still unclear what this expression entailed at the time, Cheney's comment appears in retrospect to almost have been prophetic for the years to come....... By analyzing official reports and testimonies from soldiers partaking in the War On Terror, the dissertation's second part—dark arts—focuses on the transformation of the dark side into a productive space in which “information” and the hunt for said information overshadowed all legal, ethical, or political...

  6. The Clinical Implications of Methylated p15 and p73 Genes in Adult Acute Lymphoblastic Leukemia

    International Nuclear Information System (INIS)

    ABD EL-HAMID, Th.M.; SHERISHER, M.A.; MOSSALLAM, Gh.I.

    2010-01-01

    Aberrant methylation of promoter associated CpG islands is an epigenetic modification of DNA which is associated with gene silencing. It plays an important role in the leukemia pathogenesis. This phenomenon is frequently observed in acute lymphoblastic leukemia (ALL) and results in the functional inactivation of its associated genes. The aim of this study is to investigate the frequency and the prognostic impact of p15 and p73 genes methylation in adult acute lymphoblastic leukemia patients. Patients and Methods: Methylation-specific polymerase chain reaction (PCR) was used to analyze methylation of the p15 and p73 genes in 51 newly diagnosed adult ALL patients. Results: The methylation frequencies of p15 and p73 genes at diagnosis were 41.2% and 27.5% respectively, while concomitant methylation was detected in 14% of the patients. Concomitant methylation of p15 and p73 genes was associated with significant lower rate of CR compared to patients without methylation (57% versus 90%), p=0.008. Overall survival (OS) was not affected by p15 methylation, but was poorer with p73 methylation and the difference was near significant (p=0.059). For patients without meyhylation, the survival benefit was significant when compared to patients with p15, p73 or both genes methylation (p=0.047). The leukemia free survival was not affected by the methylation status of single gene p15 or p73, but tended to be worse in patients with methylated p15, p73 or both genes when compared to patients without methylation (p= 0.08). Conclusion: Aberrant p73 promoter methylation is a potential prognostic factor in adult ALL patients. P15 methylation is frequent in Egyptian adult ALL patients, its concomitant methylation with p73 is of poor prognostic significance. Identification of these molecular targets improve risk assessment and selection of appropriate therapy.

  7. THERMODYNAMICS OF MICELLE FORMATION BY 1-METHYL-4-ALKYLPYRIDINIUM HALIDES

    NARCIS (Netherlands)

    BIJMA, K; ENGBERTS, JBFN; HAANDRIKMAN, G; VANOS, NM; BLANDAMER, MJ; BUTT, MD; CULLIS, PM

    This paper reports enthalpies of micellization for a series of 1-methyl-4-alkylpyridinium halide surfactants at 303.2 K with different lengths and degrees of branching of the 4-alkyl chain and different sizes of counterions using two microcalorimeters (LKB 2277 and Omega Microcal). The standard

  8. Methyl vinyl glycolate as a diverse platform molecule

    DEFF Research Database (Denmark)

    Sølvhøj, Amanda Birgitte; Taarning, Esben; Madsen, Robert

    2016-01-01

    and various long-chain terminal olefins give unsaturated α-hydroxy fatty acid methyl esters in good yields. [3,3]-Sigmatropic rearrangements of MVG also proceed in good yields to give unsaturated adipic acid derivatives. Finally, rearrangement of the allylic acetate of MVG proceeds in acceptable yield...

  9. Forskningens personlige side

    DEFF Research Database (Denmark)

    Hansen, Finn Thorbjørn

    2008-01-01

    Artiklen omhandler den ontologiske vending inden for universitetspædagogisk forskning, og redegør for hvorfor en mere personlig og eksistentiel side ved forskningen må medtænkes i universitetspædagogikken og -vejledningen. Udgivelsesdato: 24.11.08...

  10. Side loading filter apparatus

    International Nuclear Information System (INIS)

    Reynolds, K.E.

    1981-01-01

    A side loading filter chamber for use with radioactive gases is described. The equipment incorporates an inexpensive, manually operated, mechanism for aligning filter units with a number of laterally spaced wall openings and for removing the units from the chamber. (U.K.)

  11. Side insertable spacer

    International Nuclear Information System (INIS)

    Patterson, J.F.; Ewing, R.H.

    1992-01-01

    This patent describes a spacer for restraining the fuel rods of a nuclear fuel assembly, the assembly being formed of a plurality of parallel, elongated fuel rods so arranged that the assembly is bounded by a polygon having an even number of sides, the rods being so arranged as to lie in a plurality of sets of parallel rows, the rows of each set being perpendicular to one of the sides of the polygon. It comprises a number of spacer combs equal to at least half the number of the sides of the polygon, the spacer combs being superposed on each other, each of the spacer combs comprising: a single base strip having a length equal to that of one of the sides of the polygon and grid strips equal in number to the spaces between rows in one of the sets, and at least a majority of the grid strips being of a length sufficient to extend substantially the full length of the rows; the grid strips being provided with spring members positioned to engage each of the rods; the grid strips being provided with spring members positioned to engage each of the rods; the grid strips being secured to and extending at right angles to the base strip; the grid strips of different combs being positioned at angles to each other, so as to occupy the spaces between rows in different sets

  12. Tuning the NLO properties of polymethineimine chains by chemical substitution

    International Nuclear Information System (INIS)

    Medved’, Miroslav; Jacquemin, Denis

    2013-01-01

    Highlights: ► Properties of the most stable isomers of polymethineimine (PMI) are investigated. ► 2nd order NLO properties of experimentally known PMI derivatives are determined. ► Structure-property relationships are unraveled for several series of oligomers. ► Performance of long-range corrected DFT methods is assessed. - Abstract: Structure and molecular electronic properties including dipole moment, polarizability and first hyperpolarizability of polymethineimine (PMI) oligomers (up to hexadecamers) and its experimentally known amino-, methyl-, and cyano-derivatives are investigated using several ab initio methods (HF, MP2 and DFT). It is shown that side-chain substitutions have significant effects both on the structure and molecular properties of PMI chains. Depending on the substitution, two types of structures have been identified. The first is characterized by a bent skeleton and encompasses PMI, polyacetonitrile (PAcN), and polycyanonitrile (PCN). The second, represented by polyaminonitrile (PAN), remains quasi-linear with the plane of the unit cell (UC) only slightly rotating around the longitudinal molecular axis. These structural differences are also reflected in molecular properties; while in case of PMI, PAcN, and PCN the longitudinal component of properties (reduced per UC) reaches its maximum value for medium-size oligomers and then decreases for longer chains, the linear and nonlinear properties of PAN steadily increase towards the polymeric limit. In addition, we have assessed the performances of long-range corrected DFT functionals (LR-DFT), namely LC-BLYP, CAM-B3LYP, and ωB97X within the present framework: they provide results in qualitative agreement with MP2, a success not reached with B3LYP

  13. Crystal structure of N′-[(E-(1S,3R-(3-isopropyl-1-methyl-2-oxocyclopentylmethylidene]-4-methylbenzenesulfonohydrazide

    Directory of Open Access Journals (Sweden)

    David Tymann

    2015-12-01

    Full Text Available The title compound, C17H24N2O3S, was synthesized in order to determine the relative configuration of the corresponding β-keto aldehyde. In the U-shaped molecule, the five-membered ring approximates an envelope, with the methylene C atom adjacent to the quaternary C atom being the flap, and the methyl and isopropyl substituents lying to the same side of the ring. The dihedral angles between the four nearly coplanar atoms of the five-membered ring and the flap and the aromatic ring are 35.74 (15 and 55.72 (9°, respectively. The bond angles around the S atom are in the range from 103.26 (12 to 120.65 (14°. In the crystal, molecules are linked via N—H...O hydrogen bonds, forming a chain along the a axis.

  14. Identification of Differentially Methylated Sites with Weak Methylation Effects

    Directory of Open Access Journals (Sweden)

    Hong Tran

    2018-02-01

    Full Text Available Deoxyribonucleic acid (DNA methylation is an epigenetic alteration crucial for regulating stress responses. Identifying large-scale DNA methylation at single nucleotide resolution is made possible by whole genome bisulfite sequencing. An essential task following the generation of bisulfite sequencing data is to detect differentially methylated cytosines (DMCs among treatments. Most statistical methods for DMC detection do not consider the dependency of methylation patterns across the genome, thus possibly inflating type I error. Furthermore, small sample sizes and weak methylation effects among different phenotype categories make it difficult for these statistical methods to accurately detect DMCs. To address these issues, the wavelet-based functional mixed model (WFMM was introduced to detect DMCs. To further examine the performance of WFMM in detecting weak differential methylation events, we used both simulated and empirical data and compare WFMM performance to a popular DMC detection tool methylKit. Analyses of simulated data that replicated the effects of the herbicide glyphosate on DNA methylation in Arabidopsis thaliana show that WFMM results in higher sensitivity and specificity in detecting DMCs compared to methylKit, especially when the methylation differences among phenotype groups are small. Moreover, the performance of WFMM is robust with respect to small sample sizes, making it particularly attractive considering the current high costs of bisulfite sequencing. Analysis of empirical Arabidopsis thaliana data under varying glyphosate dosages, and the analysis of monozygotic (MZ twins who have different pain sensitivities—both datasets have weak methylation effects of <1%—show that WFMM can identify more relevant DMCs related to the phenotype of interest than methylKit. Differentially methylated regions (DMRs are genomic regions with different DNA methylation status across biological samples. DMRs and DMCs are essentially the same

  15. DNA methylation in obesity

    Directory of Open Access Journals (Sweden)

    Małgorzata Pokrywka

    2014-11-01

    Full Text Available The number of overweight and obese people is increasing at an alarming rate, especially in the developed and developing countries. Obesity is a major risk factor for diabetes, cardiovascular disease, and cancer, and in consequence for premature death. The development of obesity results from the interplay of both genetic and environmental factors, which include sedentary life style and abnormal eating habits. In the past few years a number of events accompanying obesity, affecting expression of genes which are not directly connected with the DNA base sequence (e.g. epigenetic changes, have been described. Epigenetic processes include DNA methylation, histone modifications such as acetylation, methylation, phosphorylation, ubiquitination, and sumoylation, as well as non-coding micro-RNA (miRNA synthesis. In this review, the known changes in the profile of DNA methylation as a factor affecting obesity and its complications are described.

  16. Repellency property of long chain aliphatic methyl ketones against ...

    African Journals Online (AJOL)

    -tridecanone and 2-pentadecanone) were more effective than compounds with even carbon atoms (2-decanone and 2- dodecanone). Comparable repellency activity of 2-tridecanone to DEET show that, it may save as Anopheles gambiae s.s. ...

  17. Supply chain reaction

    International Nuclear Information System (INIS)

    Snieckus, Darius

    2000-01-01

    'Logic' (Leading Oil and Gas Industry Competitiveness) is a government-industry supply chain management initiative which aims to improve the competitiveness of the UK's North Sea business by 1 billion UK pounds by 2002 and its export performance by 50% inside 5 years. Much of the article is devoted to the background and views of Logic's chief executive Chris. Freeman. Freeman makes clear that 'unlike Crine, we are not a cost-reduction initiative: that may be one of the outcomes, but we are really focusing on the co-operation side of things'. Logic aims to change the culture of the UK offshore industry through example. Freeman believes that the creation of collaborative success will flag up industry and give credence to Logics objectives

  18. CpG island methylator phenotype (CIMP) of colorectal cancer is best characterised by quantitative DNA methylation analysis and prospective cohort studies.

    Science.gov (United States)

    Ogino, S; Cantor, M; Kawasaki, T; Brahmandam, M; Kirkner, G J; Weisenberger, D J; Campan, M; Laird, P W; Loda, M; Fuchs, C S

    2006-07-01

    The concept of CpG island methylator phenotype (CIMP) is not universally accepted. Even if specific clinicopathological features have been associated with CIMP, investigators often failed to demonstrate a bimodal distribution of the number of methylated markers, which would suggest CIMP as a distinct subtype of colorectal cancer. Previous studies primarily used methylation specific polymerase chain reaction which might detect biologically insignificant low levels of methylation. To demonstrate a distinct genetic profile of CIMP colorectal cancer using quantitative DNA methylation analysis that can distinguish high from low levels of DNA methylation. We developed quantitative real time polymerase chain reaction (MethyLight) assays and measured DNA methylation (percentage of methylated reference) of five carefully selected loci (promoters of CACNA1G, CDKN2A (p16), CRABP1, MLH1, and NEUROG1) in 460 colorectal cancers from large prospective cohorts. There was a clear bimodal distribution of 80 microsatellite instability-high (MSI-H) tumours according to the number of methylated promoters, with no tumours showing 3/5 methylated loci. Thus we defined CIMP as having >or=4/5 methylated loci, and 17% (78) of the 460 tumours were classified as CIMP. CIMP was significantly associated with female sex, MSI, BRAF mutations, and wild-type KRAS. Both CIMP MSI-H tumours and CIMP microsatellite stable (MSS) tumours showed much higher frequencies of BRAF mutations (63% and 54%) than non-CIMP counterparts (non-CIMP MSI-H (0%, pCIMP MSS tumours (6.6%, pCIMP is best characterised by quantitative DNA methylation analysis. CIMP is a distinct epigenotype of colorectal cancer and may be less frequent than previously reported.

  19. Methylation-sensitive amplified polymorphism-based genome-wide analysis of cytosine methylation profiles in Nicotiana tabacum cultivars.

    Science.gov (United States)

    Jiao, J; Wu, J; Lv, Z; Sun, C; Gao, L; Yan, X; Cui, L; Tang, Z; Yan, B; Jia, Y

    2015-11-26

    This study aimed to investigate cytosine methylation profiles in different tobacco (Nicotiana tabacum) cultivars grown in China. Methylation-sensitive amplified polymorphism was used to analyze genome-wide global methylation profiles in four tobacco cultivars (Yunyan 85, NC89, K326, and Yunyan 87). Amplicons with methylated C motifs were cloned by reamplified polymerase chain reaction, sequenced, and analyzed. The results show that geographical location had a greater effect on methylation patterns in the tobacco genome than did sampling time. Analysis of the CG dinucleotide distribution in methylation-sensitive polymorphic restriction fragments suggested that a CpG dinucleotide cluster-enriched area is a possible site of cytosine methylation in the tobacco genome. The sequence alignments of the Nia1 gene (that encodes nitrate reductase) in Yunyan 87 in different regions indicate that a C-T transition might be responsible for the tobacco phenotype. T-C nucleotide replacement might also be responsible for the tobacco phenotype and may be influenced by geographical location.

  20. Methylated β-Cyclodextrins

    DEFF Research Database (Denmark)

    Schönbeck, Jens Christian Sidney; Westh, Peter; Madsen, Jens Christian

    2011-01-01

    The complexation of 6 bile salts with various methylated β-cyclodextrins was studied to elucidate how the degree and pattern of substitution affects the binding. The structures of the CDs were determined by mass spectrometry and NMR techniques, and the structures of the inclusion complexes were...

  1. Chain reaction

    International Nuclear Information System (INIS)

    Balogh, Brian.

    1991-01-01

    Chain Reaction is a work of recent American political history. It seeks to explain how and why America came to depend so heavily on its experts after World War II, how those experts translated that authority into political clout, and why that authority and political discretion declined in the 1970s. The author's research into the internal memoranda of the Atomic Energy Commission substantiates his argument in historical detail. It was not the ravages of American anti-intellectualism, as so many scholars have argued, that brought the experts back down to earth. Rather, their decline can be traced to the very roots of their success after World War II. The need to over-state anticipated results in order to garner public support, incessant professional and bureaucratic specialization, and the sheer proliferation of expertise pushed arcane and insulated debates between experts into public forums at the same time that a broad cross section of political participants found it easier to gain access to their own expertise. These tendencies ultimately undermined the political influence of all experts. (author)

  2. Application of multiplex nested methylated specific PCR in early diagnosis of epithelial ovarian cancer.

    Science.gov (United States)

    Wang, Bi; Yu, Lei; Yang, Guo-Zhen; Luo, Xin; Huang, Lin

    2015-01-01

    To explore the application of multiplex nested methylated specific polymerase chain reaction (PCR) in the early diagnosis of epithelial ovarian carcinoma (EOC). Serum and fresh tissue samples were collected from 114 EOC patients. RUNX3, TFPI2 and OPCML served as target genes. Methylation levels of tissues were assessed by multiplex nested methylated specific PCR, the results being compared with those for carcinoma antigen 125 (CA125). The serum free deoxyribose nucleic acid (DNA) methylation spectrum of EOC patients was completely contained in the DNA spectrum of cancer tissues, providing an accurate reflection of tumor DNA methylation conditions. Serum levels of CA125 and free DNA methylation in the EOC group were evidently higher than those in benign lesion and control groups (p0.05). The sensitivity, specificity and positive predicative value (PPV) of multiplex nested methylated specific PCR were significantly higher for detection of all patients and those with early EOC than those for CA125 (pnested methylated specific PCR (p>0.05), but there was no significant difference in sensitivity (p>0.05). Serum free DNA methylation can be used as a biological marker for EOC and multiplex nested methylated specific PCR should be considered for early diagnosis since it can accurately determine tumor methylation conditions.

  3. Thermoresponsive Poly(2-Oxazoline) Molecular Brushes by Living Ionic Polymerization: Modulation of the Cloud Point by Random and Block Copolymer Pendant Chains

    KAUST Repository

    Zhang, Ning; Luxenhofer, Robert; Jordan, Rainer

    2012-01-01

    random and block copolymers. Their aqueous solutions displayed a distinct thermoresponsive behavior as a function of the side-chain composition and sequence. The cloud point (CP) of MBs with random copolymer side chains is a linear function

  4. Protein methylation in pea chloroplasts

    International Nuclear Information System (INIS)

    Niemi, K.J.; Adler, J.; Selman, B.R.

    1990-01-01

    The methylation of chloroplast proteins has been investigated by incubating intact pea (Pisum sativum) chloroplasts with [ 3 H-methyl]-S-adenosylmethionine. Incubation in the light increases the amount of methylation in both the thylakoid and stromal fractions. Numerous thylakoid proteins serve as substrates for the methyltransfer reactions. Three of these thylakoid proteins are methylated to a significantly greater extent in the light than in the dark. The primary stromal polypeptide methylated is the large subunit of ribulose bisphosphate carboxylase/oxygenase. One other stromal polypeptide is also methylated much more in the light than in the dark. Two distinct types of protein methylation occur. One methylinkage is stable to basic conditions whereas a second type is base labile. The base-stable linkage is indicative of N-methylation of amino acid residues while base-lability is suggestive of carboxymethylation of amino acid residues. Labeling in the light increases the percentage of methylation that is base labile in the thylakoid fraction while no difference is observed in the amount of base-labile methylations in light-labeled and dark-labeled stromal proteins. Also suggestive of carboxymethylation is the detection of volatile [ 3 H]methyl radioactivity which increases during the labeling period and is greater in chloroplasts labeled in the light as opposed to being labeled in the dark; this implies in vivo turnover of the [ 3 H]methyl group

  5. Methylation of food commodities during fumigation with methyl bromide

    International Nuclear Information System (INIS)

    Starratt, A.N.; Bond, E.J.

    1990-01-01

    Sites of methylation in several commodities (wheat, oatmeal, peanuts, almonds, apples, oranges, maize, alfalfa and potatoes) during fumigation with 14 C-methyl bromide were studied. Differences were observed in levels of the major volatiles: methanol, dimethyl sulphide and methyl mercaptan, products of O- and S-methylation, resulting from treatment of the fumigated materials with 1N sodium hydroxide. In studies of maize and wheat, histidine was the amino acid which underwent the highest level of N-methylation. (author). 24 refs, 3 tabs

  6. Fragrance material review on cyclohexyl methyl pentanone.

    Science.gov (United States)

    Scognamiglio, J; Letizia, C S; Api, A M

    2013-12-01

    A toxicologic and dermatologic review of cyclohexyl methyl pentanone when used as a fragrance ingredient is presented. Cyclohexyl methyl pentanone is a member of the fragrance structural group Alkyl Cyclic Ketones. These fragrances can be described as being composed of an alkyl, R1, and various substituted and bicyclic saturated or unsaturated cyclic hydrocarbons, R2, in which one of the rings may include up to 12 carbons. Alternatively, R2 may be a carbon bridge of C2-C4 carbon chain length between the ketone and cyclic hydrocarbon. This review contains a detailed summary of all available toxicology and dermatology papers that are related to this individual fragrance ingredient and is not intended as a stand-alone document. Available data for cyclohexyl methyl pentanone were evaluated then summarized and includes physical properties, acute toxicity, skin irritation, mucous membrane (eye) irritation, skin sensitization, phototoxicity, photoallergy, and genotoxicity data. A safety assessment of the entire Alkyl Cyclic Ketones will be published simultaneously with this document; please refer to Belsito et al. (Belsito, D., Bickers, D., Bruze, M., Calow, P., Dagli, M., Fryer, A.D., Greim, H., Miyachi, Y., Saurat, J.H., Sipes, I.G., 2013. A toxicologic and dermatologic assessment of alkyl cyclic ketones when used as fragrance ingredients (submitted for publication).) for an overall assessment of the safe use of this material and all Alkyl Cyclic Ketones in fragrances. Copyright © 2013. Published by Elsevier Ltd.

  7. Methylation screening of the TGFBI promoter in human lung and prostate cancer by methylation-specific PCR

    International Nuclear Information System (INIS)

    Shah, Jinesh N; Shao, Genze; Hei, Tom K; Zhao, Yongliang

    2008-01-01

    Hypermethylation of the TGFBI promoter has been shown to correlate with decreased expression of this gene in human tumor cell lines. In this study, we optimized a methylation-specific polymerase chain reaction (MSP) method and investigated the methylation status of the TGFBI promoter in human lung and prostate cancer specimens. Methylation-specific primers were designed based on the methylation profiles of the TGFBI promoter in human tumor cell lines, and MSP conditions were optimized for accurate and efficient amplification. Genomic DNA was isolated from lung tumors and prostatectomy tissues of prostate cancer patients, bisulfite-converted, and analyzed by MSP. Among 50 lung cancer samples, 44.0% (22/50) harbored methylated CpG sites in the TGFBI promoter. An analysis correlating gene methylation status with clinicopathological cancer features revealed that dense methylation of the TGFBI promoter was associated with a metastatic phenotype, with 42.9% (6/14) of metastatic lung cancer samples demonstrating dense methylation vs. only 5.6% (2/36) of primary lung cancer samples (p < 0.05). Similar to these lung cancer results, 82.0% (41/50) of prostate cancer samples harbored methylated CpG sites in the TGFBI promoter, and dense methylation of the promoter was present in 38.9% (7/18) of prostate cancer samples with the feature of locoregional invasiveness vs. only 19.4% (6/31) of prostate cancer samples without locoregional invasiveness (p < 0.05). Furthermore, promoter hypermethylation correlated with highly reduced expression of the TGFBI gene in human lung and prostate tumor cell lines. We successfully optimized a MSP method for the precise and efficient screening of TGFBI promoter methylation status. Dense methylation of the TGFBI promoter correlated with the extent of TGFBI gene silencing in tumor cell lines and was related to invasiveness of prostate tumors and metastatic status of lung cancer tumors. Thus, TGFBI promoter methylation can be used as a potential

  8. Crystallisation and chain conformation of long chain n-alkanes

    International Nuclear Information System (INIS)

    Gorce, J.

    2000-06-01

    Hydrocarbon chains are a basic component in a number of systems as diverse as biological membranes, phospholipids and polymers. A better understanding of the physical properties of n-alkane chains should provide a better understanding of these more complex systems. With this aim, vibrational spectroscopy has been extensively used. This technique, sensitive to molecular details, is the only one able to both identify and quantify conformational disorder present in paraffinic systems. To achieve this, methyl deformations have been widely used as ''internal standards'' for the normalisation of peak areas. However, in the case of n-alkanes with short chain length, such as n-C 44 H 90 for example, the infrared spectra recorded at liquid nitrogen temperature and reported here show the sensitivity of these latter peaks to the various crystal structures formed. Indeed, the main frequencies of the symmetric methyl bending mode were found between 1384 cm -1 and 1368 cm -1 as a function of the crystal form. Changes in the frequency of the first order of the L.A.M. present in the Raman spectra were also observed. At higher temperatures, non all-trans conformers, inferred from different infrared bands present in the wagging mode region, were found to be essentially placed at the end of the n-alkane chains. At the monoclinic phase transition, the concentration of end-gauche conformers, proportional to the area of the infrared band at 1342 cm -1 , increases abruptly. On the contrary, in the spectra recorded at liquid nitrogen temperature no such band is observed. We also studied the degree of disorder in two purely monodisperse long chain n-alkanes, namely n-C 198 H 398 and n-C 246 H 494 . The chain conformation as well as the tilt angle of the chains from the crystal surfaces were determined by means of low frequency Raman spectroscopy and S.A.X.S. measurements on solution-crystallised samples. The increase in the number of end-gauche conformers which was expected to occur with

  9. Study of radiation formation of methyl-iodide Part 2

    International Nuclear Information System (INIS)

    Bartonicek, B.; Schweiner, Z.; Bednar, J.; Hladky, E.

    1975-01-01

    Purified methane, ethylene, iodine, methyl iodide, ethyl iodide and hydrogen iodide were irradiated and/or pyrolyzed in Pyrex ampoules by 60 Co-γ-radiation at temperatures between 150 and 450 deg C. The results on radiolysis and pyrolysis were as follows: 1., The most thermally stable product is hydrogen iodide in which already at 450 deg C essen-tially all originally present iodine appears. 2., The radiolytic formation of methyl iodide and hydrogen iodide is positively influenced by the rise in temperature, This and the absolute values of yields indicate a chain mechanism of radiolytic (and pyrolytic) decomposition of the mixture. 3., The ratio of equilibrium concentrations [HI]/[CH 3 I] increases with increasing temperature of pyrolysis showing that HI is the end product of the thermal chain reaction. Methyl iodide is likely to contribute (by its thermal decomposition) to the initiation and propagation of this chain reaction. 4., The negligible temperature dependence of G(H 2 ) and the absence of molecular hydrogen among the products of pyrolytic decomposition of methane-iodine mixtures shows, that (up to 450 deg C) H atoms do not play any role in the thermal chain decomposition of these mixtures. (K.A.)

  10. Survey of Differentially Methylated Promoters in Prostate Cancer Cell Lines

    Directory of Open Access Journals (Sweden)

    Yipeng Wang

    2005-08-01

    Full Text Available DNA methylation, copy number in the genomes of three immortalized prostate epithelial, five cancer cell lines (LNCaP, PC3, PC3M, PC3M-Pro4, PC3MLN4 were compared using a microarray-based technique. Genomic DNA is cut with a methylation-sensitive enzyme Hpall, followed by linker ligation, polymerase chain reaction (PCR amplification, labeling, hybridization to an array of promoter sequences. Only those parts of the genomic DNA that have unmethylated restriction sites within a few hundred base pairs generate PCR products detectable on an array. Of 2732 promoter sequences on a test array, 504 (18.5% showed differential hybridization between immortalized prostate epithelial, cancer cell lines. Among candidate hypermethylated genes in cancer-derived lines, there were eight (CD44, CDKN1A, ESR1, PLAU, RARB, SFN, TNFRSF6, TSPY previously observed in prostate cancer, 13 previously known methylation targets in other cancers (ARHI, bcl-2, BRCA1, CDKN2C, GADD45A, MTAP, PGR, SLC26A4, SPARC, SYK, TJP2, UCHL1, WIT-1. The majority of genes that appear to be both differentially methylated, differentially regulated between prostate epithelial, cancer cell lines are novel methylation targets, including PAK6, RAD50, TLX3, PIR51, MAP2K5, INSR, FBN1, GG2-1, representing a rich new source of candidate genes used to study the role of DNA methylation in prostate tumors.

  11. The altered promoter methylation of oxytocin receptor gene in autism.

    Science.gov (United States)

    Elagoz Yuksel, Mine; Yuceturk, Betul; Karatas, Omer Faruk; Ozen, Mustafa; Dogangun, Burak

    Autism spectrum disorder (ASD) is one of the lifelong existing disorders. Abnormal methylation status of gene promoters of oxytonergic system has been implicated as among the etiologic factors of ASDs. We, therefore, investigated the methylation frequency of oxytocin receptor gene (OXTR) promoter from peripheral blood samples of children with autistic features. Our sample includes 66 children in total (22-94 months); 27 children with ASDs according to the DSM-IV-TR and the Childhood Autism Rating Scale (CARS) and 39 children who do not have any autistic like symptoms as the healthy control group. We investigated the DNA methylation status of OXTR promoter by methylation specific enzymatic digestion of genomic DNA and polymerase chain reaction. A significant relationship has been found between ASDs and healthy controls for the reduction of methylation frequency of the regions MT1 and MT3 of OXTR. We could not find any association in the methylation frequency of MT2 and MT4 regions of OXTR. Although our findings indicate high frequency of OXTR promoter hypomethylation in ASDs, there is need for independent replication of the results for a bigger sample set. We expect that future studies with the inclusion of larger, more homogeneous samples will attempt to disentangle the causes of ASDs.

  12. Quantitative analysis of DNA methylation in chronic lymphocytic leukemia patients.

    Science.gov (United States)

    Lyko, Frank; Stach, Dirk; Brenner, Axel; Stilgenbauer, Stephan; Döhner, Hartmut; Wirtz, Michaela; Wiessler, Manfred; Schmitz, Oliver J

    2004-06-01

    Changes in the genomic DNA methylation level have been found to be closely associated with tumorigenesis. In order to analyze the relation of aberrant DNA methylation to clinical and biological risk factors, we have determined the cytosine methylation level of 81 patients diagnosed with chronic lymphocytic leukemia (CLL). The analysis was based on DNA hydrolysis followed by derivatization of the 2'-desoxyribonucleoside-3'-monophosphates with BODIPY FL EDA. Derivatives were separated by micellar electrokinetic chromatography, and laser-induced fluorescence was used for detection. We analyzed potential correlations between DNA methylation levels and numerous patient parameters, including clinical observations and biological data. As a result, we observed a significant correlation with the immunoglobulin variable heavy chain gene (VH) mutation status. This factor has been repeatedly proposed as a reliable prognostic marker for CLL, which suggests that the methylation level might be a valuable factor in determining the prognostic outcome of CLL. We are now in the process of refining our method to broaden its application potential. In this context, we show here that the oxidation of the fluorescence marker in the samples and the evaporation of methanol in the electrolytes can be prevented by a film of paraffin oil. In summary, our results thus establish capillary electrophoresis as a valuable tool for analyzing the DNA methylation status of clinical samples.

  13. Novel fatty acid methyl esters from the actinomycete Micromonospora aurantiaca

    Science.gov (United States)

    Bruns, Hilke; Riclea, Ramona

    2011-01-01

    Summary The volatiles released by Micromonospora aurantiaca were collected by means of a closed-loop stripping apparatus (CLSA) and analysed by GC–MS. The headspace extracts contained more than 90 compounds from different classes. Fatty acid methyl esters (FAMEs) comprised the major compound class including saturated unbranched, monomethyl and dimethyl branched FAMEs in diverse structural variants: Unbranched, α-branched, γ-branched, (ω−1)-branched, (ω−2)-branched, α- and (ω−1)-branched, γ- and (ω−1)-branched, γ- and (ω−2)-branched, and γ- and (ω−3)-branched FAMEs. FAMEs of the last three types have not been described from natural sources before. The structures for all FAMEs have been suggested based on their mass spectra and on a retention index increment system and verified by the synthesis of key reference compounds. In addition, the structures of two FAMEs, methyl 4,8-dimethyldodecanoate and the ethyl-branched compound methyl 8-ethyl-4-methyldodecanoate were deduced from their mass spectra. Feeding experiments with isotopically labelled [2H10]leucine, [2H10]isoleucine, [2H8]valine, [2H5]sodium propionate, and [methyl-2H3]methionine demonstrated that the responsible fatty acid synthase (FAS) can use different branched and unbranched starter units and is able to incorporate methylmalonyl-CoA elongation units for internal methyl branches in various chain positions, while the methyl ester function is derived from S-adenosyl methionine (SAM). PMID:22238549

  14. HIV Medicines and Side Effects

    Science.gov (United States)

    ... medicines, talk to your health care provider about possible side effects. Tell your health care provider about your lifestyle and point out any possible side effects that would be especially hard for you to ...

  15. Probiotics: Safety and Side Effects

    Science.gov (United States)

    ... of this page please turn JavaScript on. Feature: Probiotics Safety and Side Effects Past Issues / Winter 2016 ... Says About the Safety and Side Effects of Probiotics Whether probiotics are likely to be safe for ...

  16. Photoorientation of a liquid crystalline polyester with azobenzene side groups

    DEFF Research Database (Denmark)

    Zebger, I; Rutloh, M; Hoffmann, U

    2002-01-01

    segments in the side- and main-chain. The very high values of the normalized linear dichroism up to 0.8 and the birefringence (above 0.3) are due to the interaction of photoorientation and thermotropic self-organization. The induction of anisotropy shows a pronounced dependence on the power density...

  17. Using demand-side management to decrease transformer ageing

    NARCIS (Netherlands)

    van der Klauw, Thijs; Gerards, Marco Egbertus Theodorus; Hurink, Johann L.

    2016-01-01

    The introduction of local, often uncontrollable, generation units as well as larger loads such as electric vehicles (EVs) causes an increasing amount of stress on our energy supply chain, specifically on the distribution grids. Demand-side management (DSM) is often seen as a potential technology to

  18. Side-View Face Recognition

    NARCIS (Netherlands)

    Santemiz, P.; Spreeuwers, Lieuwe Jan; Veldhuis, Raymond N.J.

    2010-01-01

    Side-view face recognition is a challenging problem with many applications. Especially in real-life scenarios where the environment is uncontrolled, coping with pose variations up to side-view positions is an important task for face recognition. In this paper we discuss the use of side view face

  19. A model compound (methyl oleate, oleic acid, triolein) study of triglycerides hydrodeoxygenation over alumina-supported NiMo sulfide

    NARCIS (Netherlands)

    Coumans, A.E.; Hensen, E.J.M.

    We studied hydrodeoxygenation of model compounds for vegetable oil into diesel-range hydrocarbons on a sulfided NiMo/γ-Al2O3 catalyst under trickle-flow conditions. Methyl oleate (methyl ester of oleic acid, a C18 fatty acid with one unsaturated bond in the chain) represented the C18 alkyl esters in

  20. Crystal structure of di­methyl­ammonium hydrogen oxalate hemi(oxalic acid)

    Science.gov (United States)

    Diallo, Waly; Gueye, Ndongo; Crochet, Aurélien; Plasseraud, Laurent; Cattey, Hélène

    2015-01-01

    Single crystals of the title salt, Me2NH2 +·HC2O4 −·0.5H2C2O4, were isolated as a side product from the reaction involving Me2NH, H2C2O4 and Sn(n-Bu)3Cl in a 1:2 ratio in methanol or by the reaction of the (Me2NH2)2C2O4 salt and Sn(CH3)3Cl in a 2:1 ratio in ethanol. The asymmetric unit comprises a di­methyl­ammonium cation (Me2NH2 +), an hydrogenoxalate anion (HC2O4 −), and half a mol­ecule of oxalic acid (H2C2O4) situated about an inversion center. From a supra­molecular point of view, the three components inter­act together via hydrogen bonding. The Me2NH2 + cations and the HC2O4 − anions are in close proximity through bifurcated N—H⋯(O,O) hydrogen bonds, while the HC2O4 − anions are organized into infinite chains via O—H⋯O hydrogen bonds, propagating along the a-axis direction. In addition, the oxalic acid (H2C2O4) mol­ecules play the role of connectors between these chains. Both the carbonyl and hydroxyl groups of each diacid are involved in four inter­molecular inter­actions with two Me2NH2 + and two HC2O4 − ions of four distinct polymeric chains, via two N—H⋯O and two O—H⋯O hydrogen bonds, respectively. The resulting mol­ecular assembly can be viewed as a two-dimensional bilayer-like arrangement lying parallel to (010), and reinforced by a C—H⋯O hydrogen bond. PMID:25995858