Sample records for side chain rotational

  1. 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


    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...

  2. Side Chain Cyclized Aromatic Amino Acids

    DEFF Research Database (Denmark)

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


    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 p...

  3. Side chain polysiloxanes with phthalocyanine moieties

    Directory of Open Access Journals (Sweden)

    T. Ganicz


    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.

  4. Side Chain Engineering in Solution-Processable Conjugated Polymers

    KAUST Repository

    Mei, Jianguo


    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.

  5. 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


    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

  6. Modelling antibody side chain conformations using heuristic database search. (United States)

    Ritchie, D W; Kemp, G J


    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.

  7. Angle Specific Analysis of Side-to-Side Asymmetry in the Shoulder Rotators

    Directory of Open Access Journals (Sweden)

    Cassio V. Ruas


    Full Text Available Although side-to-side asymmetry of the shoulder rotators calculated by independent peak torque (IPT has been used for interpretation of injury risks in athletes, it may not measure strength through the entire range of motion (ROM tested. The aim of this study was to compare side-to-side asymmetry of the shoulder rotators between independent peak torque (IPT and ten-degree angle specific torque (AST. Twenty healthy adult males (24.65 ± 2.4 years performed concentric and eccentric internal rotation (IR and external rotation (ER of the preferred and non-preferred arms on an isokinetic dynamometer at 60°/s through 150° of total ROM. The total ROM was divided into 14 ten-degree angles of the physiological ROM from −90° of ER to 60° of IR. Concentric and eccentric IR IPT (10.5% ± 8.7% and 12.1% ± 7.2% and ER IPT (13.6% ± 9.8% and 8.7% ± 5.6% were significantly less than AST at several angles (p < 0.05. IPT might lead to erroneous interpretations of side-to-side asymmetry in the shoulder rotators and does not represent the entire ROM tested. This information could be used to prescribe strength exercises to enhance overhead performance and reduce risk of shoulder injuries.

  8. Simultaneous in vivo truncation of pectic side chains

    DEFF Research Database (Denmark)

    Øbro, Jens; Borkhardt, Bernhard; Harholt, Jesper


    . 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...

  9. Holographic Gratings in Azobenzene Side-Chain Polymethacrylates

    DEFF Research Database (Denmark)

    Andruzzi, Luisa; Altomare, Angelina; Ciardelli, Francesco


    Optical storage properties of thin unoriented liquid crystalline and amorphous side-chain azobenzene polymethacrylate films are examined by polarization holographic measurements. The investigated materials are free radical copolymers derived from two photochromic monomers, 6-(4-oxy-4...

  10. Antibody side chain conformations are position-dependent. (United States)

    Leem, Jinwoo; Georges, Guy; Shi, Jiye; Deane, Charlotte M


    Side chain prediction is an integral component of computational antibody design and structure prediction. Current antibody modelling tools use backbone-dependent rotamer libraries with conformations taken from general proteins. Here we present our antibody-specific rotamer library, where rotamers are binned according to their immunogenetics (IMGT) position, rather than their local backbone geometry. We find that for some amino acid types at certain positions, only a restricted number of side chain conformations are ever observed. Using this information, we are able to reduce the breadth of the rotamer sampling space. Based on our rotamer library, we built a side chain predictor, position-dependent antibody rotamer swapper (PEARS). On a blind test set of 95 antibody model structures, PEARS had the highest average χ 1 and χ1+2 accuracy (78.7% and 64.8%) compared to three leading backbone-dependent side chain predictors. Our use of IMGT position, rather than backbone ϕ/ψ, meant that PEARS was more robust to errors in the backbone of the model structure. PEARS also achieved the lowest number of side chain-side chain clashes. PEARS is freely available as a web application at © 2018 Wiley Periodicals, Inc.

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

    KAUST Repository

    Bhuyan, M.S.


    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.

  12. Effect of Rotational Speed on the Stability of Two Rotating Side-by-side Circular Cylinders at Low Reynolds Number (United States)

    Dou, Huashu; Zhang, Shuo; Yang, Hui; Setoguchi, Toshiaki; Kinoue, Yoichi


    Flow around two rotating side-by-side circular cylinders of equal diameter D is numerically studied at the Reynolds number 40≤ Re ≤200 and various rotation rate θ i . The incoming flow is assumed to be two-dimensional laminar flow. The governing equations are the incompressible Navier-Stokes equations and solved by the finite volume method (FVM). The ratio of the center-to-center spacing to the cylinder diameter is T/D=2. The objective of the present work is to investigate the effect of rotational speed and Reynolds number on the stability of the flow. The simulation results are compared with the experimental data and a good agreement is achieved. The stability of the flow is analyzed by using the energy gradient theory, which produces the energy gradient function K to identify the region where the flow is the most prone to be destabilized and the degree of the destabilization. Numerical results reveal that K is the most significant at the separated shear layers of the cylinder pair. With Re increases, the length of the wake is shorter and the vortex shedding generally exhibits a symmetrical distribution for θ i < θ crit . It is also shown that the unsteady vortex shedding can be suppressed by rotating the cylinders in the counter-rotating mode.

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

    Indian Academy of Sciences (India)

    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. Such a scenario arises in several practical applications. In particular, we consider a contract manufacturer who procures ...

  14. Three entropic classes of side chain in a globular protein

    Energy Technology Data Exchange (ETDEWEB)

    Glass, Dennis C. [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Krishnan, Marimuthu [International Institute of Information Technology, Hyderbad (India); Smith, Jeremy C. [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Baudry, Jerome Y. [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)


    The relationship between the NMR methyl group axial order parameter and the side chain conformational entropy is investigated in inhibitor-bound and apo human HIV protease using molecular dynamics simulation. Three distinct entropic classes of methyl-bearing side chains, determined by the topological distance of the methyl group from the protein backbone (i.e., the number of -bonds between the C and the carbon of the CH3 group), are revealed by atomistic trajectory analyses performed in the local frame of reference of individual methyl probes. The results demonstrate that topologically equivalent methyl groups experience similar nonbonded microenvironments regardless of the type of residues to which they are attached. Similarly, methyl groups that belong to the same side chain but that are not topologically equivalent exhibit different thermodynamic and dynamic properties. As a result, the two-parameter classification (based upon entropy and methyl axial order parameter) of side chains described here permits improved estimates of the conformational entropies of proteins from NMR motional parameters.

  15. Access to Functionalized Steroid Side Chains via Modified Julia Olefination (United States)

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


    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

  16. Mapping side chain interactions at protein helix termini. (United States)

    Newell, Nicholas E


    Interactions that involve one or more amino acid side chains near the ends of protein helices stabilize helix termini and shape the geometry of the adjacent loops, making a substantial contribution to overall protein structure. Previous work has identified key helix-terminal motifs, such as Asx/ST N-caps, the capping box, and hydrophobic and electrostatic interactions, but important questions remain, including: 1) What loop backbone geometries are favoured by each motif? 2) To what extent are multi-amino acid motifs likely to represent genuine cooperative interactions? 3) Can new motifs be identified in a large, recent dataset using the latest bioinformatics tools? Three analytical tools are applied here to answer these questions. First, helix-terminal structures are partitioned by loop backbone geometry using a new 3D clustering algorithm. Next, Cascade Detection, a motif detection algorithm recently published by the author, is applied to each cluster to determine which sequence motifs are overrepresented in each geometry. Finally, the results for each motif are presented in a CapMap, a 3D conformational heatmap that displays the distribution of the motif's overrepresentation across loop geometries, enabling the rapid isolation and characterization of the associated side chain interaction. This work identifies a library of geometry-specific side chain interactions that provides a new, detailed picture of loop structure near the helix terminus. Highlights include determinations of the favoured loop geometries for the Asx/ST N-cap motifs, capping boxes, "big" boxes, and other hydrophobic, electrostatic, H-bond, and pi stacking interactions, many of which have not been described before. This work demonstrates that the combination of structural clustering and motif detection in the sequence space can efficiently identify side chain motifs and map them to the loop geometries which they support. Protein designers should find this study useful, because it identifies side

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

    DEFF Research Database (Denmark)

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


    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 characteris...... 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.......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...

  18. Einstein -coefficients for rotational transitions in the ring-chain ...

    Indian Academy of Sciences (India)

    tection of the ring-chain isomer (isomer 1) of C5H2 in cosmic objects has been suggested. For identification of a ... stein A-coefficients for electric dipole transitions in the ring-chain isomer of C5H2 among the rotational levels ..... Larger value of radiative lifetime of the upper level than that of the lower one support the idea of ...

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

    DEFF Research Database (Denmark)

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


    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...

  20. Highly conductive side chain block copolymer anion exchange membranes. (United States)

    Wang, Lizhu; Hickner, Michael A


    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.

  1. Role of Side-Chain Conformational Entropy in Transmembrane Helix Dimerization of Glycophorin A (United States)

    Liu, Wei; Crocker, Evan; Siminovitch, David J.; Smith, Steven O.


    Dimerization of the transmembrane domain of glycophorin A is mediated by a seven residue motif LIxxGVxxGVxxT through a combination of van der Waals and hydrogen bonding interactions. One of the unusual features of the motif is the large number of β-branched amino acids that may limit the entropic cost of dimerization by restricting side-chain motion in the monomeric transmembrane helix. Deuterium NMR spectroscopy is used to characterize the dynamics of fully deuterated Val80 and Val84, two essential amino acids of the dimerization motif. Deuterium spectra of the glycophorin A transmembrane dimer were obtained using synthetic peptides corresponding to the transmembrane sequence containing either perdeuterated Val80 or Val84. These data were compared with spectra of monomeric glycophorin A peptides deuterated at Val84. In all cases, the deuterium line shapes are characterized by fast methyl group rotation with virtually no motion about the Cα-Cβ bond. This is consistent with restriction of the side chain in both the monomer and dimer due to intrahelical packing interactions involving the β-methyl groups, and indicates that there is no energy cost associated with dimerization due to loss of conformational entropy. In contrast, deuterium NMR spectra of Met81 and Val82, in the lipid interface, reflected greater motional averaging and fast exchange between different side-chain conformers. PMID:12547806

  2. 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


    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...

  3. 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)


    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.

  4. Rotational dynamics of gold nanoparticle chains in water solution

    Energy Technology Data Exchange (ETDEWEB)

    Zimbone, M.; Musumeci, P.; Baeri, P. [Dipartimento di Fisica ed Astronomia (Italy); Messina, E. [Dipartimento di Scienze Chimiche (Italy); Boninelli, S. [MATIS IMM CNR (Italy); Compagnini, G. [Dipartimento di Scienze Chimiche (Italy); Calcagno, L., E-mail: [Dipartimento di Fisica ed Astronomia (Italy)


    In this work we report a study on the determination of the shape of aggregated gold colloids, obtained by adding pyridine to a solution of pure gold nanoparticles prepared by laser ablation in water studying their dynamic behavior. We have simultaneously measured the translational and rotational diffusion coefficients of dilute solutions of the as-prepared and aggregated gold nanoparticles by polarized and depolarized dynamic light scattering. An increase of the hydrodynamic radius from 26 to 135 nm and a decrease of the rotational diffusion coefficient of two order of magnitude are measured with increasing the pyridine concentration, both correlated to the aggregate formation. The dynamic properties of nanoaggregates have been interpreted by applying a model which allows a direct evaluation of translation and rotational diffusion coefficients of a chain of spherical particles by changing the number and the relative position of each nanoparticle in the aggregate. The comparison between experimental and calculated values indicates that an aggregation of less than ten isolated nanoparticles produces mainly rod-like chains, while aggregate morphology approaches the fractal-like configuration with increasing aggregation number.

  5. The pulsation-rotation interaction: Greatest hits and the B-side (United States)

    Townsend, Rich


    It has long been known that rotation can have an appreciable impact on stellar pulsation - by modifying the usual p and g modes found in the non-rotating case, and by introducing new classes of modes. However, it's only relatively recently that advances in numerical simulations and complementary theoretical treatments have enabled us to model these phenomena in any great detail. In this talk I'll review highlights in this area (the `Greatest Hits'), before considering the flip side (or the `B-side', for those of us old enough to remember vinyl records) of the pulsation-rotation interaction: how pulsation can itself influence internal rotation profiles.

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

    International Nuclear Information System (INIS)

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


    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

  7. 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 ...

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

    International Nuclear Information System (INIS)

    Terwilliger, Thomas C.


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

    Indian Academy of Sciences (India)

    Keywords. Supply chain management; dynamic pricing; partner selection; supply chain planning; electronic marketplaces. ... Author Affiliations. Roshan Gaonkar1 N Viswanadham1. The Logistics Institute – Asia Pacific, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260 ...

  10. The isotridecanyl side chain of plusbacin-A3 is essential for the transglycosylase inhibition of peptidoglycan biosynthesis. (United States)

    Kim, Sung Joon; Singh, Manmilan; Wohlrab, Aaron; Yu, Tsyr-Yan; Patti, Gary J; O'Connor, Robert D; VanNieuwenhze, Michael; Schaefer, Jacob


    Plusbacin-A3 (pb-A3) is a cyclic lipodepsipeptide that exhibits antibacterial activity against multidrug-resistant Gram-positive pathogens. Plusbacin-A3 is thought not to enter the cell cytoplasm, and its lipophilic isotridecanyl side chain is presumed to insert into the membrane bilayer, thereby facilitating either lipid II binding or some form of membrane disruption. Analogues of pb-A3, [(2)H]pb-A3 and deslipo-pb-A3, were synthesized to test membrane insertion as a key to the mode of action. [(2)H]pb-A3 has an isotopically (2)H-labeled isopropyl subunit of the lipid side chain, and deslipo-pb-A3 is missing the isotridecanyl side chain. Both analogues have the pb-A3 core structure. The loss of antimicrobial activity in deslipo-pb-A3 showed that the isotridecanyl side chain is crucial for the mode of action of the drug. However, rotational-echo double-resonance nuclear magnetic resonance characterization of [(2)H]pb-A3 bound to [1-(13)C]glycine-labeled whole cells of Staphylococcus aureus showed that the isotridecanyl side chain does not insert into the lipid membrane but instead is found in the staphylococcal cell wall, positioned near the pentaglycyl cross-bridge of the cell-wall peptidoglycan. Addition of [(2)H]pb-A3 during the growth of S. aureus resulted in the accumulation of Park's nucleotide, consistent with the inhibition of the transglycosylation step of peptidoglycan biosynthesis.

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

    KAUST Repository

    Li, Huawei


    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. Side-chain crystallization in alkyl-substituted cellulose esters and hydroxypropyl cellulose esters. (United States)

    Chen, Xi; Zheng, Nan; Wang, Qiao; Liu, Lingzhi; Men, Yongfeng


    The differences in side chain crystallization behavior between cellulose esters (CEs) and hydroxypropyl cellulose esters (HPCEs) were systematically investigated by a combination of differential scanning calorimetry (DSC) and small and wide-angle X-ray scattering techniques. DSC investigation indicated that under the same side chain length, the fusion enthalpy and the number of crystallized CH 2 of CEs were smaller than HPCEs. At the same time, their d-spacing and molecular arrangements were also different from each other. For the CEs, the side chains are perpendicular to the main chain, while the side chains most probably tend to tilt to main chain in the HPCEs as was evidenced by X-ray scattering results. The phenomenon can be understood as a consequence of different flexibility of attachment bridges in both kinds of side chain polymers and the steric hindrance of methyl group in the hydroxypropyl group in HPCEs. In addition, the added hydroxypropyl substituents make the side chain length increasing. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    African Journals Online (AJOL)

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    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 stable by ...

  14. 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 ...

  15. Ambipolar charge transport in polymer:fullerene bulk heterojunctions for different polymer side-chains (United States)

    Fall, S.; Biniek, L.; Leclerc, N.; Lévêque, P.; Heiser, T.


    We use field-effect transistors to investigate electron and hole mobilities in polymer:fullerene blends. Low-band-gap polymers with a common conjugated backbone and differing side-chains are utilized in order to clarify the link between the side-chain molecular structure and grafting position, and the power-conversion efficiency of related bulk heterojunction solar cells. The results show that, at a fixed polymer:fullerene weight ratio, the electron mobility increases by more than four orders of magnitude when changing from linear to branched side-chains. As a consequence, the photovoltaic performances are highest at low fullerene contents for branched chains while the opposite is true for linear chains.

  16. Synthesis and solution self-assembly of side-chain cobaltocenium-containing block copolymers. (United States)

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


    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.

  17. Five new triterpene bisglycosides with acyclic side chains from the rhizomes of Cimicifuga foetida L. (United States)

    Lu, Lu; Chen, Jian-Chao; Song, He-Jiao; Li, Yan; Nian, Yin; Qiu, Ming-Hua


    Five new triterpene bisglycosides, foetidinosides A (1), B (2), C (3), D (4) and E (5), including three of the cycloartane type, one of its derivative, and one of the lanostane type were isolated from the rhizomes of Cimicifuga foetida. Their structures were elucidated on the basis of spectroscopic data and chemical evidence. They were the first bisglycosides with acyclic side chains which were different from the typical triterpenes with side chains epoxidized with ring D in Cimicifuga species.

  18. Searching for low percolation thresholds within amphiphilic polymer membranes: The effect of side chain branching (United States)

    Dorenbos, G.


    Percolation thresholds for solvent diffusion within hydrated model polymeric membranes are derived from dissipative particle dynamics in combination with Monte Carlo (MC) tracer diffusion calculations. The polymer backbones are composed of hydrophobic A beads to which at regular intervals Y-shaped side chains are attached. Each side chain is composed of eight A beads and contains two identical branches that are each terminated with a pendant hydrophilic C bead. Four types of side chains are considered for which the two branches (each represented as [C], [AC], [AAC], or [AAAC]) are splitting off from the 8th, 6th, 4th, or 2nd A bead, respectively. Water diffusion through the phase separated water containing pore networks is deduced from MC tracer diffusion calculations. The percolation threshold for the architectures containing the [C] and [AC] branches is at a water volume fraction of ˜0.07 and 0.08, respectively. These are much lower than those derived earlier for linear architectures of various side chain length and side chain distributions. Control of side chain architecture is thus a very interesting design parameter to decrease the percolation threshold for solvent and proton transports within flexible amphiphilic polymer membranes.

  19. Side-chain modification and "grafting onto" via olefin cross-metathesis. (United States)

    de Espinosa, Lucas Montero; Kempe, Kristian; Schubert, Ulrich S; Hoogenboom, Richard; Meier, Michael A R


    Olefin cross-metathesis is introduced as a versatile polymer side-chain modification technique. The reaction of a poly(2-oxazoline) featuring terminal double bonds in the side chains with a variety of functional acrylates has been successfully performed in the presence of Hoveyda-Grubbs second-generation catalyst. Self-metathesis, which would lead to polymer-polymer coupling, can be avoided by using an excess of the cross-metathesis partner and a catalyst loading of 5 mol%. The results suggest that bulky acrylates reduce chain-chain coupling due to self-metathesis. Moreover, different functional groups such as alkyl chains, hydroxyl, and allyl acetate groups, as well as an oligomeric poly(ethylene glycol) and a perfluorinated alkyl chain have been grafted with quantitative conversions. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Asparagine and glutamine side-chain conformation in solution and crystal: A comparison for hen egg-white lysozyme using residual dipolar ouplings

    International Nuclear Information System (INIS)

    Higman, Victoria A.; Boyd, Jonathan; Smith, Lorna J.; Redfield, Christina


    Experimental 15 N- 1 H and 1 H- 1 H residual dipolar couplings (RDCs) for the asparagine (Asn) and glutamine (Gln) side chains of hen egg-white lysozyme are measured and analysed in conjunction with 1 N relaxation data, information about χ 1 torsion angles in solution and molecular dynamics simulations. The RDCs are compared to values predicted from 16 high-resolution crystal structures. Two distinct groups of Asn and Gln side chains are identified. The first contains residues whose side chains show a fixed, relatively rigid, conformation in solution. For these residues there is good agreement between the experimental and predicted RDCs. This agreement improves when the experimental order parameter, S, is included in the calculation of the RDCs from the crystal structures. The comparison of the experimental RDCs with values calculated from the X-ray structures shows that the similarity between the oxygen and nitrogen electron densities is a limitation to the correct assignment of the Asn and Gln side-chain orientation in X-ray structures. In the majority of X-ray structures a 180 deg. rotation about χ 2 or χ 3 , leading to the swapping of N δε2 and O δε1 , is necessary for at least one Asn or Gln residue in order to achieve good agreement between experimental and predicted RDCs. The second group contains residues whose side chains do not adopt a single, well-defined, conformation in solution. These residues do not show a correlation between the experimental and predicted RDCs. In many cases the family of crystal structures shows a range of orientations for these side chains, but in others the crystal structures show a well-defined side-chain position. In the latter case, this is found to arise from crystallographic contacts and does not represent the behaviour of the side chain in solution

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

    Energy Technology Data Exchange (ETDEWEB)

    López-Barrón, Carlos R., E-mail:; Brant, Patrick; Crowther, Donna J. [ExxonMobil Chemical Company, Baytown, Texas 77520 (United States); Eberle, Aaron P. R. [ExxonMobil Research and Engineering Company, Annandale, New Jersey 08801 (United States)


    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{sub w}/M{sub 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{sub 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{sub SC}). Therefore, the glassy behavior of these polymers as well as their molecular friction and dynamic properties are influenced by their N{sub SC} values. The apparent flow activation energies are a decreasing function of N{sub SC}, and their values explain the differences in zero-shear viscosity measured at different temperatures.

  2. Sparse networks of directly coupled, polymorphic, and functional side chains in allosteric proteins. (United States)

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


    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.

  3. 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


    of carbonyls (including formaldehyde, acetone, isobutyraldehyde, and glyoxylic acid) via the formation, and subsequent beta-scission of alkoxyl radicals. The concentration of these products increases with the HO(*) flux. The release of multiple carbonyls confirms the occurrence of oxidation at C-3 and C-4...... cleavage) and formaldehyde, via the formation and subsequent beta-scission, of C-3 alkoxyl radicals. We now show that this side-chain to backbone damage transfer, is a general mechanism for aliphatic side-chains. Oxidation of Val, Leu, and Asp residues by HO(*)/O(2) results in the release of a family...... for Val, and these sites, plus C-5, for Leu. The detection of glyoxylic acid and CO(2)(-*) from Asp demonstrates the occurrence of competing beta-scission processes for the Asp C-3 alkoxyl radical. The yield of hydroperoxides and released carbonyls account for 10-145% of the initial HO(*). The greater...

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

    International Nuclear Information System (INIS)

    King, S.T.; Garces, J.


    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

  5. Assessment of Protein Side-Chain Conformation Prediction Methods in Different Residue Environments (United States)

    Peterson, Lenna X.; Kang, Xuejiao; Kihara, Daisuke


    Computational prediction of side-chain conformation is an important component of protein structure prediction. Accurate side-chain prediction is crucial for practical applications of protein structure models that need atomic detailed resolution such as protein and ligand design. We evaluated the accuracy of eight side-chain prediction methods in reproducing the side-chain conformations of experimentally solved structures deposited to the Protein Data Bank. Prediction accuracy was evaluated for a total of four different structural environments (buried, surface, interface, and membrane-spanning) in three different protein types (monomeric, multimeric, and membrane). Overall, the highest accuracy was observed for buried residues in monomeric and multimeric proteins. Notably, side-chains at protein interfaces and membrane-spanning regions were better predicted than surface residues even though the methods did not all use multimeric and membrane proteins for training. Thus, we conclude that the current methods are as practically useful for modeling protein docking interfaces and membrane-spanning regions as for modeling monomers. PMID:24619909

  6. Beyond rotamers: a generative, probabilistic model of side chains in proteins

    Directory of Open Access Journals (Sweden)

    Frellsen Jes


    Full Text Available Abstract Background Accurately covering the conformational space of amino acid side chains is essential for important applications such as protein design, docking and high resolution structure prediction. Today, the most common way to capture this conformational space is through rotamer libraries - discrete collections of side chain conformations derived from experimentally determined protein structures. The discretization can be exploited to efficiently search the conformational space. However, discretizing this naturally continuous space comes at the cost of losing detailed information that is crucial for certain applications. For example, rigorously combining rotamers with physical force fields is associated with numerous problems. Results In this work we present BASILISK: a generative, probabilistic model of the conformational space of side chains that makes it possible to sample in continuous space. In addition, sampling can be conditional upon the protein's detailed backbone conformation, again in continuous space - without involving discretization. Conclusions A careful analysis of the model and a comparison with various rotamer libraries indicates that the model forms an excellent, fully continuous model of side chain conformational space. We also illustrate how the model can be used for rigorous, unbiased sampling with a physical force field, and how it improves side chain prediction when used as a pseudo-energy term. In conclusion, BASILISK is an important step forward on the way to a rigorous probabilistic description of protein structure in continuous space and in atomic detail.

  7. Beyond rotamers: a generative, probabilistic model of side chains in proteins. (United States)

    Harder, Tim; Boomsma, Wouter; Paluszewski, Martin; Frellsen, Jes; Johansson, Kristoffer E; Hamelryck, Thomas


    Accurately covering the conformational space of amino acid side chains is essential for important applications such as protein design, docking and high resolution structure prediction. Today, the most common way to capture this conformational space is through rotamer libraries - discrete collections of side chain conformations derived from experimentally determined protein structures. The discretization can be exploited to efficiently search the conformational space. However, discretizing this naturally continuous space comes at the cost of losing detailed information that is crucial for certain applications. For example, rigorously combining rotamers with physical force fields is associated with numerous problems. In this work we present BASILISK: a generative, probabilistic model of the conformational space of side chains that makes it possible to sample in continuous space. In addition, sampling can be conditional upon the protein's detailed backbone conformation, again in continuous space - without involving discretization. A careful analysis of the model and a comparison with various rotamer libraries indicates that the model forms an excellent, fully continuous model of side chain conformational space. We also illustrate how the model can be used for rigorous, unbiased sampling with a physical force field, and how it improves side chain prediction when used as a pseudo-energy term. In conclusion, BASILISK is an important step forward on the way to a rigorous probabilistic description of protein structure in continuous space and in atomic detail.

  8. 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


    functional phenotypes that are different from those observed previously in Kv VSDs. In contrast, and similar to results obtained with Kv channels, individually neutralizing acidic side chains with synthetic derivatives and with natural amino acid substitutions in the INC had little or no effect......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...

  9. Record high hole mobility in polymer semiconductors via side-chain engineering. (United States)

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


    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.

  10. Can understanding the packing of side chains improve the design of protein-protein interactions? (United States)

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


    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.

  11. Posttranslational mutagenesis: A chemical strategy for exploring protein side-chain diversity. (United States)

    Wright, Tom H; Bower, Ben J; Chalker, Justin M; Bernardes, Gonçalo J L; Wiewiora, Rafal; Ng, Wai-Lung; Raj, Ritu; Faulkner, Sarah; Vallée, M Robert J; Phanumartwiwath, Anuchit; Coleman, Oliver D; Thézénas, Marie-Laëtitia; Khan, Maola; Galan, Sébastien R G; Lercher, Lukas; Schombs, Matthew W; Gerstberger, Stefanie; Palm-Espling, Maria E; Baldwin, Andrew J; Kessler, Benedikt M; Claridge, Timothy D W; Mohammed, Shabaz; Davis, Benjamin G


    Posttranslational modification of proteins expands their structural and functional capabilities beyond those directly specified by the genetic code. However, the vast diversity of chemically plausible (including unnatural but functionally relevant) side chains is not readily accessible. We describe C (sp 3 )-C (sp 3 ) bond-forming reactions on proteins under biocompatible conditions, which exploit unusual carbon free-radical chemistry, and use them to form Cβ-Cγ bonds with altered side chains. We demonstrate how these transformations enable a wide diversity of natural, unnatural, posttranslationally modified (methylated, glycosylated, phosphorylated, hydroxylated), and labeled (fluorinated, isotopically labeled) side chains to be added to a common, readily accessible dehydroalanine precursor in a range of representative protein types and scaffolds. This approach, outside of the rigid constraints of the ribosome and enzymatic processing, may be modified more generally for access to diverse proteins. Copyright © 2016, American Association for the Advancement of Science.

  12. Side-Chain Effects on the Thermoelectric Properties of Fluorene-Based Copolymers. (United States)

    Liang, Ansheng; Zhou, Xiaoyan; Zhou, Wenqiao; Wan, Tao; Wang, Luhai; Pan, Chengjun; Wang, Lei


    Three conjugated polymers with alkyl chains of different lengths are designed and synthesized, and their structure-property relationship as organic thermoelectric materials is systematically elucidated. All three polymers show similar photophysical properties, thermal properties, and mechanical properties; however, their thermoelectric performance is influenced by the length of their side chains. The length of the alkyl chain significantly influences the electrical conductivity of the conjugated polymers, and polymers with a short alkyl chain exhibit better conductivity than those with a long alkyl chain. The length of the alkyl chain has little effect on the Seebeck coefficient. Only a slight increase in the Seebeck coefficient is observed with the increasing length of the alkyl chain. The purpose of this study is to provide comprehensive insight into fine-tuning the thermoelectric properties of conjugated polymers as a function of side-chain engineering, thereby providing a novel perspective into the design of high-performance thermoelectric conjugated polymers. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. 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


    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...

  14. Synthesis and antimalarial activity of new chloroquine analogues carrying a multifunctional linear side chain (United States)

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


    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 structure proved detrimental to the activity against the CQR strain. PMID:19703776

  15. Electro-optic side-chain polyimide system with large optical nonlinearity and high thermal stability (United States)

    Sotoyama, Wataru; Tatsuura, Satoshi; Yoshimura, Tetsuzo


    We report electro-optic (EO) efficiency and thermal stability of a poled polyimide system with nonlinear optical dyes as side chains. The side-chain polyimide system is synthesized from a dianhydride containing azobenzene dye and a diamine. The dye in the polymer is chemically stable for temperatures below 250 °C. The polymer can be poled simultaneously with or after imidization of the polyamic acid. Our sample poled after imidization shows a large EO coefficient (r33=10.8 pm/V at λ=1.3 μm) and long-term thermal stability at 120 °C.

  16. Exploring backbone-cation alkyl spacers for multi-cation side chain anion exchange membranes (United States)

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


    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.

  17. side chains

    African Journals Online (AJOL)


    The deactivation was then varied slowly with the increasing number of cumene pulses and was distinct for studied temperatures and for different exchanged samples. This could be explained from a part, by a strength and distribution of acidity catalysts and from another part by a rapid desorption process of coke deposited ...

  18. side chains

    African Journals Online (AJOL)


    Department of Chemistry, Addis Ababa University, P.O. Box. 1176 ... Due to their fundamental importance in many chemical and biological processes aqueous ... form of the potentials together with their parameters are displayed in Table 1. For water-water interactions, the CF2 potential [45] was used, as this model is more ...

  19. Controllable rotation of microsphere chain in dual-beam fiber-optic trap with transverse offset (United States)

    Chen, Xinlin; Xiao, Guangzong; Han, Xiang; Xiong, Wei; Luo, Hui; Yang, Kaiyong


    Controllable rotation of the trapped microscopic objects has traditionally been thought of one of the most valuable optical manipulation techniques. The controllable rotation of a microsphere chain was achieved by the dual-beam fiber-optic trap with transverse offset. The experimental device was made up of a PDMS chip housing two counter-propagating fibers across a microfluidic flow channel. Each fiber was coupled with different laser diode source to avoid the generation of coherent interference, both operating at a wavelength of 980 nm. Each fiber was attached to a translation stage to adjust the transverse offset distance. The polystyrene microspheres with diameter of 10 μm were chosen as the trapped particles. The microfluidic flow channel of the device was flushed with the polystyrene microspheres solution by the mechanical fluid pump. At the beginning, the two fibers were strictly aligned to each other. Five microspheres were captured as a chain parallel to the axis of the fibers. When introducing a transverse offset to the counter-propagating fibers by adjusting the translation stages, the microsphere chain was observed to rotating in the trap center. When the offset distance was set as 9 μm, the rotation period is approximately 1.2s. A comprehensive analysis has been presented of the characteristics of the rotation. The functionality of rotated chain could be extended to applications requiring microfluidic mixing or to improving the reaction speed in a localized environment, and is generally applicable to biological and medical research.

  20. Chiro-and photooptical properties of a novel side-chain azobenzene-containing LC polymer

    Czech Academy of Sciences Publication Activity Database

    Bobrovsky, A.; Shibaev, V.; Hamplová, Věra; Kašpar, Miroslav; Glogarová, Milada


    Roč. 140, č. 7 (2009), s. 789-799 ISSN 0026-9247 R&D Projects: GA MŠk OC 175 Institutional research plan: CEZ:AV0Z10100520 Keywords : photooptical properties * side-chain polymer, * iquid crystalline * helical supermolecular structure Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.312, year: 2009

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

    DEFF Research Database (Denmark)

    Naydenova, I; Nikolova, L; Todorov, T


    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...... in the appearance of a surface relief with doubled frequency....

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

  3. Determination of monounsaturated alkyl side chain 2-alkylcyclobutanones in irradiated foods

    NARCIS (Netherlands)

    Horvatovich, Péter; Miesch, Michel; Hasselmann, Claude; Delincée, Henry; Marchioni, Eric


    The 2-alkylcyclobutanones (2-ACBs) are formed from triglycerides by irradiation treatment and may be used as markers for this type of food processing. This paper describes a detection method for the analysis of monounsaturated alkyl side chain 2-ACBs, which is formed upon irradiation from

  4. Ion pair formation of phosphorylated amino acids and lysine and arginine side chains : A theoretical study

    NARCIS (Netherlands)

    Mavri, J; Vogel, HJ

    Protein phosphorylation is one of the major signal transduction mechanisms for controlling and regulating intracellular processes, Phosphorylation of specific hydroxylated amino acid side chains (Ser, Thr, Tyr) by protein kinases can activate numerous enzymes; this effect can be reversed by the

  5. Side-chain Liquid Crystal Polymers (SCLCP: Methods and Materials. An Overview

    Directory of Open Access Journals (Sweden)

    Włodzimierz Stańczyk


    Full Text Available This review focuses on recent developments in the chemistry of side chain liquid crystal polymers. It concentrates on current trends in synthetic methods and novel, well defined structures, supramolecular arrangements, properties, and applications. The review covers literature published in this century, apart from some areas, such as dendritic and elastomeric systems, which have been recently reviewed.

  6. 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


    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

  7. Energetic, Structural, and Antimicrobial Analyses of [beta]-Lactam Side Chain Recognition by [beta]-Lactamases

    Energy Technology Data Exchange (ETDEWEB)

    Caselli, E.; Powers, R.A.; Blaszczak, L.C.; Wu, C.Y.E.; Prati, F.; Shoichet, B.K. (NWU)


    Penicillins and cephalosporins are among the most widely used and successful antibiotics. The emergence of resistance to these {beta}-lactams, most often through bacterial expression of {beta}-lactamases, threatens public health. To understand how {beta}-lactamases recognize their substrates, it would be helpful to know their binding energies. Unfortunately, these have been difficult to measure because {beta}-lactams form covalent adducts with {beta}-lactamases. This has complicated functional analyses and inhibitor design. To investigate the contribution to interaction energy of the key amide (R1) side chain of {beta}-lactam antibiotics, eight acylglycineboronic acids that bear the side chains of characteristic penicillins and cephalosporins, as well as four other analogs, were synthesized. These transition-state analogs form reversible adducts with serine {beta}-lactamases. Therefore, binding energies can be calculated directly from K{sub i} values. The K{sub i} values measured span four orders of magnitude against the Group I {beta}-lactamase AmpC and three orders of magnitude against the Group II {beta}-lactamase TEM-1. The acylglycineboronic acids have K{sub i} values as low as 20 nM against AmpC and as low as 390 nM against TEM-1. The inhibitors showed little activity against serine proteases, such as chymotrypsin. R1 side chains characteristic of {beta}-lactam inhibitors did not have better affinity for AmpC than did side chains characteristic of {beta}-lactam substrates. Two of the inhibitors reversed the resistance of pathogenic bacteria to {beta}-lactams in cell culture. Structures of two inhibitors in their complexes with AmpC were determined by X-ray crystallography to 1.90 {angstrom} and 1.75 {angstrom} resolution; these structures suggest interactions that are important to the affinity of the inhibitors. Acylglycineboronic acids allow us to begin to dissect interaction energies between {beta}-lactam side chains and {beta}-lactamases. Surprisingly

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

    DEFF Research Database (Denmark)

    Hvilsted, Søren; Pedersen, M; Holme, NCR


    . Atomic force and scanning near-held optical microscopic investigations of gratings prepared with orthogonally polarized overlapping beams have demonstrated that the anisotropy is preserved in the film despite extensive mass transport and surface corrugation after the irradiation process. However......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...... on azobenzene, iii- the methylene main-chain segment length, and iv-the polyester molecular mass, all influence the optical storage properties. A general synthetic route to novel mesogenic azobenzene diols comprising parameters i and ii is outlined. Polyesters with molecular masses (parameter iv) up to 100...

  9. Modulation of the transglycosylation activity of plant family GH18 chitinase by removing or introducing a tryptophan side chain. (United States)

    Umemoto, Naoyuki; Ohnuma, Takayuki; Osawa, Takuo; Numata, Tomoyuki; Fukamizo, Tamo


    Transglycosylation (TG) activity of a family GH18 chitinase from the cycad, Cycas revoluta, (CrChiA) was modulated by removing or introducing a tryptophan side chain. The removal from subsite +3 through mutation of Trp168 to alanine suppressed TG activity, while introduction into subsite +1 through mutation of Gly77 to tryptophan (CrChiA-G77W) enhanced TG activity. The crystal structures of an inactive double mutant of CrChiA (CrChiA-G77W/E119Q) with one or two N-acetylglucosamine residues occupying subsites +1 or +1/+2, respectively, revealed that the Trp77 side chain was oriented toward +1 GlcNAc to be stacked with it face-to-face, but rotated away from subsite +1 in the absence of GlcNAc at the subsite. Aromatic residues in the aglycon-binding site are key determinants of TG activity of GH18 chitinases. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  10. Arginine side chain interactions and the role of arginine as a gating charge carrier in voltage sensitive ion channels (United States)

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


    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.

  11. 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


    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.

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

    KAUST Repository

    Giovannitti, Alexander


    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.

  13. Preparation of Quinolinium Salts Differing in the Length of the Alkyl Side Chain

    Directory of Open Access Journals (Sweden)

    Kamil Kuca


    Full Text Available Quaternary quinolinium salts differing in alkyl chain length are members of a widespread group of cationic surfactants. These compounds have numerous applications in various branches of industry and research. In this work, the preparation of quinoline-derived cationic surface active agents differing in the length of the side alkyl chains (from C8 to C20 is described. An HPLC method was successfully developed for distinction of all members of the series of prepared long-chain quinolinium derivatives. In conclusion, some possibilities of intended tests or usage have been summarized. In vitro testing using a microdilution broth method showed good activity of a substance with a C12 chain length against Gram-positive cocci and Candida species.

  14. 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


    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

  15. Producing high-accuracy lattice models from protein atomic coordinates including side chains. (United States)

    Mann, Martin; Saunders, Rhodri; Smith, Cameron; Backofen, Rolf; Deane, Charlotte M


    Lattice models are a common abstraction used in the study of protein structure, folding, and refinement. They are advantageous because the discretisation of space can make extensive protein evaluations computationally feasible. Various approaches to the protein chain lattice fitting problem have been suggested but only a single backbone-only tool is available currently. We introduce LatFit, a new tool to produce high-accuracy lattice protein models. It generates both backbone-only and backbone-side-chain models in any user defined lattice. LatFit implements a new distance RMSD-optimisation fitting procedure in addition to the known coordinate RMSD method. We tested LatFit's accuracy and speed using a large nonredundant set of high resolution proteins (SCOP database) on three commonly used lattices: 3D cubic, face-centred cubic, and knight's walk. Fitting speed compared favourably to other methods and both backbone-only and backbone-side-chain models show low deviation from the original data (~1.5 Å RMSD in the FCC lattice). To our knowledge this represents the first comprehensive study of lattice quality for on-lattice protein models including side chains while LatFit is the only available tool for such models.

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


    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.

  17. Separation of cannabinoid receptor affinity and efficacy in delta-8-tetrahydrocannabinol side-chain analogues (United States)

    Griffin, Graeme; Williams, Stephanie; Aung, Mie Mie; Razdan, Raj K; Martin, Billy R; Abood, Mary E


    The activities of a number of side-chain analogues of delta-8-tetrahydrocannabinol (Δ8-THC) in rat cerebellar membrane preparations were tested.The affinities of each compound for the CB1 receptor were compared by their respective abilities to displace [3H]-SR141716A and their efficacies compared by stimulation of [35S]-GTPγS binding.It was found that the affinities varied from 0.19±0.03 nM for 3-norpentyl-3-[6′-cyano,1′,1′-dimethyl]hexyl-Δ8-THC to 395±66.3 nM for 5′-[N-(4-chlorophenyl)]-1′,1′-dimethyl-carboxamido-Δ8-THC.The efficacies of these compounds varied greatly, ranging from the very low efficacy exhibited to acetylenic compounds such as 1′-heptyn-Δ8-THC and 4′-octyn-Δ8-THC to higher efficacy compounds such as 5′-(4-cyanophenoxy)-1′,1′-dimethyl-Δ8-THC and 5′-[N-(4-aminosulphonylphenyl)]-1′,1′ dimethyl-carboxamido Δ8-THC. All agonist activities were antagonized by the CB1-selective antagonist SR141716A.It was found that a ligand's CB1 affinity and efficacy are differentially altered by modifications in the side-chain. Decreasing the flexibility of the side-chain reduced efficacy but largely did not alter affinity. Additionally, the positioning of electrostatic moieties, such as cyano groups, within the side-chain also has contrasting effects on these two properties.In summary, this report details the characterization of a number of novel Δ8-THC analogues in rat cerebellar membranes. It provides the first detailed pharmacological analysis of how the inclusion of electrostatic moieties in the side-chain and also how alteration of the side-chain's flexibility may differentially affect a CB1 cannabinoid receptor ligand's affinity and efficacy. PMID:11159703

  18. Correlation between protein secondary structure, backbone bond angles, and side-chain orientations (United States)

    Lundgren, Martin; Niemi, Antti J.


    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.

  19. Polypeptides with quaternary phosphonium side chains: synthesis, characterization, and cell-penetrating properties. (United States)

    Song, Ziyuan; Zheng, Nan; Ba, Xiaochu; Yin, Lichen; Zhang, Rujing; Ma, Liang; Cheng, Jianjun


    Polypeptides bearing quaternary phosphonium side chains were synthesized via controlled ring-opening polymerization of chlorine-functionalized amino acid N-carboxyanhydride monomers followed by one-step nucleophilic substitution reaction with triethylphosphine. The conformation of the resulting polypeptides can be controlled by modulating the side-chain length and α-carbon stereochemistry. The phosphonium-based poly(l-glutamate) derivatives with 11 σ-bond backbone-to-charge distance adopt stable α-helical conformation against pH and ionic strength changes. These helical, quaternary phosphonium-bearing polypeptides exhibit higher cell-penetrating capability than their racemic and random-coiled analogues. They enter cells mainly via an energy-independent, nonendocytic cell membrane transduction mechanism and exhibit low cytotoxicity, substantiating their potential use as a safe and effective cell-penetrating agent.

  20. 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


    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

  1. 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


    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

  2. 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


    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

  3. 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.


    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)

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

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


    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.

  5. Synthesis and coupling reactions of alpha,alpha-dialkylated amino acids with nucleobase side chains.


    Azumaya, I; Aebi, R; Kubik, S; Rebek, J


    Several di- and tripeptides containing protected purine (adenine) and pyrimidine (thymine) residues on their side chains were synthesized. The parent amino acids alpha, alpha-dialkylated in a symmetrical manner. An effective coupling procedure was developed for these sterically hindered amino acids: the fluoren-9-ylmethyloxycarbonyl-protected amino acid was dehydrated to its oxazolinone form, which was coupled in good yields with amino esters in hot tetrachloroethane.

  6. Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins. (United States)

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


    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.

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

    DEFF Research Database (Denmark)

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


    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....

  8. Applying Thienyl Side Chains and Different π-Bridge to Aromatic Side-Chain Substituted Indacenodithiophene-Based Small Molecule Donors for High-Performance Organic Solar Cells. (United States)

    Wang, Jin-Liang; Liu, Kai-Kai; Liu, Sha; Liu, Feng; Wu, Hong-Bin; Cao, Yong; Russell, Thomas P


    A pair of linear tetrafluorinated small molecular donors, named as ThIDTTh4F and ThIDTSe4F, which are with tetrathienyl-substituted IDT as electron-rich central core, electron-deficient difluorobenzothiadiazole as acceptor units, and donor end-capping groups, but having differences in the π-bridge (thiophene and selenophene), were successfully synthesized and evaluated as donor materials in organic solar cells. Such π-bridge and core units in these small molecules play a decisive role in the formation of the nanoscale separation of the blend films, which were systematically investigated through absorption spectra, grazing incidence X-ray diffraction pattern, transmission electron microscopy images, resonant soft X-ray scattering profiles, and charge mobility measurement. The ThIDTSe4F (with selenophene π-bridge)-based device exhibited superior performance than devices based on ThIDTh4F (with thiophene π-bridge) after post annealing treatment owing to optimized film morphology and improved charge transport. Power conversion efficiency of 7.31% and fill factor of ∼0.70 were obtained by using a blend of ThIDTSe4F and PC 71 BM with thermal annealing and solvent vapor annealing treatments, which is the highest PCE from aromatic side-chain substituted IDT-based small molecular solar cells. The scope of this study is to reveal the structure-property relationship of the aromatic side-chain substituted IDT-based donor materials as a function of π-bridge and the post annealing conditions.

  9. All solid-state polymer electrolytes prepared from a graft copolymer consisting of a polyimide main chain and poly(ethylene oxide) based side chains

    Energy Technology Data Exchange (ETDEWEB)

    Higa, Mitsuru, E-mail: [Graduate School of Science and Engineering, Yamaguchi University, 2-16-1 Tokiwadai, Ube City, Yamaguchi 755-8611 (Japan); Yaguchi, Kazuaki; Kitani, Ryousuke [Graduate School of Science and Engineering, Yamaguchi University, 2-16-1 Tokiwadai, Ube City, Yamaguchi 755-8611 (Japan)


    We prepare an all solid-state, liquid-free, polymer electrolyte (ASPE) from a lithium salt and a graft copolymer consisting of a polyimide main chain and poly(ethylene glycol) methyl ether methacrylate side chains using atom transfer radical polymerization method. The ionic conductivity of ASPEs increases with increasing the side chain length. The ionic conductivity of the ASPE whose POEM content = 60 wt% shows 6.5 x 10{sup -6} S/cm at 25 deg. C. The ASPEs having shorter average distance between side chains and/or shorter side chain length show higher mechanical strength. The tensile strength of the ASPEs is more than 10 MPa and about 20 times higher than that of the ASPEs in the previous study [Electrochim. Acta, 50 (1998) 3832]; hence, the ASPEs have sufficiently high mechanical strength for a polymer electrolyte of lithium secondary batteries.

  10. Contribution of cutinase serine 42 side chain to the stabilization of the oxyanion transition state. (United States)

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


    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.

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

    Directory of Open Access Journals (Sweden)

    Carl Henrik Görbitz


    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.

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

    KAUST Repository

    Giovannitti, Alexander


    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.

  13. Improving proton conduction pathways in di- and triblock copolymer membranes: Branched versus linear side chains (United States)

    Dorenbos, G.


    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.

  14. Regulation of the thermal sensitivity of hydroxypropyl cellulose by poly(N-isopropylacryamide) side chains. (United States)

    Jin, Xin; Kang, Hongliang; Liu, Ruigang; Huang, Yong


    Hydroxyproyl cellulose graft poly(N-isopropylacryamide) (HPC-g-PNIPAm) copolymers were synthesized by single-electron transfer living radical polymerization (SET-LRP) in water and THF mixture solvent and characterized. The controllability and polymerization rate of SET-LRP can be adjusted by the water/THF ratio in the mixture solvent. The monomer conversion rate is relatively low in the solvent with low water content. The thermal responsive property of HPC-g-PNIPAm copolymers in aqueous solution depends on the length of the graft chains. The relatively short PNIPAm side chains (<150 repeat units) can effectively regulate the low critical solution temperature (LCST) of the HPC-g-PNIPAm copolymers in aqueous solution due to the hydrophilic properties of the short PNIPAm chains. This work provides an approach for the regulation of the LCST to body temperature region by graft copolymerization. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

    KAUST Repository

    Zhang, Hefeng


    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.

  16. 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


    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.

  17. Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains. (United States)

    Makowski, Mariusz; Liwo, Adam; Scheraga, Harold A


    The physics-based potentials of side-chain-side-chain interactions corresponding to pairs composed of charged and polar, polar and polar, charged and hydrophobic, and hydrophobic and hydrophobic side chains have been determined. A total of 144 four-dimensional potentials of mean force (PMFs) of all possible pairs of molecules modeling these pairs were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation, and the analytical expressions were then fitted to the PMFs. Depending on the type of interacting sites, the analytical approximation to the PMF is a sum of terms corresponding to van der Waals interactions and cavity-creation involving the nonpolar sections of the side chains and van der Waals, cavity-creation, and electrostatic (charge-dipole or dipole-dipole) interaction energies and polarization energies involving the charged or polar sections of the side chains. The model used in this work reproduces all features of the interacting pairs. The UNited RESidue force field with the new side-chain-side-chain interaction potentials was preliminarily tested with the N-terminal part of the B-domain of staphylococcal protein A (PDBL 1BDD ; a three-α-helix bundle) and UPF0291 protein YnzC from Bacillus subtilis (PDB: 2HEP ; an α-helical hairpin).

  18. Peramivir analogues bearing hydrophilic side chains exhibit higher activities against H275Y mutant than wild-type influenza virus. (United States)

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


    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.

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

    KAUST Repository

    El Labban, Abdulrahman


    (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.

  20. 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


    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

  1. Accessing ns-{mu}s side chain dynamics in ubiquitin with methyl RDCs

    Energy Technology Data Exchange (ETDEWEB)

    Fares, Christophe [University of Toronto, University Health Network, Max Bell Research Center (Canada); Lakomek, Nils-Alexander [National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Walter, Korvin F. A.; Frank, Benedikt T. C. [Max-Planck Institute for Biophysical Chemistry, Department of NMR-based Structural Biology (Germany); Meiler, Jens [Vanderbilt University, Department of Chemistry, Center of Structural Biology (United States); Becker, Stefan; Griesinger, Christian [Max-Planck Institute for Biophysical Chemistry, Department of NMR-based Structural Biology (Germany)], E-mail:


    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-{tau}{sub 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 {tau}{sub c}. In fact, the average amplitude of motion expressed in terms of order parameters S{sup 2} associated with the supra-{tau}{sub 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.

  2. 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.


    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

  3. Stability of photochromism in new bifunctional copolymers containing spiropyran and chalcone moiety in the side chain

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Dong Hoon; Ban, Si Young; Kim, Jae Hong [Kyunghee Univ., Suwon (Korea, Republic of)


    We synthesized three copolymers bearing photochromic spiropyran dye and chalcone moiety in the side chain for studying the dynamic properties of their photochromism. They contain methacrylate-spiropyran (MA-spiropyran) and methacrylate-chalcone) (MA-chalcone) with the different concentration. The photosensitivity of the newly synthesized copolymers was investigated by using UV-Vis absorption spectroscopy. We absorbed photodimerization and phtochromic behavior under UV irradiation at the same time. The effect of photocrosslink on the rate and stability of photochromism in three copolymers was considered in this study. This study might be helpful to design photochromic materials for irreversible optical memory by virtue of photocrosslinking reaction.

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

    DEFF Research Database (Denmark)

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


    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...... molecules. We believe that this technique would have a great potential in the recording of thousands of holograms in a two-dimensional plane, as for instance in text retrieval systems and in the fabrication of high density interconnects in optical neural networks....

  5. Side chain packing below the fusion peptide strongly modulates triggering of the Hendra virus F protein. (United States)

    Smith, Everett Clinton; Dutch, Rebecca Ellis


    Triggering of the Hendra virus fusion (F) protein is required to initiate the conformational changes which drive membrane fusion, but the factors which control triggering remain poorly understood. Mutation of a histidine predicted to lie near the fusion peptide to alanine greatly reduced fusion despite wild-type cell surface expression levels, while asparagine substitution resulted in a moderate restoration in fusion levels. Slowed kinetics of six-helix bundle formation, as judged by sensitivity to heptad repeat B-derived peptides, was observed for all H372 mutants. These data suggest that side chain packing beneath the fusion peptide is an important regulator of Hendra virus F triggering.

  6. Selectively deuterated liquid crystalline cyanoazobenzene side-chain polyesters. 2. Preparation and characterization of polyesters

    DEFF Research Database (Denmark)

    Kulinna, Christian; Hvilsted, Søren; Hendann, Claudia


    Two sets of specifically deuterated cyanoazobenzene side-chain polyadipates and polytetrade-canedioates have been prepared by transesterification in the melt. Combinations of three different, selectively deuterium labeled 2-[6-[4-[(4-cyanophenyl)azo]phenoxy]hexyl]-1,3-propanediols or the non...... calorimetry. Whereas the polytetradecanedioates show a complex thermal behaviour with a number of different phases, the polyadipates are less complex and both nematic and smectic A phases have been identified by polarizing optical microscopy. Solution 1H, 13C and 2H NMR spectroscopy have been utilized...

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

    Directory of Open Access Journals (Sweden)

    Arlette A. Santiago


    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.

  8. Two New Prenylated Stilbenes with an Irregular Sesquiterpenyl Side Chain from Propolis from Fiji Islands

    Directory of Open Access Journals (Sweden)

    Boryana Trusheva


    Full Text Available Two new prenylated stilbenes with an irregular sesquiterpenyl side chain, solomonin B (1 and solomonin C (2, together with four known compounds, glyasperin A (3, isolated for the first time from propolis, kumatakenin (4, macarangin (5 and mangiferolic acid (6 were isolated from ethanol extract of propolis from Fiji islands. The compounds structures were determined based on their spectral data analysis (1D- and 2D NMR, UV and HREIMS and comparison with literature data. The chemical composition of propolis from Fiji islands was determined for the first time.

  9. 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


    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

  10. Side-chain alkylation of toluene with methanol over Zn-modified KX zeolite


    Song, Lanlan; Yu, Yue; Li, Zhenrong; Guo, Shaoqing; Zhao, Liangfu; Li, Wen


    The effect of Zn on side-chain alkylation of toluene with methanol over KX zeolite was investigated. It was found that the addition of Zn with a low content over KX could enhance toluene conversion significantly. In addition, the results showed that the conversion of toluene over ZnKX (0.8 wt. %) catalyst was almost twice as high as that over KX. The catalysts were characterized by X-ray diffraction (XRD), N2 physisorption, NH3-temperature-programmed desorption (TPD), pyridine absorption infr...

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

    DEFF Research Database (Denmark)

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


    . 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...

  12. Shoulder rotator muscle dynamometry characteristics: side asymmetry and correlations with ball-throwing speed in adolescent handball players. (United States)

    Pontaga, Inese; Zidens, Janis


    1) compare shoulder external/internal rotator muscles' peak torques and average power values and their ratios in the dominant and non-dominant arm; 2) determine correlations between shoulder rotator muscles' peak torques, average power and ball-throwing speed in handball players. Fourteen 14 to 15-year-old male athletes with injury-free shoulders participated in the study (body height: 176 ± 7 cm, body mass 63 ± 9 kg). The tests were carried out by an isokinetic dynamometer system in the shoulder internal and external rotation movements at angular velocities of 60°/s, 90°/s and 240°/s during concentric contractions. The eccentric external- concentric internal rotator muscle contractions were performed at the velocity of 90°/s. The player threw a ball at maximal speed keeping both feet on the floor. The speed was recorded with reflected light rays. Training in handball does not cause significant side asymmetry in shoulder external/internal rotator muscle peak torques or the average power ratio. Positive correlations between isokinetic characteristics of the shoulder internal and external rotator muscles and ball-throwing speed were determined. The power produced by internal rotator muscles during concentric contractions after eccentric contractions of external rotator muscles was significantly greater in the dominant than in the non-dominant arm. Thus, it may be concluded that the shoulder eccentric external/concentric internal rotator muscle power ratio is significantly greater than this ratio in the concentric contractions of these muscles.

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

    CSIR Research Space (South Africa)

    Reddy, GSM


    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...

  14. Side chain engineering of poly-thiophene and its impact on crystalline silicon based hybrid solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Zellmeier, M.; Rappich, J.; Nickel, N. H. [Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute for Silicon Photovoltaics, Kekuléstr. 5, 12489 Berlin (Germany); Klaus, M.; Genzel, Ch. [Department of Microstructure and Residual Stress Analysis, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Straße 15, 12489 Berlin (Germany); Janietz, S. [Department of Polymer Electronics, Fraunhofer Institute for Applied Polymer Research, Geiselbergstr. 69, 14476 Potsdam (Germany); Frisch, J.; Koch, N. [Humboldt Universität zu Berlin, Brook-Taylor-Straße 6, 12489 Berlin (Germany)


    The influence of ether groups in the side chain of spin coated regioregular polythiophene derivatives on the polymer layer formation and the hybrid solar cell properties was investigated using electrical, optical, and X-ray diffraction experiments. The polymer layers are of high crystallinity but the polymer with 3 ether groups in the side chain (P3TOT) did not show any vibrational fine structure in the UV-Vis spectrum. The presence of ether groups in the side chains leads to better adhesion resulting in thinner and more homogeneous polymer layers. This, in turn, enhances the electronic properties of the planar c-Si/poly-thiophene hybrid solar cell. We find that the power conversion efficiency increases with the number of ether groups in the side chains, and a maximum power conversion efficiency of η = 9.6% is achieved even in simple planar structures.

  15. Effect of side-chain asymmetry on the intermolecular structure and order-disorder transition in alkyl-substituted polyfluorenes

    DEFF Research Database (Denmark)

    Knaapila, Matti; Stepanyan, R.; Torkkeli, M.


    into alternating side-chain and backbone layers that transform into an isotropic phase at TODT(PF6) and TODTbi(PF1−8). We interpret polymers in terms of monodisperse and bidisperse brushes and predict scenarios TODT

  16. Systematic review: what surgical technique provides the best outcome for symptomatic partial articular-sided rotator cuff tears? (United States)

    Bollier, Matthew; Shea, Kevin


    There is no consensus in the literature regarding the optimal surgical treatment of symptomatic partial rotator cuff tears. We attempted to determine the optimal surgical treatment for partial articular-sided rotator cuff tears through a systematic review of appropriate studies. Medline®, PubMed, Ovid, and the cochrane register of controlled trials were searched for all studies published between January 1991 to March 2010 that used the key words "shoulder", "partial rotator cuff tear", "PASTA", "articularsided rotator cuff tear", "incomplete rotator cuff tear", "arthroscopic" and "repair". Inclusion criteria were studies (Level I to IV) that reported clinical outcomes in patients who had arthroscopic evaluation and arthroscopic or mini-open treatment of a symptomatic partial articular-sided rotator cuff tear. One of three surgical treatments was used: debridement with or without acromioplasty; transtendon arthroscopic repair; or tear completion with repair. Exclusion criteria included studies with over 50% overhead throwers or athletes, studies that involved an open approach to the rotator cuff without arthroscopy, and data presented in technical notes or review papers. Data abstracted from the studies included patient demographics, tear characteristics, surgical procedure(s), and clinical outcomes. Of 588 studies involving partial rotator cuff tears, 14 studies were identified which met our inclusion and exclusion criteria. All studies were Level IV retrospective case-series studies. Seven studies reported outcomes after rotator cuff debridement. Tear completion and repair was performed in three studies. Transtendon repair of a partial articular-sided rotator cuff tear was performed in three studies. Although different outcome measures were used, each study reported subjective and objective improvement postoperatively. One study compared outcomes in patients who underwent arthroscopic debridement versus another group where patients had tear completion and mini

  17. Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data3 (United States)

    Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall


    One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called NASCA (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), NASCA extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that NASCA assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by NASCA have backbone RMSD 0

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

    Directory of Open Access Journals (Sweden)

    X. Liu


    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.

  19. Preferred side-chain constellations at antiparallel coiled-coil interfaces. (United States)

    Hadley, Erik B; Testa, Oliver D; Woolfson, Derek N; Gellman, Samuel H


    Reliable predictive rules that relate protein sequence to structure would facilitate postgenome predictive biology and the engineering and de novo design of peptides and proteins. Through a combination of experiment and analysis of the protein data bank (PDB), we have deciphered and rationalized new rules for helix-helix interfaces of a common protein-folding and association motif, the antiparallel dimeric coiled coil. These interfaces are defined by a specific pattern of interactions among largely hydrophobic side chains often referred to as knobs-into-holes (KIH) packing: a knob from one helix inserts into a hole formed by four residues on the partner. Previous work has focused on lateral interactions within the KIH motif, for example, between an a position on one helix and a d' position on the other in an antiparallel coiled coil. We show that vertical interactions within the KIH motif, such as a'-a-a', are energetically important as well. The experimental and database analyses concur regarding preferred vertical combinations, which can be rationalized as leading to favorable side-chain interactions that we call constellations. The findings presented here highlight an unanticipated level of complexity in coiled-coil interactions, and our analysis of a few specific constellations illustrates a general, multipronged approach to addressing this complexity.

  20. Histidine side-chain dynamics and protonation monitored by {sup 13}C CPMG NMR relaxation dispersion

    Energy Technology Data Exchange (ETDEWEB)

    Hass, Mathias A. S. [Leiden University, Institute of Chemistry (Netherlands); Yilmaz, Ali [University of Copenhagen, Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences (Denmark); Christensen, Hans E. M. [Technical University of Denmark, Department of Chemistry (Denmark); Led, Jens J. [University of Copenhagen, Department of Chemistry (Denmark)], E-mail:


    The use of {sup 13}C NMR relaxation dispersion experiments to monitor micro-millisecond fluctuations in the protonation states of histidine residues in proteins is investigated. To illustrate the approach, measurements on three specifically {sup 13}C labeled histidine residues in plastocyanin (PCu) from Anabaena variabilis (A.v.) are presented. Significant Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion is observed for {sup 13}C{sup {epsilon}}{sup 1} nuclei in the histidine imidazole rings of A.v. PCu. The chemical shift changes obtained from the CPMG dispersion data are in good agreement with those obtained from the chemical shift titration experiments, and the CPMG derived exchange rates agree with those obtained previously from {sup 15}N backbone relaxation measurements. Compared to measurements of backbone nuclei, {sup 13}C{sup {epsilon}}{sup 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 {sup 13}C{sup {epsilon}}{sup 1} dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains are discussed.

  1. Subcritical Water Hydrolysis of Peptides: Amino Acid Side-Chain Modifications (United States)

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


    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.

  2. 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


    , 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......) x s(-1)) > backbone amides (10-10(-3) M(-1) x s(-1)) > Gln(0.03 M(-1) x s(-1)) approximately Asn (0.03 M(-1) x s(-1)). The rate constants for reaction of HOCl with backbone amides (peptide bonds) vary by 4 orders of magnitude with uncharged peptide bonds reacting more readily with HOCl than those....... 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...

  3. Free Energy Perturbation Calculations of the Thermodynamics of Protein Side-Chain Mutations. (United States)

    Steinbrecher, Thomas; Abel, Robert; Clark, Anthony; Friesner, Richard


    Protein side-chain mutation is fundamental both to natural evolutionary processes and to the engineering of protein therapeutics, which constitute an increasing fraction of important medications. Molecular simulation enables the prediction of the effects of mutation on properties such as binding affinity, secondary and tertiary structure, conformational dynamics, and thermal stability. A number of widely differing approaches have been applied to these predictions, including sequence-based algorithms, knowledge-based potential functions, and all-atom molecular mechanics calculations. Free energy perturbation theory, employing all-atom and explicit-solvent molecular dynamics simulations, is a rigorous physics-based approach for calculating thermodynamic effects of, for example, protein side-chain mutations. Over the past several years, we have initiated an investigation of the ability of our most recent free energy perturbation methodology to model the thermodynamics of protein mutation for two specific problems: protein-protein binding affinities and protein thermal stability. We highlight recent advances in the field and outline current and future challenges. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. A Major Role for Side-Chain Polyglutamine Hydrogen Bonding in Irreversible Ataxin-3 Aggregation (United States)

    Relini, Annalisa; Apicella, Alessandra; Invernizzi, Gaetano; Casari, Carlo; Gliozzi, Alessandra; Doglia, Silvia Maria; Tortora, Paolo; Regonesi, Maria Elena


    The protein ataxin-3 consists of an N-terminal globular Josephin domain (JD) and an unstructured C-terminal region containing a stretch of consecutive glutamines that triggers the neurodegenerative disorder spinocerebellar ataxia type 3, when it is expanded beyond a critical threshold. The disease results from misfolding and aggregation, although the pathway and structure of the aggregation intermediates are not fully understood. In order to provide insight into the mechanism of the process, we monitored the aggregation of a normal (AT3Q24) ataxin-3, an expanded (AT3Q55) ataxin-3, and the JD in isolation. We observed that all of them aggregated, although the latter did so at a much slower rate. Furthermore, the expanded AT3Q55 displayed a substantially different behavior with respect to the two other variants in that at the latest stages of the process it was the only one that did the following: i) lost its reactivity towards an anti-oligomer antibody, ii) generated SDS-insoluble aggregates, iii) gave rise to bundles of elongated fibrils, and iv) displayed two additional bands at 1604 and 1656 cm−1 in FTIR spectroscopy. Although these were previously observed in other aggregated polyglutamine proteins, no one has assigned them unambiguously, yet. By H/D exchange experiments we show for the first time that they can be ascribed to glutamine side-chain hydrogen bonding, which is therefore the hallmark of irreversibly SDS-insoluble aggregated protein. FTIR spectra also showed that main-chain intermolecular hydrogen bonding preceded that of glutamine side-chains, which suggests that the former favors the latter by reorganizing backbone geometry. PMID:21533208

  5. A major role for side-chain polyglutamine hydrogen bonding in irreversible ataxin-3 aggregation.

    Directory of Open Access Journals (Sweden)

    Antonino Natalello


    Full Text Available The protein ataxin-3 consists of an N-terminal globular Josephin domain (JD and an unstructured C-terminal region containing a stretch of consecutive glutamines that triggers the neurodegenerative disorder spinocerebellar ataxia type 3, when it is expanded beyond a critical threshold. The disease results from misfolding and aggregation, although the pathway and structure of the aggregation intermediates are not fully understood. In order to provide insight into the mechanism of the process, we monitored the aggregation of a normal (AT3Q24 ataxin-3, an expanded (AT3Q55 ataxin-3, and the JD in isolation. We observed that all of them aggregated, although the latter did so at a much slower rate. Furthermore, the expanded AT3Q55 displayed a substantially different behavior with respect to the two other variants in that at the latest stages of the process it was the only one that did the following: i lost its reactivity towards an anti-oligomer antibody, ii generated SDS-insoluble aggregates, iii gave rise to bundles of elongated fibrils, and iv displayed two additional bands at 1604 and 1656 cm(-1 in FTIR spectroscopy. Although these were previously observed in other aggregated polyglutamine proteins, no one has assigned them unambiguously, yet. By H/D exchange experiments we show for the first time that they can be ascribed to glutamine side-chain hydrogen bonding, which is therefore the hallmark of irreversibly SDS-insoluble aggregated protein. FTIR spectra also showed that main-chain intermolecular hydrogen bonding preceded that of glutamine side-chains, which suggests that the former favors the latter by reorganizing backbone geometry.

  6. Bioreducible poly(amido amine)s with oligoamine side chains: synthesis, characterization, and structural effects on gene delivery

    NARCIS (Netherlands)

    Lin, C.; Blaauboer, Cees-Jan; Mateos timoneda, Miguel; Lok, Martin C.; Steenbergen, Mies; Hennink, Wim E.; Zhong, Zhiyuan; Feijen, Jan; Engbersen, Johannes F.J.


    A group of bioreducible poly(amido amine)s containing multiple disulfide linkages in main chain and oligoamines in side chain (SS–PAOAs) were prepared by Michael-type polyaddition of N-tert-butyloxycarbonyl (N-Boc) protected oligoamine to the disulfide-containing cystaminebisacrylamide, followed by

  7. 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.


    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

  8. Physics-based side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials for coarse-grained UNRES force field. 2. Comparison with statistical potentials and implementation (United States)

    Kozłowska, Urszula; Maisuradze, Gia G.; Liwo, Adam; Scheraga, Harold A.


    Using the harmonic-approximation approach of the accompanying paper and AM1 energy surfaces of terminally-blocked amino-acid residues, we determined physics-based side-chain-rotamer potentials and the side-chain virtual-bond-deformation potentials of 19 natural amino-acid residues with side chains. The potentials were approximated by analytical formulas and implemented in the UNRES mesoscopic dynamics program. For comparison, the corresponding statistical potentials were determined from 19,682 high-resolution protein structures. The low-free-energy region of both the AM1-derived and the statistical potentials is determined by the valence geometry and the L-chirality, and its size increases with side-chain flexibility and decreases with increasing virtual-bond-angle θ. The differences between the free energies of rotamers are greater for the AM1-derived potentials compared to the statistical potentials and, for alanine and other residues with small side chains, a region corresponding to the Cax7 conformation has remarkably low free energy for the AM1-derived potentials, as opposed to the statistical potentials. These differences probably result from the interactions between neighboring residues and indicate the need for introduction of cooperative terms accounting for the coupling between side-chain-rotamer and backbone interactions. Both AM1-derived and statistical virtual-bond-deformation potentials are multimodal for flexible side chains and are topologically similar; however, the regions of minima of the statistical potentials are much narrower, which probably results from imposing restraints in structure determination. The force field with the new potentials was preliminarily optimized using the FBP WW domain (1E0L) and the engrailed homeodomain (1ENH) as training proteins and assessed to be reasonably transferable. PMID:20017135

  9. 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


    )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......-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...

  10. Different hip rotations influence hip abductor muscles activity during isometric side-lying hip abduction in subjects with gluteus medius weakness. (United States)

    Lee, Ji-Hyun; Cynn, Heon-Seock; Kwon, Oh-Yun; Yi, Chung-Hwi; Yoon, Tae-Lim; Choi, Woo-Jeong; Choi, Sil-Ah


    The purpose of this study was to establish the effects of different hip rotations during isometric side-lying hip abduction (SHA) in subjects with gluteus medius (Gmed) weakness by investigating the electromyographic (EMG) amplitude of the Gmed, tensor fasciae latae (TFL) activity, and gluteus maximus (Gmax), and the activity ratio of the Gmed/TFL, Gmax/TFL, and Gmed/Gmax. Nineteen subjects with Gmed weakness were recruited for this study. Subjects performed three isometric hip abductions: frontal SHA with neutral hips (SHA-N), frontal SHA with hip medial rotation (SHA-MR), and frontal SHA with hip lateral rotation (SHA-LR). Surface EMG amplitude was measured to collect the EMG data from the Gmed, TFL, and Gmax. A one-way repeated-measures analysis of variance was used to determine the statistical significance of the Gmed, TFL, and Gmax EMG activity and the Gmed/TFL, Gmax/TFL, and Gmed/Gmax EMG activity ratios. Gmed EMG activity was significantly greater in SHA-MR than in SHA-N. TFL EMG activity was significantly greater in SHA-LR than in SHA-N. The Gmed/TFL and Gmed/Gmax EMG activity ratios were also significantly greater in SHA-MR than in SHA-N or SHA-LR. The results of this study suggest that SHA-MR can be used as an effective method to increase Gmed activation and to decrease TFL activity during SHA exercises. Published by Elsevier Ltd.

  11. 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.


    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

  12. Characterization of counter-rotating streamwise vortices in flat rectangular channel with one-sided wavy wall

    KAUST Repository

    Bouremel, Yann


    Particle Image Velocimetry (PIV) has been used to characterize the evolution of counter-rotating streamwise vortices in a rectangular channel with one sided wavy surface. The vortices were created by a uniform set of saw-tooth carved over the leading edge of a flat plate at the entrance of a flat rectangular channel with one-sided wavy wall. PIV measurements were taken over the spanwise and streamwise planes at different locations and at Reynolds number of 2500. Two other Reynolds numbers of 2885 and 3333 have also been considered for quantification purpose. Pairs of counter-rotating streamwise vortices have been shown experimentally to be centred along the spanwise direction at the saw-tooth valley where the vorticity ωz=0ωz=0. It has also been found that the vorticity ωzωz of the pairs of counter-rotating vortices decreases along the streamwise direction, and increases with the Reynolds number. Moreover, different quantifications of such counter-rotating vortices have been discussed such as their size, boundary layer, velocity profile and vorticity. The current study shows that the mixing due to the wall shear stress of counter-rotating streamwise vortices as well as their averaged viscous dissipation rate of kinetic energy decrease over flat and adverse pressure gradient surfaces while increasing over favourable pressure gradient surfaces. Finally, it was also demonstrated that the main direction of stretching is orientated at around 45° with the main flow direction.

  13. Multi-responsive carboxymethyl polysaccharide crosslinked hydrogels containing Jeffamine side-chains. (United States)

    Mocanu, Georgeta; Souguir, Zied; Picton, Luc; Le Cerf, Didier


    The paper studies the synthesis and characterization of crosslinked carboxymethylpullulan hydrogels containing Jeffamine (Jef) (M-600 and M-2005) [polyoxyalkyleneamines (polyethylene oxide, polypropylene oxide)] units as side chains, linked through amide bonds. These hydrogels present pH sensitive properties due to the presence of anionic functional groups and thermoassociative properties due to the Jeff units. They were characterized through FTIR spectra, swelling behavior in various media, at various pH or temperatures, retention of hydrophobic molecules, to appreciate their pH-sensitive and thermoassociative (multi-responsive) properties. The interaction with biomolecules as proteins: lysozyme, BSA and antioxidants as: lutein and alpha-tocopherol was studied, to estimate some potential application domains of these new synthesized hydrogels. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

    DEFF Research Database (Denmark)

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


    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...

  15. 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)


    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.

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

    KAUST Repository

    Zhou, Yan


    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.

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

  18. Poly-dimethylsiloxane derivates side chains effect on syntan functionalized Polyamide fabric (United States)

    Migani, V.; Weiss, H.; Massafra, M. R.; Merlo, A.; Colleoni, C.; Rosace, G.


    Poly-dimethylsiloxane (PDMS) polymers finishing of Polyamide-6,6 (PA66) fabrics involves ionic interactions between reactive groups on the PDMS polymers and the ones of the textile fabric. Such interactions could be strengthened by a pretreatment with a fixing agent to promote either ion-ion and H-bonding and ion-dipole forces. These forces could contribute towards the building of substantial PDMS-PA66 systems and the achieving of better adhesion properties to fabrics. Four different silicone polymers based on PDMS were applied on a synthetic tanning agent (syntan) finished Polyamide-6,6 fabric under acid conditions. Soxhlet extraction method and ATR FT-IR technique were used to investigate the application conditions. The finishing parameters such as pH and temperature together with fastness, mechanical and performance properties of the treated samples were studied and related to PDMS side chains effect on syntan functionalized Polyamide fabric.

  19. Selective side-chain oxidation of alkyl aromatic compounds catalyzed by cerium modified silver catalysts

    DEFF Research Database (Denmark)

    Beier, Matthias Josef; Schimmoeller, Bjoern; Hansen, Thomas Willum


    . In addition, flame-made catalysts were more stable against silver leaching compared to the impregnated catalysts. The structure of the silver catalysts was studied in detail both by X-ray absorption spectroscopy and transmission electron microscopy suggesting metallic silver to be required for catalytic......Silver supported on silica effectively catalyzes the aerobic side-chain oxidation of alkyl aromatic compounds under solvent-free conditions. Toluene, p-xylene, ethylbenzene and cumene were investigated as model substrates. Typically, the reaction was performed at ambient pressure; only for toluene...... an elevated pressure was required. Carboxylic acids, such as benzoic acid or p-toluic acid, additionally increased the reaction rate while CeO2 could act both as a promoter and an inhibitor depending on the substrate and the reaction conditions. Silver catalysts were prepared both by standard impregnation...

  20. Liquid crystalline polybutadiene diols with chiral thiol side-chain units

    Czech Academy of Sciences Publication Activity Database

    Kašpar, Miroslav; Bubnov, Alexej M.; Sedláková, Zdeňka; Stojanović, M.; Havlíček, J.; Obadović, D.; Ilavský, Michal


    Roč. 44, č. 1 (2008), s. 233-243 ISSN 0014-3057 R&D Projects: GA ČR GP202/03/P011; GA ČR GA202/05/0431; GA MŠk OC 175; GA AV ČR IAA100100710; GA AV ČR IAA4112401 Grant - others:MSEP(CS) 141020; ESF-COST(XE) D35 WG13-05 Institutional research plan: CEZ:AV0Z10100520; CEZ:AV0Z40500505 Keywords : chiral thiols * liquid crystal * polybutadiene * diols * side-chain polymer * polarizing optical microscopy * X-ray * dielectric spectroscopy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.143, year: 2008

  1. The different interactions of lysine and arginine side chains with lipid membranes. (United States)

    Li, Libo; Vorobyov, Igor; Allen, Toby W


    The basic amino acids lysine (Lys) and arginine (Arg) play important roles in membrane protein activity, the sensing of membrane voltages, and the actions of antimicrobial, toxin, and cell-penetrating peptides. These roles are thought to stem from the strong interactions and disruptive influences of these amino acids on lipid membranes. In this study, we employ fully atomistic molecular dynamics simulations to observe, quantify, and compare the interactions of Lys and Arg with saturated phosphatidylcholine membranes of different thickness. We make use of both charged (methylammonium and methylguanidinium) and neutral (methylamine and methylguanidine) analogue molecules, as well as Lys and Arg side chains on transmembrane helix models. We find that the free energy barrier experienced by a charged Lys crossing the membrane is strikingly similar to that of a charged Arg (to within 2 kcal/mol), despite the two having different chemistries, H-bonding capability, and hydration free energies that differ by ∼10 kcal/mol. In comparison, the barrier for neutral Arg is higher than that for neutral Lys by around 5 kcal/mol, being more selective than that for the charged species. This can be explained by the different transport mechanisms for charged or neutral amino acid side chains in the membrane, involving membrane deformations or simple dehydration, respectively. As a consequence, we demonstrate that Lys would be deprotonated in the membrane, whereas Arg would maintain its charge. Our simulations also reveal that Arg attracts more phosphate and water in the membrane, and can form extensive H-bonding with its five H-bond donors to stabilize Arg-phosphate clusters. This leads to enhanced interfacial binding and membrane perturbations, including the appearance of a trans-membrane pore in a thinner membrane. These results highlight the special role played by Arg as an amino acid to bind to, disrupt, and permeabilize lipid membranes, as well as to sense voltages for a range

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

    KAUST Repository

    Junnila, Susanna


    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.

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

    Ghani, Nur Syatila Ab; Firdaus-Raih, Mohd


    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.

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

    Directory of Open Access Journals (Sweden)

    Inbar Yuval


    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 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.

  5. Shoulder Rotator Muscle Dynamometry Characteristics: Side Asymmetry and Correlations with Ball-Throwing Speed in Adolescent Handball Players

    Directory of Open Access Journals (Sweden)

    Pontaga Inese


    Full Text Available The aim of the investigation was to: 1 compare shoulder external/internal rotator muscles’ peak torques and average power values and their ratios in the dominant and non-dominant arm; 2 determine correlations between shoulder rotator muscles’ peak torques, average power and ball-throwing speed in handball players. Fourteen 14 to 15- year-old male athletes with injury-free shoulders participated in the study (body height: 176 ± 7 cm, body mass 63 ± 9 kg. The tests were carried out by an isokinetic dynamometer system in the shoulder internal and external rotation movements at angular velocities of 60°/s, 90°/s and 240°/s during concentric contractions. The eccentric external- concentric internal rotator muscle contractions were performed at the velocity of 90°/s. The player threw a ball at maximal speed keeping both feet on the floor. The speed was recorded with reflected light rays. Training in handball does not cause significant side asymmetry in shoulder external/internal rotator muscle peak torques or the average power ratio. Positive correlations between isokinetic characteristics of the shoulder internal and external rotator muscles and ball-throwing speed were determined. The power produced by internal rotator muscles during concentric contractions after eccentric contractions of external rotator muscles was significantly greater in the dominant than in the non-dominant arm. Thus, it may be concluded that the shoulder eccentric external/concentric internal rotator muscle power ratio is significantly greater than this ratio in the concentric contractions of these muscles

  6. 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


    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.

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

  8. The power of hard-sphere models: explaining side-chain dihedral angle distributions of Thr and Val. (United States)

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


    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.

  9. 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


    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.

  10. Selective carbon 13 enrichment of side chain carbons of ginkgo lignin traced by carbon 13 nuclear magnetic resonance

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Y. (Nagoya Univ. (Japan). Faculty of Agriculture); Robert, D.R. (CEA Centre d' Etudes de Grenoble, 38 (France). Dept. de Recherche Fondamentale sur la Matiere Condensee); Terashima, N. (Forest Products Lab., Madison, WI (United States))

    Although carbon 13 nuclear magnetic resonance spectroscopy ([sup 13]C-NMR) is widely used in lignin structural studies, serious difficulties are encountered in the assignments of [sup 13]C signals because of their extensive overlaps resulting from the complex structure of lignin and of delicate detection of minor structures. To overcome these difficulties, specifically [sup 13]C-enriched precursors of lignin biosynthesis, coniferin-[side chain-[beta]-[sup 13]C] and coniferin-[side chain-[gamma]-[sup 13]C], were administered to growing stems of ginkgo (Ginkgo biloba). The NMR analysis of the milled wood lignins isolated from the newly formed xylem showed that selective enrichment of specific carbons of protolignin in the cell wall was achieved without seriously disturbing the lignin biosynthesis. The presence of saturated methylene side chains in the protolignin was shown for the first time by this selective enrichment technique in combination with NMR analysis. (authors). 23 refs., 3 figs., 1 tab.

  11. Synthesis, Structural Studies and Antitumoral Evaluation of C-6 Alkyl and Alkenyl Side Chain Pyrimidine Derivatives S

    Directory of Open Access Journals (Sweden)

    Marijeta Kralj


    Full Text Available The synthetic route for introduction of fluorophenylalkyl (compounds 5, 7, 14 and 15 and fluorophenylalkenyl (compounds 4E and 13 side chains at C-6 of the pyrimidine nucleus involved the lithiation of the pyrimidine derivatives 1, 2 and 11 and subsequent nucleophilic addition or substitution reactions of the organolithium intermediate thus obtained with 2-fluorophenylacetone, 4-fluoroacetophenone or ethyl 4-fluorobenzoate as electrophiles. The structures of novel compounds were confirmed by 1H-, 19F- and 13C-NMR and MS. Compounds 8 and 10 containing unsaturated fluorophenylalkyl side chains showed better inhibitory effect than their saturated fluorophenylalkylated pyrimidine counterparts 7 and 9. A conformational study based on NOE enhancements showed the importance of the double bond and substitution in the side chain for the conformational preferences in relation to inhibitory activity. Among all tested compounds, C-5 furyl (12 and phenyl (13 and 15 substituted pyrimidine derivatives showed significant cytostatic activities against all tested tumor cell lines.

  12. Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures. (United States)

    Yesselman, Joseph D; Horowitz, Scott; Brooks, Charles L; Trievel, Raymond C


    The propensity of backbone Cα atoms to engage in carbon-oxygen (CH · · · O) hydrogen bonding is well-appreciated in protein structure, but side chain CH · · · O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH · · · O hydrogen bonding is examined through a survey of neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, methyl groups were observed to form stabilizing CH · · · O hydrogen bonds within protein structure that are maintained through protein dynamics and participate in correlated motion. Collectively, these findings illustrate that side chain methyl CH · · · O hydrogen bonding contributes to the energetics of protein structure and folding. © 2014 Wiley Periodicals, Inc.

  13. Prediction of closed-chain human arm dynamics in a crank-rotation task. (United States)

    Davoudabadi Farahani, Saeed; Svinin, Mikhail; Andersen, Michael Skipper; de Zee, Mark; Rasmussen, John


    This paper deals with the analysis of human arm movement in a crank-rotation task that is an example of environmentally constrained movements. Opening a door, rotating a steering wheel, and pushing a carriage are other typical examples of movements where the physical constraints, imposed on the hand position/orientation, influence the joint angles of the shoulder and the elbow. To predict kinematic and kinetic patterns for human arm movement in crank-rotation tasks, we use an optimization-based technique. The method enables dynamic prediction of closed-chain movements and force exertion using inverse dynamics musculoskeletal simulation. An anatomically detailed musculoskeletal model is parameterized by means of time functions controlling selected degrees-of-freedom. Subsequently, the parameters of these functions are optimized to produce an optimal motion according to a user-defined objective function and constraints given by the anthropometry of the body and physics of the environment. In this study, we use a physiology-based objective function expressing the muscle metabolic energy expenditure and validation metrics to assess the accuracy of the computational model. Qualitative and quantitative comparisons between predicted results and experimental data from a group of four healthy males indicate that the method reproduces natural kinetic and kinematic patterns. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. A Study on the Impact of Poly(3-hexylthiophene Chain Length and Other Applied Side-Chains on the NO2 Sensing Properties of Conducting Graft Copolymers

    Directory of Open Access Journals (Sweden)

    Marcin Procek


    Full Text Available The detection and concentration measurements of low concentrations of nitrogen dioxide (NO2 are important because of its negative effects on human health and its application in many fields of industry and safety systems. In our approach, conducting graft copolymers based on the poly(3-hexylthiophene (P3HT conducting polymer and other side-chains, polyethylene glycol (PEG and dodec-1-en, grafted on a poly(methylhydrosiloxane backbone, were investigated. The grafts containing PEG (PEGSil and dodec-1-en (DodecSil in two variants, namely, fractions with shorter (hexane fraction -H and longer (chloroform fraction -CH side-chains of P3HT, were tested as receptor structures in NO2 gas sensors. Their responses to NO2, within the concentration range of 1–20 ppm, were investigated in an nitrogen atmosphere at different operating temperatures—room temperature (RT = 25 °C, 50 °C, and 100 °C. The results indicated that both of the copolymers with PEG side-chains had higher responses to NO2 than the materials with dodec-1-en side-chains. Furthermore, the results indicated that, in both cases, H fractions were more sensitive than CH fractions. The highest response to 1 ppm of NO2, from the investigated graft copolymers, had PEGSil H, which indicated a response of 1330% at RT and 1980% at 100 °C. The calculated lower-limit of the detection of this material is lower than 300 ppb of NO2 at 100 °C. This research indicated that graft copolymers of P3HT had great potential for low temperature NO2 sensing, and that the proper choice of other side-chains in graft copolymers can improve their gas sensing properties.

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


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


    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 dif...

  16. 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.


    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

  17. Side chain: backbone projections in aromatic and ASX residues from NMR cross-correlated relaxation

    Energy Technology Data Exchange (ETDEWEB)

    Voegeli, Beat, E-mail:; Riek, Roland [Swiss Federal Institute of Technology, Laboratory of Physical Chemistry (Switzerland)


    The measurements of cross-correlated relaxation rates between H{sup N}-N and C{sup {beta}}-C{sup {gamma}} intraresidual and sequential dipolar interactions is demonstrated in ASN, ASP and aromatic residues. The experiment can be used for deuterated samples and no additional knowledge such as Karplus parametrizations is required for the analysis. The data constitutes a new type of information since no other method relates the C{sup {beta}}-C{sup {gamma}} bond to H{sup N}-N. Using this method the dominant populations of rotamer states of {chi}1 can be readily cross checked provided that {phi} or {psi} are known. In addition, dynamics on all timescales can be probed. As opposed to standard dynamics analysis of isolated bonds, the presented observables depend on relative dynamics with an interesting prospect to analyze correlated fluctuations of the two torsion angles {phi} or {psi} with {chi}1. Experimental rates are compared to single conformer and ensemble representations of GB3 and ubiquitin. In particular, it is found that the recently published ubiquitin ensemble 2k39 improves the agreement obtained for 1UBQ. In general, however, input data restricting ASX and aromatic side chains in structure calculation is sparse highlighting the need for new NMR observables.

  18. Side chain: backbone projections in aromatic and ASX residues from NMR cross-correlated relaxation. (United States)

    Vögeli, Beat; Riek, Roland


    The measurements of cross-correlated relaxation rates between H(N)-N and C(beta)-C(gamma) intraresidual and sequential dipolar interactions is demonstrated in ASN, ASP and aromatic residues. The experiment can be used for deuterated samples and no additional knowledge such as Karplus parametrizations is required for the analysis. The data constitutes a new type of information since no other method relates the C(beta)-C(gamma) bond to H(N)-N. Using this method the dominant populations of rotamer states of chi 1 can be readily cross checked provided that phi or psi are known. In addition, dynamics on all timescales can be probed. As opposed to standard dynamics analysis of isolated bonds, the presented observables depend on relative dynamics with an interesting prospect to analyze correlated fluctuations of the two torsion angles phi or psi with chi 1. Experimental rates are compared to single conformer and ensemble representations of GB3 and ubiquitin. In particular, it is found that the recently published ubiquitin ensemble 2k39 improves the agreement obtained for 1UBQ. In general, however, input data restricting ASX and aromatic side chains in structure calculation is sparse highlighting the need for new NMR observables.

  19. Improving ranking of models for protein complexes with side chain modeling and atomic potentials. (United States)

    Viswanath, Shruthi; Ravikant, D V S; Elber, Ron


    An atomically detailed potential for docking pairs of proteins is derived using mathematical programming. A refinement algorithm that builds atomically detailed models of the complex and combines coarse grained and atomic scoring is introduced. The refinement step consists of remodeling the interface side chains of the top scoring decoys from rigid docking followed by a short energy minimization. The refined models are then re-ranked using a combination of coarse grained and atomic potentials. The docking algorithm including the refinement and re-ranking, is compared favorably to other leading docking packages like ZDOCK, Cluspro, and PATCHDOCK, on the ZLAB 3.0 Benchmark and a test set of 30 novel complexes. A detailed analysis shows that coarse grained potentials perform better than atomic potentials for realistic unbound docking (where the exact structures of the individual bound proteins are unknown), probably because atomic potentials are more sensitive to local errors. Nevertheless, the atomic potential captures a different signal from the residue potential and as a result a combination of the two scores provides a significantly better prediction than each of the approaches alone. Copyright © 2012 Wiley Periodicals, Inc.

  20. Phase Behavior and Magnetic Alignment of Hydrogen Bonded Side Chain Liquid Crystalline Block Copolymers (United States)

    Gopinadhan, Manesh; Majewski, Pawel; Beach, Evan; Anastas, Paul; Osuji, Chinedum


    Hydrogen bonding between a poly(styrene-b-acrylic acid) backbone and an imidazole terminated biphenyl mesogen results in the formation of a side-group liquid crystalline block copolymer (LC BCP).We use a combination of FTIR, X-ray scattering and DSC to characterize the phase behavior of the PAA-LC system, which is largely dominated by the sub-stoichiometric saturation of the binding capacity of the chain. In the melt, the self assembled materials exhibited composition and temperature dependent smectic LC phases along with characteristic birefringence and multiple thermal transitions associated with LC polymers. The diblock copolymers (LC BCP) microphase separated into lamellar microdomains with homeotropic anchoring at the IMDS. Alignment of a hierarchically ordered lamellar BCP was performed using a 5 T magnetic field at elevated temperature in the melt state and characterized by SAXS. The system exhibits a tilted smectic structure, which on alignment by the field displays scattering patterns akin to those observed in bookshelf or chevron-type structures. These results demonstrate that simple non-covalent interactions can be used to generate LC order and thus provide a convenient handle for subsequent alignment of BCP structures by magnetic fields.

  1. Photo-induced deformations in azobenzene-containing side-chain polymers: molecular dynamics study

    Directory of Open Access Journals (Sweden)



    Full Text Available We perform molecular dynamics simulations of azobenzene containing side-chain liquid crystalline polymer subject to an external model field that mimicks the reorientations of the azobenzenes upon irradiation with polarized light. The smectic phase of the polymer is studied with the field applied parallel to the nematic director, forcing the trans isomers to reorient perpendicularly to the field (the direction of which can be assosiated with the light polarization. The coupling between the reorientation of azobenzenes and mechanical deformation of the sample is found to depend on the field strength. In a weak field the original smectic order is melted gradually with no apparent change in the simulation box shape, whereas in a strong field two regimes are observed. During the first one a rapid melting of the liquid crystalline order is accompanied by the contraction of the polymer along the field direction (the effect similar to the one observed experimentally in azobenzene containing elastomers. During the slower second regime, the smectic layers are rebuilt to accomodate the preferential direction of chromophores perperdicular to the field.

  2. Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains. (United States)

    Makowski, Mariusz; Liwo, Adam; Sobolewski, Emil; Scheraga, Harold A


    A new model of side-chain-side-chain interactions for charged side-chains of amino acids, to be used in the UNRES force-field, has been developed, in which a side chain consists of a nonpolar and a charged site. The interaction energy between the nonpolar sites is composed of a Gay-Berne and a cavity term; the interaction energy between the charged sites consists of a Lennard-Jones term, a Coulombic term, a generalized-Born term, and a cavity term, while the interaction energy between the nonpolar and charged sites is composed of a Gay-Berne and a polarization term. We parametrized the energy function for the models of all six pairs of natural like-charged amino-acid side chains, namely propionate-propionate (for the aspartic acid-aspartic acid pair), butyrate-butyrate (for the glutamic acid-glutamic acid pair), propionate-butyrate (for the aspartic acid-glutamic acid pair), pentylamine cation-pentylamine cation (for the lysine-lysine pair), 1-butylguanidine cation-1-butylguanidine cation (for the arginine-arginine pair), and pentylamine cation-1-butylguanidine cation (for the lysine-arginine pair). By using umbrella-sampling molecular dynamics simulations in explicit TIP3P water, we determined the potentials of mean force of the above-mentioned pairs as functions of distance and orientation and fitted analytical expressions to them. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules were well represented by analytical expressions for all systems. The values of the parameters of all the energy components are physically reasonable, which justifies use of such potentials in coarse-grain protein-folding simulations. © 2011 American Chemical Society

  3. Azapeptide Synthesis Methods for Expanding Side-Chain Diversity for Biomedical Applications. (United States)

    Chingle, Ramesh; Proulx, Caroline; Lubell, William D


    Mimicry of bioactive conformations is critical for peptide-based medicinal chemistry because such peptidomimetics may augment stability, enhance affinity, and increase specificity. Azapeptides are peptidomimetics in which the α-carbon(s) of one or more amino acid residues are substituted by nitrogen. The resulting semicarbazide analogues have been shown to reinforce β-turn conformation through the combination of lone pair-lone pair repulsion of the adjacent hydrazine nitrogen and urea planarity. Substitution of a semicarbazide for an amino amide residue in a peptide may retain biological activity and add benefits such as improved metabolic stability. The applications of azapeptides include receptor ligands, enzyme inhibitors, prodrugs, probes, and imaging agents. Moreover, azapeptides have proven therapeutic utility. For example, the aza-glycinamide analogue of the luteinizing hormone-releasing hormone analogue Zoladex is a potent long-acting agonist currently used in the clinic for the treatment of prostate and breast cancer. However, the use of azapeptides was hampered by tedious solution-phase synthetic routes for selective hydrazine functionalization. A remarkable stride to overcome this bottleneck was made in 2009 through the introduction of the submonomer procedure for azapeptide synthesis, which enabled addition of diverse side chains onto a common semicarbazone intermediate, providing a means to construct azapeptide libraries by solution- and solid-phase chemistry. In brief, aza residues are introduced into the peptide chain using the submonomer strategy by semicarbazone incorporation, deprotonation, N-alkylation, and orthogonal deprotection. Amino acylation of the resulting semicarbazide and elongation gives the desired azapeptide. Since the initial report, a number of chemical transformations have taken advantage of the orthogonal chemistry of semicarbazone residues (e.g., Michael additions and N-arylations). In addition, libraries have been synthesized

  4. 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


    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 ...


    NARCIS (Netherlands)


    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

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


    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.

  7. Quantifying millisecond time-scale exchange in proteins by CPMG relaxation dispersion NMR spectroscopy of side-chain carbonyl groups

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, Alexandar L.; Kay, Lewis E., E-mail: [University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry (Canada)


    A new pulse sequence is presented for the measurement of relaxation dispersion profiles quantifying millisecond time-scale exchange dynamics of side-chain carbonyl groups in uniformly {sup 13}C labeled proteins. The methodology has been tested using the 87-residue colicin E7 immunity protein, Im7, which is known to fold via a partially structured low populated intermediate that interconverts with the folded, ground state on the millisecond time-scale. Comparison of exchange parameters extracted for this folding 'reaction' using the present methodology with those obtained from more 'traditional' {sup 15}N and backbone carbonyl probes establishes the utility of the approach. The extracted excited state side-chain carbonyl chemical shifts indicate that the Asx/Glx side-chains are predominantly unstructured in the Im7 folding intermediate. However, several crucial salt-bridges that exist in the native structure appear to be already formed in the excited state, either in part or in full. This information, in concert with that obtained from existing backbone and side-chain methyl relaxation dispersion experiments, will ultimately facilitate a detailed description of the structure of the Im7 folding intermediate.

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

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


    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. 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


    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. Biodegradable cationic poly(carbonates): Effect of varying side chain hydrophobicity on key aspects of gene transfection. (United States)

    Ong, Zhan Yuin; Yang, Chuan; Cheng, Wei; Voo, Zhi Xiang; Chin, Willy; Hedrick, James L; Yang, Yi Yan


    The degree of hydrophobicity in cationic polymers plays an important but often underappreciated role in the safety and efficacy of gene delivery processes. In order to further elucidate structure-activity relationships of biodegradable cationic poly(carbonate) gene carriers, we synthesized a series of narrowly dispersed homo-polymers via metal-free organocatalytic living ring-opening polymerization (ROP) of cyclic carbonate monomers bearing either alkyl (propyl, hexyl or nonyl) or 4-methyl benzyl halide side chains. The polymers were then quaternized using bis-tertiary amines to install both quaternary ammoniums and tertiary amines for DNA binding and endosomal escape, respectively. Among the polymers with similar molecular lengths and charge densities, it was found that an increase in side chain alkyl spacer length from 3 to 6 carbons significantly enhanced cellular uptake and luciferase gene expression in HepG2 and HeLa cell lines without causing overt hemolysis and cytotoxicity. A further increase of side chain alkyl length to 9 carbons, however, led to a drastic decline in gene expression due to increased cellular toxicity, which was correlated with an increased disruption and lysis of red blood cell membranes. Interestingly, the incorporation of an aromatic 4-methyl benzyl spacer increased DNA binding strength, reduced particle sizes of resultant DNA complexes, and enhanced cellular uptake, leading to improved luciferase gene expression, albeit with higher levels of hemolysis and cytotoxicity. Taken together, the findings of this study demonstrate that a delicate balance between cationic charge density and hydrophobicity could be achieved by utilizing a hexyl spacer in the side chains of cationic poly(carbonates), hence providing insights on the future development of non-viral cationic polymeric gene delivery systems. Owing to their ease of synthesis and well-controlled polymerization, biodegradable cationic poly(carbonates) have emerged as a highly promising

  11. 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


    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...

  12. Enhancing the Performance of Polymer Solar Cells by Using Donor Polymers Carrying Discretely Distributed Side Chains. (United States)

    Gong, Xue; Li, Guangwu; Wu, Yang; Zhang, Jicheng; Feng, Shiyu; Liu, Yahui; Li, Cuihong; Ma, Wei; Bo, Zhishan


    Conjugated polymers with three components, P1-1 and P1-2, were prepared by one-pot Stille polymerization. The two-component polymer P1-0 is only composed of a 5-fluoro-6-alkyloxybenzothiadiazole (AFBT) acceptor unit and a thiophene donor unit, while the three-component polymers P1-1 and P1-2 contain 10% and 20% 5,6-difluorobenzothiadiazole (DFBT), respectively, as the third component. The incorporation of the third component, 5,6-difluorobenzothiadiazole, makes the side chains discretely distributed in the polymer backbones, which can enhance the π-π stacking of polymers in film, markedly increase the hole mobility of active layers, and improve the power-conversion efficiency (PCE) of devices. Influence of the third component on the morphology of active layer was also studied by X-ray diffraction (XRD), resonant soft X-ray scattering (R-SoXS), and transmission electron microscopy (TEM) experiments. P1-1/PC 71 BM-based PSCs gave a high PCE up to 7.25%, whereas similarly fabricated devices for P1-0/PC 71 BM only showed a PCE of 3.46%. The PCE of P1-1/PC 71 BM-based device was further enhanced to 8.79% after the use of 1,8-diiodooctane (DIO) as the solvent additive. Most importantly, after the incorporation of 10% 5,6-difluorobenzothiadiazole unit, P1-1 exhibited a marked tolerance to the blend film thickness. Devices with a thickness of 265 nm still showed a PCE above 8%, indicating that P1-1 is promising for future applications.

  13. Heterologous Expression of Hen Egg White Lysozyme and Resonance Assignment of Tryptophan Side Chains in its Non-native States

    International Nuclear Information System (INIS)

    Schloerb, Christian; Ackermann, Katrin; Richter, Christian; Wirmer, Julia; Schwalbe, Harald


    A new protocol is described for the isotope ( 15 N and 13 C, 15 N) enrichment of hen egg white lysozyme. Hen egg white lysozyme and an all-Ala-mutant of this protein have been expressed in E. coli. They formed inclusion bodies from which mg quantities of the proteins were purified and prepared for NMR spectroscopic investigations. 1 H, 13 C and 15 N main chain resonances of disulfide reduced and S-methylated lysozyme were assigned and its residual structure in water pH 2 was characterized by chemical shift perturbation analysis. A new NMR experiment has been developed to assign tryptophan side chain indole resonances by correlation of side chain and backbone NH resonances with the C γ resonances of these residues. Assignment of tryptophan side chains enables further residue specific investigations on structural and dynamical properties, which are of significant interest for the understanding of non-natives states of lysozyme stabilized by hydrophobic interactions between clusters of tryptophan residues

  14. Asymmetric Alkyl Side-Chain Engineering of Naphthalene Diimide-Based n-Type Polymers for Efficient All-Polymer Solar Cells. (United States)

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


    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.

  15. "There is a chain of connections": using syndemics theory to understand HIV treatment side effects. (United States)

    Gagnon, Marilou


    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.

  16. Phase equilibria of polymer solutions using the chain-of-rotators equation of state (United States)

    Novenario, Carlos Rull


    Equations of state (eos) have become the prevalent means for thermodynamic and phase equilibrium calculations as both vapor and liquid phases are described over wide ranges of conditions by the same equation. Whereas most eos theories are developed to represent the behavior of volatile fluids, extension of these theories to systems containing large chain molecules is necessary in a variety of industrial applications. In this thesis, the Chain-of-Rotators (COR) eos derived from the rotational partition function for polyatomic molecular fluids is used to describe phase equilibria of polymer + solvent systems. New parameterization is proposed for COR to extend the equation to a wide variety of solvents encountered in practice, from nonpolar to highly polar and associating. A group contribution approach is adopted to obtain the segmental parameters that are applicable to polymers of varying molecular weights. Parameters a and b for a polymer are obtained from the small molecule of the same chemical structure as the polymer segment. Parameter c is then fitted from pure polymer pressure-volume-temperature data. Generally excellent correlation of vapor-liquid equilibrium (vle) data is obtained for all mixtures investigated by using only one constant interaction coefficient in the van der Waals mixing rule for the attractive parameter independent of temperature or polymer molecular weight. For the majority of systems studied, vle predictions from COR by setting the van der Waals binary interaction parameter to zero and by using UNIFAC free energy matched mixing rules are better than or comparable to those of the recommended UNIFAC-FV model for polymer solutions. The van der Waals mixing rules, however, are inadequate for description of the experimentally observed liquid-liquid phase equilibrium behavior of polymer solutions. Good correlation of polymer + solvent liquid-liquid equilibrium data is obtained upon incorporation of a modified Flory-Huggins solution model into

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

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


    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.

  18. Side chain dynamics of carboxyl and carbonyl groups in the catalytic function of Escherichia coli ribonuclease H (United States)

    Stafford, Kate A.; Ferrage, Fabien; Cho, Jae-Hyun; Palmer, Arthur G.


    Many proteins use Asx and Glx (x = n, p, or u) side chains as key functional groups in enzymatic catalysis and molecular recognition. In this study, NMR spin relaxation experiments and molecular dynamics (MD) simulations are used to measure the dynamics of the side chain amide and carboxyl groups, 13Cγ/δ, in Escherichia coli ribonuclease HI (RNase H). Model-free analysis shows that the catalytic residues in RNase H are pre-organized on ps-ns timescales via a network of electrostatic interactions. However, chemical exchange line broadening shows that these residues display significant conformational dynamics on μs – ms timescales upon binding of Mg2+ ions. Two groups of catalytic residues exhibit differential linebroadening, implicating distinct reorganizational processes upon binding of metal ions. These results support the “mobile metal ion” hypothesis, which was inferred from structural studies of RNase H. PMID:24219366

  19. 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


    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...... and pharmacology has proven to be exceedingly difficult in such large and complex proteins. Using the in vivo nonsense suppression approach, we report the first successful incorporation of the isosteric, titratable Arg analog, canavanine, into a neurotransmitter receptor in a living cell, utilizing a glutamate......-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...

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

    KAUST Repository

    Mei, Jianguo


    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.

  1. Multi-layer mucilage of Plantago ovata seeds: Rheological differences arise from variations in arabinoxylan side chains. (United States)

    Yu, Long; Yakubov, Gleb E; Zeng, Wei; Xing, Xiaohui; Stenson, John; Bulone, Vincent; Stokes, Jason R


    Mucilages are hydrocolloid solutions produced by plants for a variety of functions, including the creation of a water-holding barrier around seeds. Here we report our discovery of the formation of three distinct mucilage layers around Plantago ovata seeds upon their hydration. Each layer is dominated by different arabinoxylans (AXs). These AXs are unusual because they are highly branched and contain β-1,3-linked xylose in their side chains. We show that these AXs have similar monosaccharide and linkage composition, but vary in their polymer conformation. They also exhibit distinct rheological properties in aqueous solution, despite analytical techniques including NMR showing little difference between them. Using enzymatic hydrolysis and chaotropic solvents, we reveal that hydrogen bonding and side chain distribution are key factors underpinning the distinct rheological properties of these complex AXs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. 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.


    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...... in high-density optical storage and high-resolution lithography....

  3. Synthesis and properties of aromatic polyethers containing poly(ethylene oxide) side chains as polymer electrolytes for lithium ion batteries

    Energy Technology Data Exchange (ETDEWEB)

    Vöge, Andrea, E-mail: [Department of Chemistry, University of Patras, 26500 Patras (Greece); Deimede, Valadoula, E-mail: [Department of Chemistry, University of Patras, 26500 Patras (Greece); Paloukis, Fotis; Neophytides, Stylianos G. [Foundation of Research and Technology – Hellas, Institute of Chemical Engineering Sciences (FORTH/ICE-HT), Patras 26504 (Greece); Kallitsis, Joannis K. [Department of Chemistry, University of Patras, 26500 Patras (Greece)


    Polymer electrolytes consisting of polar pyridine units in the backbone and poly(ethylene oxide) (PEO) side chains are designed for possible application in lithium ion batteries. In particular, aromatic polyethers bearing PEO side chains with varying length are synthesized either by copolymerization of the corresponding PEO based diols with different arylfluorides or by modification of dihydroxyl functionalized precursor polymers with poly(ethylene oxide) methyl ether tosylate. The formation of free standing films is dependent on the PEO content, polymers' composition as well as on the different monomers used. The mechanical properties study shows that the glass transition temperature can be controlled by varying the PEO content. Thermal stability is also influenced by the PEO length: the shorter the PEO side chain, the higher the stability. XRD analysis gives information about the desired amorphous character of these polymers, which is independent of the PEO content. Solid polymer electrolytes prepared by blending the PEO-based polymers with lithium salt and PEO 2000 (used as plasticizer) show ambient temperature conductivities in the range of 10{sup −6} S/cm. To further improve conductivity doping of PEO-based polymers in liquid electrolyte (1 M LiPF{sub 6} in EC/DMC 1/1) in some cases results in high conductivities in the range of 10{sup −3} S cm{sup −1} at 80 °C. - Highlights: • Polymer electrolytes bearing PEO side chains of varying lengths were designed. • DMA and TGA show that T{sub g} and T{sub d} can be controlled by varying the PEO content. • XRD confirms polymers amorphous character, independent of the PEO content. • Membranes doped in liquid electrolyte have high conductivities (10{sup −3} S cm{sup −1}, 80 °C)

  4. Side Chain Engineering on Medium Bandgap Copolymers to Suppress Triplet Formation for High-Efficiency Polymer Solar Cells. (United States)

    Xue, Lingwei; Yang, Yankang; Xu, Jianqiu; Zhang, Chunfeng; Bin, Haijun; Zhang, Zhi-Guo; Qiu, Beibei; Li, Xiaojun; Sun, Chenkai; Gao, Liang; Yao, Jia; Chen, Xiaofeng; Yang, Yunxu; Xiao, Min; Li, Yongfang


    Suppression of carrier recombination is critically important in realizing high-efficiency polymer solar cells. Herein, it is demonstrated difluoro-substitution of thiophene conjugated side chain on donor polymer can suppress triplet formation for reducing carrier recombination. A new medium bandgap 2D-conjugated D-A copolymer J91 is designed and synthesized with bi(alkyl-difluorothienyl)-benzodithiophene as donor unit and fluorobenzotriazole as acceptor unit, for taking the advantages of the synergistic fluorination on the backbone and thiophene side chain. J91 demonstrates enhanced absorption, low-lying highest occupied molecular orbital energy level, and higher hole mobility, in comparison with its control polymer J52 without fluorination on the thiophene side chains. The transient absorption spectra indicate that J91 can suppress the triplet formation in its blend film with n-type organic semiconductor acceptor m-ITIC (3,9-bis(2-methylene-(3-(1,1-dicyanomethylene)-indanone)-5,5,11,11-tetrakis(3-hexylphenyl)-dithieno[2,3-d:2,3'-d']-s-indaceno[1,2-b:5,6-b']-dithiophene). With these favorable properties, a higher power conversion efficiency of 11.63% with high V OC of 0.984 V and high J SC of 18.03 mA cm -2 is obtained for the polymer solar cells based on J91/m-ITIC with thermal annealing. The improved photovoltaic performance by thermal annealing is explained from the morphology change upon thermal annealing as revealed by photoinduced force microscopy. The results indicate that side chain engineering can provide a new solution to suppress carrier recombination toward high efficiency, thus deserves further attention. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. One-sided time constraints routing problem in supply chain management- An Ant colony optimization based heuristic


    Tiwari, Dr. Sandeep Kumar; Acharya, Sopnamayee


    Transportation costs constitute a significant fraction of total logistics cost in Supply Chain Management (SCM). To reduce transportation costs, improve customer service and to achieve maximum customer satisfaction, the optimal selection of the vehicle route is a frequent decision problem and this is commonly known as vehicle routing problem. Vehicle routing problem with one-sided time constraint, where the delivery of products from depots to distribution centers has to take place within the ...

  6. Dehydroanthrasesamones A and B, anthraquinone derivatives containing a dienyl side-chain from Sesamum indicum hairy roots. (United States)

    Furumoto, Toshio; Hoshikuma, Arata


    Two additional anthraquinone derivatives containing a (Z)-dienyl side-chain, dehydroanthrasesamones A (2) and B (3), were isolated from a hairy root culture of Sesamum indicum after preventing light throughout all experimental procedures. Their respective structures were determined to be 1-hydroxy-2-[(Z)-4-methylpenta-1,3-dien-1-yl]anthraquinone and 1,4-dihydroxy-2-[(Z)-4-methylpenta-1,3-dien-1-yl]anthraquinone by spectroscopic methods.

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

    KAUST Repository

    Dyer-Smith, Clare


    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.

  8. 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


    To explore the structure essential for the catalysis in 26 kDa endochitinase from barley seeds, we calculated theoretical pKa values of the ionizable groups based on the crystal structure, and then the roles of ionizable side chains located near the catalytic residue were examined by site......-directed mutagenesis. The pKa value calculated for Arg215, which is located at the bottom of the catalytic cleft, is abnormally high (>20.0), indicating that the guanidyl group may interact strongly with nearby charges. No enzymatic activity was found in the Arg215-mutated chitinase (R215A) produced by the Escherichia...... coli expression system. The transition temperature of thermal unfolding (T(m)) of R215A was lower than that of the wild type protein by about 6.2 degrees C. In the crystal structure, the Arg215 side chain is in close proximity to the Glu203 side chain, whose theoretical pKa value was found...

  9. 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


    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.

  10. 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


    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

  11. Fine-tuning blend morphology via alkylthio side chain engineering towards high performance non-fullerene polymer solar cells (United States)

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


    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.

  12. 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


    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.

  13. Inversion of the stereochemistry around the sulfur atom of the axial methionine side chain through alteration of amino acid side chain packing in Hydrogenobacter thermophilus cytochrome C552 and its functional consequences. (United States)

    Tai, Hulin; Tonegawa, Ken; Shibata, Tomokazu; Hemmi, Hikaru; Kobayashi, Nagao; Yamamoto, Yasuhiko


    In cytochrome c, the coordination of the axial Met Sδ atom to the heme Fe atom occurs in one of two distinctly different stereochemical manners, i.e., R and S configurations, depending upon which of the two lone pairs of the Sδ atom is involved in the bond; hence, the Fe-coordinated Sδ atom becomes a chiral center. In this study, we demonstrated that an alteration of amino acid side chain packing induced by the mutation of a single amino acid residue, i.e., the A73V mutation, in Hydrogenobacter thermophilus cytochrome c552 (HT) forces the inversion of the stereochemistry around the Sδ atom from the R configuration [Travaglini-Allocatelli, C., et al. (2005) J. Biol. Chem. 280, 25729-25734] to the S configuration. Functional comparison between the wild-type HT and the A73V mutant possessing the R and S configurations as to the stereochemistry around the Sδ atom, respectively, demonstrated that the redox potential (Em) of the mutant at pH 6.00 and 25 °C exhibited a positive shift of ∼20 mV relative to that of the wild-type HT, i.e., 245 mV, in an entropic manner. Because these two proteins have similar enthalpically stabilizing interactions, the difference in the entropic contribution to the Em value between them is likely to be due to the effect of the conformational alteration of the axial Met side chain associated with the inversion of the stereochemistry around the Sδ atom due to the effect of mutation on the internal mobility of the loop bearing the axial Met. Thus, the present study demonstrated that the internal mobility of the loop bearing the axial Met, relevant to entropic control of the redox function of the protein, is affected quite sensitively by the contextual stereochemical packing of amino acid side chains in the proximity of the axial Met.

  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


    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. Polypropylene non-woven meshes with conformal glycosylated layer for lectin affinity adsorption: the effect of side chain length. (United States)

    Ye, Xiang-Yu; Huang, Xiao-Jun; Xu, Zhi-Kang


    The unique characteristics of polypropylene non-woven meshes (PPNWMs), like random network of overlapped fibers, multiple connected pores and overall high porosity, make them high potentials for use as separation or adsorption media. Meanwhile, carbohydrates can specifically recognize certain lectin through multivalent interactions. Therefore glycosylated PPNWMs, combing the merits of both, can be regarded as superior affinity membranes for lectin adsorption and purification. Here, we describe a versatile strategy for the glycosylation of PPNWMs. Two hydrophilic polymers with different side chain length, poly(2-hydroxyethyl methacrylate) (PHEMA) and poly(oligo(ethylene glycol) methacrylate) (POEGMA), were first conformally tethered on the polypropylene fiber surface by a modified plasma pretreatment and benzophenone (BP) entrapment UV irradiation process. Then glucose ligands were bound through the reaction between the hydroxyl group and acetyl glucose. Chemical changes of the PPNWMs surface were monitored by FT-IR/ATR. SEM pictures show that conformal glucose ligands can be achieved through the modified process. After deprotection, the glycosylated PPNWMs became superhydrophilic and had high specific recognition capability toward Concanavalin A (Con A). Static Con A adsorption experiments were further performed and the results indicate that fast adsorption kinetics and high binding capacity can be accomplished at the same time. We also found that increasing the side chain length of polymer brushes had positive effect on protein binding capacity due to improved chain mobility. Model studies suggest a multilayer adsorption behavior of Con A. Copyright © 2013 Elsevier B.V. All rights reserved.

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

  17. Naphthalenetetracarboxylic diimide layer-based transistors with nanometer oxide and side chain dielectrics operating below one volt. (United States)

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


    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.

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


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


    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...

  19. Proton clouds to measure long-range contacts between nonexchangeable side chain protons in solid-state NMR. (United States)

    Sinnige, Tessa; Daniëls, Mark; Baldus, Marc; Weingarth, Markus


    We show that selective labeling of proteins with protonated amino acids embedded in a perdeuterated matrix, dubbed 'proton clouds', provides general access to long-range contacts between nonexchangeable side chain protons in proton-detected solid-state NMR, which is important to study protein tertiary structure. Proton-cloud labeling significantly improves spectral resolution by simultaneously reducing proton line width and spectral crowding despite a high local proton density in clouds. The approach is amenable to almost all canonical amino acids. Our method is demonstrated on ubiquitin and the β-barrel membrane protein BamA.

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

    KAUST Repository

    Mondal, Rajib


    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.

  1. 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


    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......, 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...

  2. Synthesis and characterisation of new types of side chain cholesteryl polymers. (United States)

    Wang, Bin; Du, Haiyan; Zhang, Junhua


    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.

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

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


    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.

  4. Side-chain and linkage-mediated effects of anthraquinone moieties on ambipolar poly(triphenylamine)-based volatile polymeric memory devices. (United States)

    Wu, Jia-Hao; Yen, Hung-Ju; Hu, Yi-Cheng; Liou, Guey-Sheng


    Two ambipolar and thermally stable poly(triphenylamine)s with pendent anthraquinone acceptors were readily synthesized and prepared for the investigation of side-chain and linkage-mediated effects on the memory behaviour.

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

    Michalak, Karol; Wicha, Jerzy


    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.

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

    KAUST Repository

    Fetsch, Corinna


    © 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.

  7. 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


    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.

  8. Amide side chain amphiphilic polymers disrupt surface established bacterial bio-films and protect mice from chronic Acinetobacter baumannii infection. (United States)

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


    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.

  9. Z-Selective olefin metathesis on peptides: investigation of side-chain influence, preorganization, and guidelines in substrate selection. (United States)

    Mangold, Shane L; O'Leary, Daniel J; Grubbs, Robert H


    Olefin metathesis has emerged as a promising strategy for modulating the stability and activity of biologically relevant compounds; however, the ability to control olefin geometry in the product remains a challenge. Recent advances in the design of cyclometalated ruthenium catalysts has led to new strategies for achieving such control with high fidelity and Z selectivity, but the scope and limitations of these catalysts on substrates bearing multiple functionalities, including peptides, remained unexplored. Herein, we report an assessment of various factors that contribute to both productive and nonproductive Z-selective metathesis on peptides. The influence of sterics, side-chain identity, and preorganization through peptide secondary structure are explored by homodimerization, cross metathesis, and ring-closing metathesis. Our results indicate that the amino acid side chain and identity of the olefin profoundly influence the activity of cyclometalated ruthenium catalysts in Z-selective metathesis. The criteria set forth for achieving high conversion and Z selectivity are highlighted by cross metathesis and ring-closing metathesis on diverse peptide substrates. The principles outlined in this report are important not only for expanding the scope of Z-selective olefin metathesis to peptides but also for applying stereoselective olefin metathesis in general synthetic endeavors.

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

    Energy Technology Data Exchange (ETDEWEB)

    Oosterhout, Stefan D.; Koster, L.J.A.; Wienk, Martijn M.; Janssen, Rene A.J. [Molecular Materials and Nanosystems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven (Netherlands); Van Bavel, Svetlana S.; Loos, Joachim [Laboratory of Materials and Interface Chemistry and Soft Matter, CryoTEM Research Unit, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven (Netherlands); Stenzel, Ole; Thiedmann, Ralf; Schmidt, Volker [Institute for Stochastics, Ulm University, D-89069 Ulm (Germany); Campo, Bert; Cleij, Thomas J.; Lutzen, Laurence; Vanderzande, Dirk [Hasselt University, Institute for Materials Research, Wetenschapspark 1, BE 3590 Diepenbeek (Belgium)


    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 chain poly(3-hexylthiophene-2,5-diyl) derivative (P3HT-E), the nanoscale morphology of ZnO:polymer solar cells is significantly more intimately mixed compared to ZnO:poly(3-hexylthiophene-2,5-diyl) (ZnO:P3HT), as evidenced experimentally from a 3D reconstruction of the phase separation using electron tomography. Photoinduced absorption reveals nearly quantitative charge generation for the ZnO:P3HT-E blend but not for ZnO:P3HT, consistent with the results obtained from solving the 3D diffusion equation for excitons formed in the polymer within the two experimental ZnO morphologies. For thin ZnO:P3HT-E active layers ({proportional_to}50 nm) this yields a significant improvement of the solar cell performance. For thicker cells, however, the reduced hole mobility and a reduced percolation of ZnO pathways hinders charge carrier collection, limiting the power conversion efficiency. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  11. Controlling the morphology of side chain liquid crystalline block copolymer thin films through variations in liquid crystalline content. (United States)

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


    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.

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


    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.

  13. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity.

    Directory of Open Access Journals (Sweden)

    Noah Ollikainen

    Full Text Available Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein-ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i prediction of enzyme specificity altering mutations and (ii prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art "fixed backbone" design methods perform poorly on these tests, we develop a new "coupled moves" design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein-ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution.

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

    KAUST Repository

    Moia, Davide


    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.

  15. 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


    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

  16. Synthesis and characterization of poly(vinylchloride type macrophotoinitiator comprising side-chain thioxanthone via click chemistry

    Directory of Open Access Journals (Sweden)


    Full Text Available Nowadays, the use of macromolecular photoinitiators provides for a good compatibility of the initiator in the formulation. Moreover, the migration of the initiator to the surface of the material is prevented, which results in low-odor and non-toxic coatings. In the present study, it has been demonstrated that polyvinylchloride macrophotoinitiator (PVC-TX containing side chain thioxanthone (2% moieties were successfully prepared by 'click chemistry'. For this purpose, propargyl thioxanthone and polyvinylchloride with side chain azide moieties were reacted in N,N-dimethylformamide for 24 hours at 25°C in order to give corresponding macrophotoinitiator. The synthesized polymer was characterized by 1H-NMR (nuclear magnetic resonance, UV (ultraviolet and fluorescence spectroscopies and water based gel permeation chromatography. Obtained macrophotoinitiator has similar absorption characteristics compared to parent thioxanthone. Its capabilities to act as initiator for the photopolymerization of methacrylic acid, methyl methacrylate, N-vinyl pyrrolidone and styrene in various solvents in the absence and presence of triethylamine media were also examined.

  17. Synthesis and Characterization of Polyacetylene with Side-chain Thiophene Functionality

    Directory of Open Access Journals (Sweden)

    Yusuf Yagci


    Full Text Available A new polyacetylene derivative with electroactive thiophene substituent, namely poly(2-methylbut-2-enyl thiophene-3-carboxylate was synthesized and characterized. For this purpose, novel acetylene monomer was synthesized by the reaction of 3- thiophenecarboxylic acid with propargyl bromide and polymerized with a Rh catalyst to give the corresponding polymer. The chemical structure of the polymer was characterized to comprise the conjugated backbone and electroactive thiophene side group. UV spectral changes of the polymer with temperature were also studied. The polymer exhibited better thermal stability than the unsubstituted polyacetylenes.

  18. Dynamic covalent side-chain cross-links via intermolecular oxime or hydrazone formation from bifunctional peptides and simple organic linkers. (United States)

    Haney, Conor M; Horne, W Seth


    Peptide cyclization via chemoselective reactions between side chains has proven a useful strategy to control folded structure. We report here a method for the synthesis of side-chain to side-chain cyclic peptides based on the intermolecular reaction between a linear peptide functionalized with two aminooxy or hydrazide side chains and an organic dialdehyde linker. A family of oxime-based and hydrazone-based cyclic products is prepared in a modular and convergent fashion by combination of unprotected linear peptide precursors and various small molecule linkers in neutral aqueous buffer. The side-chain to side-chain linkages that result can alter peptide folding behavior. The dynamic covalent nature of the Schiff bases in the cyclic products can be utilized to create mixtures where product composition changes in response to experimental conditions. Thus, a linear peptide precursor can select one organic linker from a mixture, and a cyclic product can dynamically exchange the small molecule component of the macrocycle. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.

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

    Directory of Open Access Journals (Sweden)

    Giulia Guidotti


    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.

  20. Haptacyclic Carbazole-Based Ladder-Type Nonfullerene Acceptor with Side-Chain Optimization for Efficient Organic Photovoltaics. (United States)

    Hsiao, Yu-Tang; Li, Chia-Hua; Chang, Shao-Ling; Heo, Soowon; Tajima, Keisuke; Cheng, Yen-Ju; Hsu, Chain-Shu


    In this research, a haptacyclic carbazole-based dithienocyclopentacarbazole (DTCC) ladder-type structure was formylated to couple with two 1,1-dicyanomethylene-3-indanone (IC) moieties, forming a new nonfullerene acceptor DTCCIC-C17 using a bulky branched 1-octylnonayl side chain at the nitrogen of the embedded carbazole and four 4-octylphenyl groups at the sp 3 -carbon bridges. The rigid and coplanar main-chain backbone of the DTCC core provides a broad light-absorbing window and a higher-lying LUMO energy level, whereas the bulky flanked side chains reduce intermolecular interactions, making DTCCIC-C17 amorphous with excellent solution processability. The DTCCIC-C17 as an acceptor is combined with a medium band gap polymer poly[(2,6-(4,8-bis(5-(2-ethylhexyl)thiophen-2-yl)-benzo[1,2-b:4,5-b']dithiophene))-alt-(5,5-(1',3'-di-2-thienyl-5',7'-bis(2-ethylhexyl)benzo[1',2'-c:4',5'-c']dithiophene-4,8-dione))] (PBDB-T) as the donor in the active layer to obtain suitable highest occupied molecular orbital/lowest unoccupied molecular orbital energy alignments and complimentary absorption. The devices with an inverted configuration (ITO/ZnO/active layer/MoO 3 /Ag) without using an aqueous poly(3,4-ethylenedioxythiophene) polystyrene sulfonate layer were fabricated for better device stability. When the diiodooctane-treated PBDB-T:DTCCIC-C17 active layer was thermally annealed at 50 °C for 10 min, the device achieved the highest efficiency of 9.48% with a high V oc of 0.98 V, a J sc of 14.27 mA cm -2 , and an FF of 0.68.

  1. De(side chain) model of epothilone: bioconformer interconversions DFT study. (United States)

    Rusinska-Roszak, Danuta; Lozynski, Marek


    Using ab initio methods, we have studied conformations of the de(sidechain)de(dioxy)difluoroepothilone model to quantify the effect of stability change between the exo and endo conformers of the epoxy ring. The DFT minimization of the macrolactone ring reveals four low energy conformers, although MP2 predicted five stable structures. The model tested with DFT hybride functional (B3LYP/6-31+G(d,p)) exhibits the global minimum for one of the exo forms (C), experimentally observed in the solid state, but unexpectedly with the MP2 electron correlation method for the virtual endo form (W). Using the QST3 technique, several pathways were found for the conversion of the low energy conformers to the other low energy exo representatives, as well as within the endo analog subset. The potential energy relationships obtained for several exo forms suggest a high conformational mobility between three, experimentally observed, conformers. The high rotational barrier, however, excludes direct equilibrium with experimental EC-derived endo form S. The highest calculated transition state for the conversion of the most stable exo M interligand to the endo S form is approximately a 28 kcal/mol above the energy of the former. The two-step interconversion of the exo H conformer to the endo S requires at least 28 kcal/mol. Surprisingly, we found that the transition state energy of the H form to the virtual endo W has the acceptable value of about 9 kcal/mol and the next energy barrier for free interconversion of endo W to endo S is 13 kcal/mol.

  2. 5-Ethynyl-2'-deoxycytidine: a DNA building block with a 'clickable' side chain. (United States)

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


    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.

  3. Synthesis of Peptides from α- and β-Tubulin Containing Glutamic Acid Side-Chain Linked Oligo-Glu with Defined Length

    Directory of Open Access Journals (Sweden)

    Werner Tegge


    Full Text Available Side-chain oligo- and polyglutamylation represents an important posttranslational modification in tubulin physiology. The particular number of glutamate units is related to specific regulatory functions. In this work, we present a method for the synthesis of building blocks for the Fmoc synthesis of peptides containing main chain glutamic acid residues that carry side-chain branching with oligo-glutamic acid. The two model peptide sequences CYEEVGVDSVEGEG-E(E-EEGEEY and CQDATADEQG-E(E-FEEEEGEDEA from the C-termini of mammalian α1- and β1-tubulin, respectively, containing oligo-glutamic acid side-chain branching with lengths of 1 to 5 amino acids were assembled in good yield and purity. The products may lead to the generation of specific antibodies which should be important tools for a more detailed investigation of polyglutamylation processes.

  4. Morphology and side-chain dynamics in hydrated hard α-keratin fibres by 1H solid-state NMR (United States)

    Melian, Claudiu; Demco, Dan E.; Istrate, Monica; Balaceanu, Andreea; Moldovan, Dumitrita; Fechete, Radu; Popescu, Crisan; Möller, Martin


    The effect of hydration on phase composition, aminoacids side-chain dynamics, and domain thickness of hard α-keratin was investigated by 1H solid-state NMR. Decomposition of wide-line 1H NMR spectra was used to determine the phase composition and to obtain information on molecular motion. Proton spin-diffusion NMR experiments using a double-quantum dipolar filter were used to estimate the rigid domain sizes for the hydrated Caucasian hair fibres. The relative domain sizes were obtained from the solution of spin-diffusion equation for cylindrical morphologies in the initial-rate approximation by a novel approach. A qualitative model describing the morphological and molecular dynamics changes induced by hydration was developed.

  5. Charge transfer between the PO4- groups of DNA and the arginine + and lysine + side chains of proteins (United States)

    Bende, A.; Bogár, F.; Ladik, J.


    Using the HF + MP2 methods with full geometry optimizations the charge transfer (CT) from the PO4- groups of DNA to the arginine or lysine side chains of the proteins forming the nuclohistone cores were calculated. (X-ray investigation shows that in the nucleohistone core there are eight histones which are wrapped around by a DNA superhelix). We have found 0.21e and 0.26e CT, respectively. Knowing the structure of nucleohistones one can estimate a charge transfer at every fourth base pair. Taking as average 0.10e CT (there are also other attractive interactions) one can compute the concentrations of holes in DNA. From these one can obtain the dc conductivity for polyguanilic acid (the mobilities are known).

  6. [Influence of hydrophobicity of amino acid side chains on volume and viscosity properties of their aqueous solutions]. (United States)

    Tiunina, E Iu; Badelin, V G


    The standard partial molar volumes (V(0)(2),phi) and coefficients of viscosity (B eta) at 298.15 K for aqueous solutions of amino acids containing hydrophobic and hydrophilic groups have been calculated. Based on the transition state theory of Feakins, the partial molar free energies of activation of the viscous flow of amino acids in water have been obtained. Correlations between the delta mu(0)(2) values and the hydrophobic contribution (logP') of amino acid molecules and the "packing density" (Dh) of water molecules in their hydration shells have been established. It was shown that delta mu(0)(2) and V(0)(2),phi values reflect changes in the hydrophobicity of amino acid side chains and their hydrogen bonding ability.

  7. Unexpected Chiro-Thermoresponsive Behavior of Helical Poly(phenylacetylene)s Bearing Elastin-Based Side Chains. (United States)

    Arias, Sandra; Freire, Felix; Calderón, Marcelo; Bergueiro, Julian


    The thermoresponsive behavior of an elastin-based polymer can be altered by the polymeric macromolecular conformation. Thus, when the elastin basic amino acid sequence VPGVG is used as a pendant group of a poly(phenylacetylene) (PPA) its thermoresponsive behavior in water can be remotely detected through conformational changes on the formed helix. Circular dichroism at different temperatures shows an inversion of the first Cotton effect (450 nm) at 25.8 °C that matches with the cloud point temperature. The elastin-based side-chain poly(phenylacetylene) shows an upper critical solution temperature with low pH and concentration dependency, not expected in elastin-based polymers. It was found that the polymer self-assembles in water into spherical nanoparticles with hydrodynamic diameters of 140 nm at the hydrophobic state. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Pressure dependence of side chain 13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH2. (United States)

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


    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.

  9. Effect of methanol in controlling defunctionalization of the propyl side chain of phenolics from catalytic upstream biorefining. (United States)

    Ferrini, Paola; Chesi, Claudio; Parkin, Nicholas; Rinaldi, Roberto


    In recent years, lignin valorization has gained upward momentum owing to advances in both plant bioengineering and catalytic processing of lignin. In this new horizon, catalysis is now applied to the 'pulping process' itself, creating efficient methods for lignocellulose fractionation or deconstruction (here referred to as Catalytic Upstream Biorefining or 'CUB'). These processes render, together with delignified pulps, lignin streams of low molecular weight (M w ) and low molecular diversity. Recently, we introduced a CUB process based on Early-stage Catalytic Conversion of Lignin (ECCL) through H-transfer reactions catalyzed by RANEY® Ni. This approach renders a lignin stream obtained as a viscous oil, comprising up to 60 wt% monophenolic compounds (M w process yields a holocellulose pulp with a low content of residual lignin (process carried out in the presence of primary alcohols, which often inhibit the catalytic activity of RANEY® Ni, as revealed in model compound studies performed at low temperature. Considering the composition of the lignin oils obtained from CUB based on ECCL, the processes commonly render ortho-(di)methoxy-4-propylphenol derivatives with a varied degree of defunctionalization of the propyl side chain. In this contribution, we present the role of the alcohol solvent (methanol or 2-propanol) and Ni catalyst (Ni/C or RANEY® Ni) in control over selectivity of phenolic products. The current results indicate that solvent effects on the catalytic processes could hold the key for improving control over the degree of functionalization of the propyl side-chain in the lignin oil obtained from CUB, offering new avenues for lignin valorization at the extraction step.

  10. Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage (United States)

    Shih, I-hung; Been, Michael D.


    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

  11. A Review: The Styrene Metabolizing Cascade of Side-Chain Oxygenation as Biotechnological Basis to Gain Various Valuable Compounds

    Directory of Open Access Journals (Sweden)

    Michel Oelschlägel


    Full Text Available Styrene is one of the most produced and processed chemicals worldwide and is released into the environment during widespread processing. But, it is also produced from plants and microorganisms. The natural occurrence of styrene led to several microbiological strategies to form and also to degrade styrene. One pathway designated as side-chain oxygenation has been reported as a specific route for the styrene degradation among microorganisms. It comprises the following enzymes: styrene monooxygenase (SMO; NADH-consuming and FAD-dependent, two-component system, styrene oxide isomerase (SOI; cofactor independent, membrane-bound protein and phenylacetaldehyde dehydrogenase (PAD; NAD+-consuming and allows an intrinsic cofactor regeneration. This specific way harbors a high potential for biotechnological use. Based on the enzymatic steps involved in this degradation route, important reactions can be realized from a large number of substrates which gain access to different interesting precursors for further applications. Furthermore, stereochemical transformations are possible, offering chiral products at high enantiomeric excess. This review provides an actual view on the microbiological styrene degradation followed by a detailed discussion on the enzymes of the side-chain oxygenation. Furthermore, the potential of the single enzyme reactions as well as the respective multi-step syntheses using the complete enzyme cascade are discussed in order to gain styrene oxides, phenylacetaldehydes, or phenylacetic acids (e.g., ibuprofen. Altered routes combining these putative biocatalysts with other enzymes are additionally described. Thus, the substrates spectrum can be enhanced and additional products as phenylethanols or phenylethylamines are reachable. Finally, additional enzymes with similar activities toward styrene and its metabolic intermediates are shown in order to modify the cascade described above or to use these enzyme independently for

  12. The effect of side-chain functionality and hydrophobicity on the gene delivery capabilities of cationic helical polypeptides. (United States)

    Zhang, Rujing; Zheng, Nan; Song, Ziyuan; Yin, Lichen; Cheng, Jianjun


    The rational design of effective and safe non-viral gene vectors is largely dependent on the understanding of the structure-property relationship. We herein report the design of a new series of cationic, α-helical polypeptides with different side charged groups (amine and guanidine) and hydrophobicity, and mechanistically unraveled the effect of polypeptide structure on the gene delivery capability. Guanidine-containing polypeptides displayed superior membrane activities to their amine-containing analogues via the pore formation mechanism, and thus possessed notably higher transfection efficiencies. Elongating the hydrophobic side chain also potentiated the membrane activities of the polypeptides, while at the meantime caused higher cytotoxicities. Upon an optimal balance between membrane activity and cytotoxicity, maximal transfection efficiency was achieved which outperformed commercial reagent Lipofectamine™ 2000 (LPF2000) by 3-6 folds. This study thus provides mechanistic insights into the rational design of non-viral gene delivery vectors, and the best-performing materials identified also serve as a promising addition to the existing systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Rotation of the swing plane of Foucault's pendulum and Thomas spin precession: two sides of one coin

    International Nuclear Information System (INIS)

    Krivoruchenko, Mikhail I


    Using elementary geometric tools, we apply essentially the same methods to derive expressions for the rotation angle of the swing plane of Foucault's pendulum and the rotation angle of the spin of a relativistic particle moving in a circular orbit (the Thomas precession effect). (methodological notes)

  14. Rotation of the swing plane of Foucault's pendulum and Thomas spin precession: two sides of one coin

    Energy Technology Data Exchange (ETDEWEB)

    Krivoruchenko, Mikhail I [Alikhanov Institute for Theoretical and Experimental Physics, Russian Federation State Scientific Center, Moscow (Russian Federation)


    Using elementary geometric tools, we apply essentially the same methods to derive expressions for the rotation angle of the swing plane of Foucault's pendulum and the rotation angle of the spin of a relativistic particle moving in a circular orbit (the Thomas precession effect). (methodological notes)

  15. 4-N, 4-S & 4-O Chloroquine Analogues: Influence of Side Chain Length and Quinolyl Nitrogen pKa on Activity vs. Chloroquine Resistant Malaria+, # (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.


    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

  16. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Dong Hoon; Cha, Young Kwan [Kyunghee Univ., Yongin (Korea, Republic of)


    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.

  18. 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


    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...... a quantitative analysis of the ensemble of ¿(2)-angles of especially leucine residues in disordered proteins. The changes in the rotamer distributions upon denaturation correlate to the changes upon helix induction by the co-solvent trifluoroethanol, suggesting that the side chain conformers are directly...

  19. An Improved Method for Separating the Kinetics of the Induction of Anisotropic and Topographic Gratings in Side-Chain Azobenzene Polyesters

    DEFF Research Database (Denmark)

    Helgert, M.; Fleck, B.; Wenke, L.


    The induction of anisotropy gratings in side-chain azobenzene polyesters is accompanied by the formation of surface relief. We introduce an improved holographic method to separate the contributions of the anisotropic and the topographic part to the diffraction efficiency by analyzing the polariza......The induction of anisotropy gratings in side-chain azobenzene polyesters is accompanied by the formation of surface relief. We introduce an improved holographic method to separate the contributions of the anisotropic and the topographic part to the diffraction efficiency by analyzing...

  20. 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


    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.

  1. 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.


    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

  2. Influence of dominant- as compared with nondominant-side symptoms on Disabilities of the Arm, Shoulder and Hand and Western Ontario Rotator Cuff scores in patients with rotator cuff tendinopathy. (United States)

    Christiansen, David Høyrup; Michener, Lori; Roy, Jean-Sébastien


    The Disabilities of the Arm, Shoulder and Hand (DASH) questionnaire and the Western Ontario Rotator Cuff (WORC) index are 2 widely used patient-reported questionnaires in individuals with rotator cuff (RC) tendinopathy. In contrast to the WORC index, for which the items are specific to the affected shoulder, the items of the DASH questionnaire assess the ability to perform activities regardless of the arm used. The objective of this study is to determine whether scores on the DASH questionnaire and WORC index are affected if the symptoms are on the dominant or nondominant side in individuals with RC tendinopathy. Given the number of items that can be influenced by dominance, the hypothesis is that DASH scores will be impacted by the side of the symptoms. Individuals with RC tendinopathy (N = 149) completed questions on symptomatology and hand dominance, the DASH questionnaire, and the WORC index. Differences in total scores (independent t test) and single items (Wilcoxon rank sum test) were compared between groups of participants with dominant-side symptoms and those without dominant-side symptoms. No significant differences were observed for WORC or DASH total scores when comparing participants with and without symptoms on their dominant side. Single-item comparison revealed more items being affected by symptom side on the DASH questionnaire (6 of 30 items) than on the WORC index (2 of 21 items). The side of the symptoms does not influence the DASH and WORC total scores, as there are no systematic differences between individuals with and without symptoms in their dominant shoulder. However, the presence of dominant symptoms does influence item scores more on the DASH questionnaire than on the WORC index. Copyright © 2018 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

  3. 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


    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.

  4. Effect of Side Chain Functional Group on Interactions in Ionic Liquid Systems: Insights from Infinite Dilution Thermodynamic Data. (United States)

    Paduszyński, Kamil; Królikowska, Marta


    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.

  5. 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: [Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH (Switzerland)


    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.

  6. Backbone and side-chain assignments for a novel CBM69 starch binding domain AmyP-SBD. (United States)

    Li, Xinxin; Yu, Jigang; Zhang, Jiahai; Sun, Hongbin; Zhang, Xuecheng


    Starch binding domains (SBDs) are important for the functions of glycoside hydrolysis enzymes such as α-amylases, they have great application potential in biotechnology and industries. AmyP is a newly identified α-amylase belonging to a new subfamily 37 of glycoside hydrolysis enzyme family 13. AmyP shows preferential degradation to soluble starch, in which its C-terminal starch binding domain, AmyP-SBD, plays an important role. AmyP-SBD shares very low sequence similarity with other biochemically characterized SBDs and was assigned to a new carbohydrate binding module family CBM69. Intriguingly, AmyP-SBD is unfolded in free form, and substrate analogue β-cyclodextrin may induce it to fold into a relatively rigid state. Structure determination for AmyP-SBD will be helpful for understanding its unique properties. Here, we report the backbone and side-chain 1 H, 13 C and 15 N resonance assignments of folded AmyP-SBD, as a basis for structure determination and further studies.

  7. Side chain modified peptide nucleic acids (PNA for knock-down of six3 in medaka embryos

    Directory of Open Access Journals (Sweden)

    Dorn Sebastian


    Full Text Available Abstract Background Synthetic antisense molecules have an enormous potential for therapeutic applications in humans. The major aim of such strategies is to specifically interfere with gene function, thus modulating cellular pathways according to the therapeutic demands. Among the molecules which can block mRNA function in a sequence specific manner are peptide nucleic acids (PNA. They are highly stable and efficiently and selectively interact with RNA. However, some properties of non-modified aminoethyl glycine PNAs (aegPNA hamper their in vivo applications. Results We generated new backbone modifications of PNAs, which exhibit more hydrophilic properties. When we examined the activity and specificity of these novel phosphonic ester PNAs (pePNA molecules in medaka (Oryzias latipes embryos, high solubility and selective binding to mRNA was observed. In particular, mixing of the novel components with aegPNA components resulted in mixed PNAs with superior properties. Injection of mixed PNAs directed against the medaka six3 gene, which is important for eye and brain development, resulted in specific six3 phenotypes. Conclusions PNAs are well established as powerful antisense molecules. Modification of the backbone with phosphonic ester side chains further improves their properties and allows the efficient knock down of a single gene in fish embryos.

  8. Side Chain-oxidized Oxysterols Regulate the Brain Renin-Angiotensin System through a Liver X Receptor-dependent Mechanism* (United States)

    Mateos, Laura; Ismail, Muhammad-Al-Mustafa; Gil-Bea, Francisco-Javier; Schüle, Rebecca; Schöls, Ludger; Heverin, Maura; Folkesson, Ronnie; Björkhem, Ingemar; Cedazo-Mínguez, Angel


    Disturbances in cholesterol metabolism have been associated with hypertension and neurodegenerative disorders. Because cholesterol metabolism in the brain is efficiently separated from plasma cholesterol by the blood-brain barrier (BBB), it is an unsolved paradox how high blood cholesterol can cause an effect in the brain. Here, we discuss the possibility that cholesterol metabolites permeable to the BBB might account for these effects. We show that 27-hydroxycholesterol (27-OH) and 24S-hydroxycholesterol (24S-OH) up-regulate the renin-angiotensin system (RAS) in the brain. Brains of mice on a cholesterol-enriched diet showed up-regulated angiotensin converting enzyme (ACE), angiotensinogen (AGT), and increased JAK/STAT activity. These effects were confirmed in in vitro studies with primary neurons and astrocytes exposed to 27-OH or 24S-OH, and were partially mediated by liver X receptors. In contrast, brain RAS activity was decreased in Cyp27a1-deficient mice, a model exhibiting reduced 27-OH production from cholesterol. Moreover, in humans, normocholesterolemic patients with elevated 27-OH levels, due to a CYP7B1 mutation, had markers of activated RAS in their cerebrospinal fluid. Our results demonstrate that side chain-oxidized oxysterols are modulators of brain RAS. Considering that levels of cholesterol and 27-OH correlate in the circulation and 27-OH can pass the BBB into the brain, we suggest that this cholesterol metabolite could be a link between high plasma cholesterol levels, hypertension, and neurodegeneration. PMID:21628469

  9. Investigation of nonfouling polypeptides of poly(glutamic acid) with lysine side chains synthesized by EDC·HCl/HOBt chemistry. (United States)

    Yang, Qinghua; Li, Wenchen; Wang, Longgang; Wang, Guangzhi; Wang, Zhen; Liu, Lingyun; Chen, Shengfu


    Nonfouling polypeptides with homogenous alternating charges draw peoples' attentions for their potential capability in biodegradation. Homogenous glutamic acid (E) and lysine (K) polypeptides were proposed and synthesized before. In this work, a new polypeptide formed by poly(glutamic acid) with lysine side chains (poly(E)-K) was synthesized by facile EDC·HCl/HOBt chemistry and investigated. Results show that these polypeptides also have good nonspecific protein resistance determined by enzyme-linked immunosorbent assay. The lowest nonspecific adsorption of the model proteins, anti-IgG and fibrinogen (Fg), on the self-assembling monolayers (SAMs) surface of poly(E)-K was only 3.3 ± 1.8 and 4.4 ± 1.6%, respectively, when protein adsorption on tissue culture polystyrene surface was set as 100%. And, the relative nonspecific protein adsorption increases when the polypeptide molecular weight increases due to the repression of low density polymer brushes. Moreover, almost no obvious cytotoxicity and hemolytic activity in vitro were detected. This work suggests that polypeptides with various formats of homogenous balanced charges could achieve excellent nonspecific protein resistance, which might be the intrinsic reason for the coexistence of high concentration serum proteins in blood.

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

    KAUST Repository

    Kiefer, David


    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


    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. Performance comparison of long and short-side chain perfluorosulfonic membranes for high temperature polymer electrolyte membrane fuel cell operation (United States)

    Stassi, A.; Gatto, I.; Passalacqua, E.; Antonucci, V.; Arico, A. S.; Merlo, L.; Oldani, C.; Pagano, E.

    A new Aquivion™ E79-03S short-side chain perfluorosulfonic membrane with a thickness of 30 μm (dry form) and an equivalent weight (EW) of 790 g/equiv recently developed by Solvay-Solexis for high-temperature operation was tested in a pressurised (3 bar abs.) polymer electrolyte membrane (PEM) single cell at a temperature of 130 °C. For comparison, a standard Nafion™ membrane (EW 1100 g/equiv) of similar thickness (50 μm) was investigated under similar operating conditions. Both membranes were tested for high temperature operation in conjunction with an in-house prepared carbon supported Pt electrocatalyst. The electrocatalyst consisted of nanosized Pt particles (particle size ∼2 nm) dispersed on a high surface area carbon black. The electrochemical tests showed better performance for the Aquivion™ membrane as compared to Nafion™ with promising properties for high temperature PEM fuel cell applications. Beside the higher open circuit voltage and lower ohmic constraints, a higher electrocatalytic activity was observed at high temperature for the electrocatalyst-Aquivion™ ionomer interface indicating a better catalyst utilization.

  13. Synthesis of amphiphilic alternating polyesters with oligo(ethylene glycol) side chains and potential use for sustained release drug delivery. (United States)

    Wang, Wei; Ding, Jianxun; Xiao, Chunsheng; Tang, Zhaohui; Li, Di; Chen, Jie; Zhuang, Xiuli; Chen, Xuesi


    Novel amphiphilic alternating polyesters, poly((N-phthaloyl-l-glutamic anhydride)-co-(2-(2-(2-methoxyethoxy)ethoxy)methyl)oxirane) (P(PGA-co-ME(2)MO)), were synthesized by alternating copolymerization of PGA and ME(2)MO. The structures of the synthesized polyesters were characterized by (1)H NMR, (13)C NMR, FT-IR, and GPC analyses. Because of the presence of oligo(ethylene glycol) (OEG) side chains, the polyesters could self-assemble into thermosensitive micelles. Dynamic light scattering (DLS) showed that these micelles underwent thermoinduced size decrease without intermicellar aggregation. In vitro methyl thiazolyl tetrazolium (MTT) assay demonstrated that the polyesters were biocompatible to Henrietta Lacks (HeLa) cells, rendering their potential for drug delivery applications. Two hydrophobic drugs, rifampin and doxorubicin (DOX), were loaded into the polyester micelles and observed to be released in a zero-order sustained manner. The sustained release could be accelerated in lower pH or in the presence of proteinase K, due to the degradation of the polyester under these conditions. Remarkably, in vitro cell experiments showed that the polyester micelles accomplished fast release of DOX inside cells and higher anticancer efficacy as compared with the free DOX. With enhanced stability during circulation condition and accelerated drug release at the target sites (e.g., low pH or enzyme presence), these novel polyesters with amphiphilic structures are promising to be used in sustained release drug delivery systems.

  14. Microbial side-chain cleavage of phytosterols by mycobacteria in vegetable oil/aqueous two-phase system. (United States)

    Xu, Yang-Guang; Guan, Yi-Xin; Wang, Hai-Qing; Yao, Shan-Jing


    Microbial side-chain cleavage of natural sterols to 4-androstene-3,17-dione (AD) and 1,4-androstadiene-3,17-dione (ADD) by Mycobacteria has received much attention in pharmaceutical industry, while low yield of the reaction owing to the strong hydrophobicity of sterols is a tough problem to be solved urgently. Eight kinds of vegetable oils, i.e., sunflower, peanut, corn, olive, linseed, walnut, grape seed, and rice oil, were used to construct oil/aqueous biphasic systems in the biotransformation of phytosterols by Mycobacterium sp. MB 3683 cells. The results indicated that vegetable oils are suitable for phytosterol biotransformation. Specially, the yield of AD carried out in sunflower biphasic system (phase ratio of 1:9, oil to aqueous) was greatly increased to 84.8 % with 10 g/L feeding concentration after 120-h transformation at 30 °C and 200 rpm. Distribution coefficients of AD in different oil/aqueous systems were also determined. Because vegetable oils are of low cost and because of their eco-friendly characters, there is a great potential for the application of oil/aqueous two-phase systems in bacteria whole cell biocatalysis.

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

    Fakhraee, Mostafa; Gholami, Mohammad Reza


    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.

  16. Residue-specific pK(a) determination of lysine and arginine side chains by indirect N-15 and C-13 NMR spectroscopy : Application to apo calmodulin

    NARCIS (Netherlands)

    Andre, Ingemar; Linse, Sara; Mulder, Frans A. A.


    Electrostatic interactions in proteins can be probed experimentally through determination of residue-specific acidity constants, We describe here triple-resonance NMR techniques for direct determination of lysine and arginine side-chain protonation states in proteins. The experiments are based on

  17. 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


    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.

  18. Side-chain liquid-crystalline poly(ketone)s : effect of spacer length, mesogen type and mesogen density on mesomorphic behavior

    NARCIS (Netherlands)

    Nieuwhof, R.P.; Marcelis, A.T.M.; Sudhölter, E.J.R.; Wursche, R.; Rieger, B.


    Novel side-chain liquid-crystalline copolymers (SCLCPs) were synthesized via the Pd(II) catalyzed alternating copolymerization of mesogenic 1-alkenes and carbon monoxide. For methoxybiphenyl mesogens, these copolymers exhibited highly ordered smectic E mesophases and high glass transition

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

    Directory of Open Access Journals (Sweden)

    Pierre J. De Clercq


    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.

  20. Asymmetric synthesis of the HMG-CoA reductase inhibitor atorvastatin calcium: an organocatalytic anhydride desymmetrization and cyanide-free side chain elongation approach. (United States)

    Chen, Xiaofei; Xiong, Fangjun; Chen, Wenxue; He, Qiuqin; Chen, Fener


    An efficient asymmetric synthesis of atorvastatin calcium has been achieved from commercially available diethyl 3-hydroxyglutarate through a novel approach that involves an organocatalytic enantioselective cyclic anhydride desymmetrization to establish C(3) stereogenicity and cyanide-free assembly of C7 amino type side chain via C5+C2 strategy as the key transformations.

  1. Synthesis and photovoltaic properties of the polymers base on thiophene derivatives with electron-deficient 3-nitro-1,2,4-triazole side chains

    International Nuclear Information System (INIS)

    Zhao, Bin; Li, Xinwei; Tang, Peng; Cao, Zhencai; Huang, Hongyan; Shen, Ping; Tan, Songting


    Three soluble alternating conjugated copolymers PT-TZN, PF-TZN, and PBDT-TZN, composed of thiophene, fluorene, benzo[1,2-b:4,5-b′]dithiophene and thiophene derivatives with 3-nitro-1,2,4-triazole side chains, were synthesized via the palladium-catalyzed Suzuki coupling reaction and Stille coupling reaction. The effects of 3-nitro-1,2,4-triazole on the thermal, photophysical, electrochemical and photovoltaic properties were investigated. The introduction of the 3-nitro-1,2,4-triazole side chains is beneficial for lowering the bandgaps of the polymers. The bulk-heterojunction polymer solar cells were fabricated based on the blend of the as-synthesized polymers and the fullerene acceptor [6, 6]-phenyl-C 61 -butyric acid methyl ester. The maximum power conversion efficiency (1.13%) was obtained with PBDT-TZN as the electron donor under the illumination of Air Mass 1.5, 100 mW/cm 2 . - Highlights: • Three conjugated polymers with 3-nitro-1,2,4-triazole side chains were synthesized. • The introduction of the side chains favors lowering the bandgaps of the polymers. • The strong electron-withdrawing nitro group likely promotes excimer quenching

  2. Metabolism of a novel side chain modified Δ8(14)-15-ketosterol, a potential cholesterol lowering drug: 28-hydroxylation by CYP27A1 (United States)

    Pettersson, Hanna; Norlina, Maria; Andersson, Ulla; Pikuleva, Irina; Björkhem, Ingemar; Misharin, Alexander Yu.; Wikvall, Kjell


    The synthetic inhibitors of sterol biosynthesis, 3β-hydroxy-5α-cholest-8(14)-en-15-one and 3β-hydroxy-24S-methyl-5α-cholesta-8(14),22-dien-15-one, are of interest as potential cholesterol lowering drugs. Rapid metabolism of synthetic 15-ketosterols may lead to a decrease, or loss, of their potency to affect lipid metabolism. 3β-Hydroxy-5α-cholest-8(14)-en-15-one is reported to be rapidly side chain oxygenated by rat liver mitochondria. In an attempt to reduce this metabolism, the novel side-chain modified 15-ketosterol 3β-Hydroxy-24S-methyl-5α-cholesta-8(14),22-dien-15-one was synthesized. We have examined the metabolism by recombinant human CYP27A1 of this novel side-chain modified 3β-hydroxy-24S-methyl-5α-cholesta-8(14),22-dien-15-one and compared the rate of metabolism with that of the previously described 3β-hydroxy-5α-cholest-8(14)-en-15-one. Both sterols were found to be efficiently metabolized by recombinant human CYP27A1. None of the two 15-ketosterols was significantly metabolized by microsomal 7α-hydroxylation. Interestingly, CYP27A1-mediated product formation was much lower with the side-chain modified 3β-hydroxy-24S-methyl-5α-cholesta-8(14),22-dien-15-one than with the previously described 3β-hydroxy-5α-cholest-8(14)-en-15-one. A surprising finding was that this novel side-chain modified sterol was metabolized mainly in the C-28 position by CYP27A1. The data on 28-hydroxylation by human CYP27A1 provide new insights on the catalytic properties and substrate specificity of this enzyme. The finding that 3β-hydroxy-24S-methyl-5α-cholesta-8(14),22-dien-15-one with a modified side chain is metabolized at a dramatically slower rate than the previously described 15-ketosterol with unmodified side chain may be important for future development of synthetic cholesterol lowering sterols. PMID:18603016

  3. Metabolism of a novel side chain modified Delta8(14)-15-ketosterol, a potential cholesterol lowering drug: 28-hydroxylation by CYP27A1. (United States)

    Pettersson, Hanna; Norlin, Maria; Andersson, Ulla; Pikuleva, Irina; Björkhem, Ingemar; Misharin, Alexander Yu; Wikvall, Kjell


    The synthetic inhibitors of sterol biosynthesis, 3beta-hydroxy-5alpha-cholest-8(14)-en-15-one and 3beta-hydroxy-24S-methyl-5alpha-cholesta-8(14),22-dien-15-one, are of interest as potential cholesterol lowering drugs. Rapid metabolism of synthetic 15-ketosterols may lead to a decrease, or loss, of their potency to affect lipid metabolism. 3beta-Hydroxy-5alpha-cholest-8(14)-en-15-one is reported to be rapidly side chain oxygenated by rat liver mitochondria. In an attempt to reduce this metabolism, the novel side chain modified 15-ketosterol 3beta-Hydroxy-24S-methyl-5alpha-cholesta-8(14),22-dien-15-one was synthesized. We have examined the metabolism by recombinant human CYP27A1 of this novel side chain modified 3beta-hydroxy-24S-methyl-5alpha-cholesta-8(14),22-dien-15-one and compared the rate of metabolism with that of the previously described 3beta-hydroxy-5alpha-cholest-8(14)-en-15-one. Both sterols were found to be efficiently metabolized by recombinant human CYP27A1. None of the two 15-ketosterols was significantly metabolized by microsomal 7alpha-hydroxylation. Interestingly, CYP27A1-mediated product formation was much lower with the side chain modified 3beta-hydroxy-24S-methyl-5alpha-cholesta-8(14),22-dien-15-one than with the previously described 3beta-hydroxy-5alpha-cholest-8(14)-en-15-one. A surprising finding was that this novel side chain modified sterol was metabolized mainly in the C-28 position by CYP27A1. The data on 28-hydroxylation by human CYP27A1 provide new insights on the catalytic properties and substrate specificity of this enzyme. The finding that 3beta-hydroxy-24S-methyl-5alpha-cholesta-8(14),22-dien-15-one with a modified side chain is metabolized at a dramatically slower rate than the previously described 15-ketosterol with unmodified side chain may be important for future development of synthetic cholesterol lowering sterols.

  4. Effect of side chain length on the stability and structural properties of 3-(2’,5’-dialkoxy-phenylthiophenes: a theoretical study

    Directory of Open Access Journals (Sweden)

    Taye Beyene Demissie


    Full Text Available We report on the effect of the alkoxy chain length on the thermodynamic properties of neutral and the corresponding radical cations of 3-(2’,5’-dibutyloxyphenylthiophene (DBOPT, 3-(2’,5’-diheptyloxyphenylthiophene (DHOPT, and 3-(2’,5’-dioctyloxyphenylthiophene (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 stable by about 61.39 kJ/mol than the ones with shorter side chains at the radical cation state. The results correlate well with the experimental observations made during the electrochemical synthesis of these polymers from their monomers.

  5. Evaluating Force Fields for the Computational Prediction of Ionized Arginine and Lysine Side-Chains Partitioning into Lipid Bilayers and Octanol. (United States)

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


    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.

  6. Interrogation of side chain biases for oligomannose recognition by antibody 2G12 via structure-guided phage display libraries. (United States)

    Lin, Tsung-Yi; Lai, Jonathan R


    Monoclonal antibodies (mAbs) are essential reagents for deciphering gene or protein function and have been a fruitful source of therapeutic and diagnostic agents. However, developing anticarbohydrate antibodies to target glycans for those purposes has been less successful because the molecular basis for glycan-mAb interactions is poorly understood relative to protein- or peptide-binding mAbs. Here, we report our investigation on glycan-mAb interactions by using the unique architectural scaffold of 2G12, an antibody that targets oligomannoses on the HIV-1 glycoprotein gp120, as the template for engineering highly specific mAbs to target glycans. We first analyzed 24 different X-ray structures of antiglycan mAbs from the Protein Data Bank to determine side chain amino acid distributions in of glycan-mAb interactions. We identified Tyr, Arg, Asn, Ser, Asp, and His as the six most prevalent residues in the glycan-mAb contacts. We then utilized this information to construct two phage display libraries ("Lib1" and "Lib2") in which positions on the heavy chain variable domains of 2G12 were allowed to vary in restricted manner among Tyr, Asp, Ser, His, Asn, Thr, Ala and Pro to interrogate the minimal physicochemical requirements for oligomannose recognition. We analyzed the sequences of 39 variants from Lib1 and 14 variants from Lib2 following selection against gp120, the results showed that there is a high degree of malleability within the 2G12 for glycan recognitions. We further characterized five unique phage clones from both libraries that exhibited a gp120-specific binding profile. Expression of two of these variants as soluble mAbs indicated that, while specificity of gp120-binding was retained, the affinity of these mutants was significantly reduced relative to WT 2G12. Nonetheless, the results indicate these is some malleability in the identity of contact residues and provide a novel insight into the nature of glycan-antibody interactions and how they may differ

  7. 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


    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.

  8. Modulated protonation of side chain aminoethylene repeats in N-substituted polyaspartamides promotes mRNA transfection. (United States)

    Uchida, Hirokuni; Itaka, Keiji; Nomoto, Takahiro; Ishii, Takehiko; Suma, Tomoya; Ikegami, Masaru; Miyata, Kanjiro; Oba, Makoto; Nishiyama, Nobuhiro; Kataoka, Kazunori


    Fine-tuning of chemical structures of polycation-based carriers (polyplexes) is an attractive strategy for safe and efficient mRNA transfaction. Here, mRNA polyplexes comprising N-substituted polyaspartamides with varied numbers of side chain aminoethylene repeats were constructed, and their transfection ability against human hepatoma cells was examined. Transfection efficacy clearly correlated with the number of aminoethylene repeats: polyplexes with odd number repeats (PA-Os) produced sustained increases in mRNA expression compared with those with even number repeats (PA-Es). This predominant efficacy of PA-Os over PA-Es was contradictory to our previous findings for pDNA polyplexes prepared from the same N-substituted polyaspartamides, that is, PA-Es revealed superior transfection efficacy of pDNA than PA-Os. Intracellular FRET analysis using flow cytometry and polyplex tracking under confocal laser scanning microscopy revealed that overall transfection efficacy was determined through the balance between endosomal escaping capability and stability of translocated mRNA in cytoplasm. PA-Es efficiently transported mRNA into the cytoplasm. However, their poor cytoplasmic stability led to facile degradation of mRNA, resulting in a less durable pattern of transfection. Alternatively, PA-Os with limited capability of endosomal escape eventually protect mRNA in the cytoplasm to induce sustainable mRNA expression. Higher cytoplasmic stability of pDNA compared to mRNA may shift the limiting step in transfection from cytoplasmic stability to endosomal escape capacity, thereby giving an opposite odd-even effect in transfection efficacy. Endosomal escaping capability and nuclease stability of polyplexes are correlated with the modulated protonation behavior in aminoethylene repeats responding to pH, appealing the substantial importance of chemistry to design polycation structures for promoted mRNA transfection.

  9. Effects of hydrophobic helix length and side chain chemistry on biomimicry in peptoid analogues of SP-C. (United States)

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


    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.

  10. The molecular mechanism of N-acetylglucosamine side-chain attachment to the Lancefield group A carbohydrate in Streptococcus pyogenes. (United States)

    Rush, Jeffrey S; Edgar, Rebecca J; Deng, Pan; Chen, Jing; Zhu, Haining; van Sorge, Nina M; Morris, Andrew J; Korotkov, Konstantin V; Korotkova, Natalia


    In many Lactobacillales species ( i.e. lactic acid bacteria), peptidoglycan is decorated by polyrhamnose polysaccharides that are critical for cell envelope integrity and cell shape and also represent key antigenic determinants. Despite the biological importance of these polysaccharides, their biosynthetic pathways have received limited attention. The important human pathogen, Streptococcus pyogenes , synthesizes a key antigenic surface polymer, the Lancefield group A carbohydrate (GAC). GAC is covalently attached to peptidoglycan and consists of a polyrhamnose polymer, with N -acetylglucosamine (GlcNAc) side chains, which is an essential virulence determinant. The molecular details of the mechanism of polyrhamnose modification with GlcNAc are currently unknown. In this report, using molecular genetics, analytical chemistry, and mass spectrometry analysis, we demonstrated that GAC biosynthesis requires two distinct undecaprenol-linked GlcNAc-lipid intermediates: GlcNAc-pyrophosphoryl-undecaprenol (GlcNAc-P-P-Und) produced by the GlcNAc-phosphate transferase GacO and GlcNAc-phosphate-undecaprenol (GlcNAc-P-Und) produced by the glycosyltransferase GacI. Further investigations revealed that the GAC polyrhamnose backbone is assembled on GlcNAc-P-P-Und. Our results also suggested that a GT-C glycosyltransferase, GacL, transfers GlcNAc from GlcNAc-P-Und to polyrhamnose. Moreover, GacJ, a small membrane-associated protein, formed a complex with GacI and significantly stimulated its catalytic activity. Of note, we observed that GacI homologs perform a similar function in Streptococcus agalactiae and Enterococcus faecalis In conclusion, the elucidation of GAC biosynthesis in S. pyogenes reported here enhances our understanding of how other Gram-positive bacteria produce essential components of their cell wall. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

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


    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

  12. Coordinate developmental expression of genes regulating sterol economy and cholesterol side-chain cleavage in the porcine ovary. (United States)

    LaVoie, H A; Benoit, A M; Garmey, J C; Dailey, R A; Wright, D J; Veldhuis, J D


    To investigate the coordinate developmental expression of low-density lipoprotein (LDL) receptor, 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase, sterol carrier protein 2 (SCP2), steroidogenic acute regulatory protein (StAR), and cytochrome P450 side-chain cleavage (P450scc) enzyme messages throughout the pig estrous cycle, RNase protection analysis was performed using homologous (partially cloned) porcine sequences. Total RNA was isolated from ovarian tissues from unstimulated prepubertal gilts and gilts stimulated with eCG (Day -3) and hCG (Day 0) to induce follicular growth and ovulation. Specific transcripts (relative to 18S rRNA) were quantified in immature ovaries, preovulatory follicles (> or = 5 mm), corpora lutea (CL), and corpora albicantia. As an index of steroidogenesis, tissue progesterone content (per microgram protein) was low in the unstimulated ovary and preovulatory follicles, and it began to increase 4 days post-hCG, peaked at 12 days, and returned to preovulatory concentrations by 20 days post-hCG. HMG-CoA reductase mRNA was expressed at low levels and did not change significantly throughout the estrous cycle. The amount of LDL receptor mRNA increased approximately 6-fold after eCG stimulation and was expressed at similar concentrations in both preovulatory follicles and functional CL. Expression of SCP2 mRNA did not differ among the four tissue types but tended to be highest in midcycle (Day 12) CL compared other stages of CL (p = 0.007). StAR mRNA expression was minimal in unstimulated ovaries, was higher in preovulatory follicles (p = 0.014), and then rose again in CL (p = 0.009 compared with unstimulated ovary). P450scc mRNA concentrations were low in unstimulated ovaries, increased in preovulatory follicles (p = 0.044), and increased further in CL (p = 0.001 compared with preovulatory follicles). P450scc and StAR mRNA levels correlated with progesterone levels (r = +0.37, p = 0.025, and r = +0.71, p StAR, and P450scc messages

  13. Ring flips revisited: (13)C relaxation dispersion measurements of aromatic side chain dynamics and activation barriers in basic pancreatic trypsin inhibitor. (United States)

    Weininger, Ulrich; Modig, Kristofer; Akke, Mikael


    Intramolecular motions of proteins are critical for biological function. Transient structural fluctuations underlie a wide range of processes, including enzyme catalysis, ligand binding to buried sites, and generic protein motions, such as 180° rotation of aromatic side chains in the protein interior, but remain poorly understood. Understanding the dynamics and molecular nature of concerted motions requires characterization of their rates and energy barriers. Here we use recently developed (13)C transverse relaxation dispersion methods to improve our current understanding of aromatic ring flips in basic pancreatic trypsin inhibitor (BPTI). We validate these methods by benchmarking ring-flip rates against the three previously characterized cases in BPTI, namely, Y23, Y35, and F45. Further, we measure conformational exchange for one additional aromatic ring, F22, which can be interpreted in terms of a flip rate of 666 s(-1) at 5 °C. Upon inclusion of our previously reported result that Y21 also flips slowly [Weininger, U., et al. (2013) J. Phys. Chem. B 117, 9241-9247], the (13)C relaxation dispersion experiments thus reveal relatively slow ring-flip rates for five of eight aromatic residues in BPTI. These results are in contrast with previous reports, which have estimated that all rings, except Y23, Y35, and F45, flip with a high rate at ambient temperature. The (13)C relaxation dispersion data result in an updated rank order of ring-flip rates in BPTI, which agrees considerably better with that estimated from a recent 1 ms molecular dynamics trajectory than do previously published NMR data. However, significant quantitative differences remain between experiment and simulation, in that the latter yields flip rates that are in many cases too fast by 1-2 orders of magnitude. By measuring flip rates across a temperature range of 5-65 °C, we determined the activation barriers of ring flips for Y23, Y35, and F45. Y23 and F45 have identical activation parameters

  14. Phenylpropanoid 2,3-dioxygenase involved in the cleavage of the ferulic acid side chain to form vanillin and glyoxylic acid in Vanilla planifolia. (United States)

    Negishi, Osamu; Negishi, Yukiko


    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.

  15. Effects of side-chain and electron exchange correlation on the band structure of perylene diimide liquid crystals: a density functional study. (United States)

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


    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.

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

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


    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.

  17. Synthesis and structure-activity relationship study of FD-891: importance of the side chain and C8-C9 epoxide for cytotoxic activity against cancer cells. (United States)

    Itagaki, Tomohiro; Kawamata, Ayano; Takeuchi, Miho; Hamada, Keisuke; Iwabuchi, Yoshiharu; Eguchi, Tadashi; Kudo, Fumitaka; Usui, Takeo; Kanoh, Naoki


    Unified synthesis of FD-891 analogs and their structure-activity relationship are described. By using stereoselective allylation/crotylation and Evans aldol chemistry, six side-chain fragments having different length and terminus were synthesized. These fragments were coupled with a macrolactone fragment, improved synthesis of which was also developed here, to generate FD-891 and five truncated analogs. These synthetic compounds as well as three analogs obtained from fermentation of gene-disrupted Streptomyces graminofaciens mutants were tested for in vitro cytotoxic activity against HeLa cells. As a result, coexistence of the C8-C9 epoxide and side-chain terminus was found to be critical for the cytotoxic activity.

  18. An efficient nitration of light alkanes and the alkyl side-chain of aromatic compounds with nitrogen dioxide and nitric acid catalyzed by N-hydroxyphthalimide. (United States)

    Nishiwaki, Yoshiki; Sakaguchi, Satoshi; Ishii, Yasutaka


    Nitration of light alkanes and the alkyl side-chain of aromatic compounds with NO(2) and HNO(3) was successfully achieved by the use of N-hydroxyphthalimide (NHPI) as a catalyst under relatively mild conditions. For example, the nitration of propane with NO(2) catalyzed by NHPI at 100 degrees C for 14 h gave 2-nitropropane in good yield without formation of 1-nitropropane and cleaved products such as nitroethane and nitromethane. Various aliphatic nitroalkanes, which are difficult to prepare by conventional methods, could be selectively obtained by means of the present methodology by using NHPI as the key catalyst. In addition, the side-chain nitration of alkylbenzenes such as toluene was selectively carried out to lead to alpha-nitrotoluene without the ring nitration. The present reaction provides an efficient selective method for the nitration of light alkanes and alkylbenzenes, which has been very difficult to carry out so far.

  19. Electrophilic heteroaromatic substitutions. 8. Studies on the mechanism of the α-side-chain aminomethylation and hydrogen/deuterium isotope exchange reactions of α-methylpyrroles

    International Nuclear Information System (INIS)

    Curulli, A.; Sleiter, G.


    A kinetic investigation of the acid-mediated α-side-chain (dimethylamino)alkylation and hydrogen/deuterium isotope exchange reactions of ethyl 1,3,4,5-tetramethylpyrrole-2-carboxylate and ethyl 4-bromo-1,3,5-trimethylpyrrole-2-carboxylate in aqueous acetonitrile has been carried out. The effect of a number of variables, such as nature and concentration of the catalyzing acid, amount of water in the reaction medium, and concentration and type of the electrophile, on the reaction rate indicates that both processes are subject to general acid catalysis and that their limiting step is electrophilic attack on an α-methylenepyrroline. The influence on the rate of the Mannich reaction of the nuclear substituent adjacent to the side chain undergoing attack is also discussed. The conditional dissociation constants of acetic and formic acid in 95% aqueous acetonitrile have been measured. 13 references, 2 tables

  20. Development of bio-based thermoplastic polyurethanes formulations using corn-derived chain extender for reactive rotational molding

    Directory of Open Access Journals (Sweden)

    K. Prashantha


    Full Text Available Partly bio-based segmented thermoplastic polyurethane (TPU formulations were developed to fulfill the requirements of the reactive rotational molding process. They were obtained by one-shot bulk polymerization between an aliphatic diisocyanate (1,6-hexamethylene diisocyanate, a polyether polyol as macrodiol (polyethylene glycol and a biobased corn-derived 1,3-propanediol as chain extender (CE, in presence of a catalyst, at an initial temperature of 45°C. Equivalent TPU formulations with classical petroleum-based 1,3-propanediol were also prepared for a purpose of comparison. TPU with different soft to hard segment (SS/HS ratios were synthesized by varying the macrodiol and CE concentrations in the formulations. For each formulation, the evolution of the reaction temperature as a function of time was monitored and the kinetics of polymerization was studied by Fourier Transform infrared spectroscopy in attenuated total reflection mode (FTIR-ATR. The morphology, thermal properties, solubility in different solvents and tensile properties of the final products were analyzed. All synthesized polyurethanes are 100% linear polymers and the extent of microphase separation, as well as the thermal and mechanical properties highly depends on the HS content, and glass transition temperature and Young modulus can be tuned by adjustment of the SS/HS ratio. All results indicate that petrochemical CE can be replaced by its recently available corn-derived homologue, without sacrificing any use properties of the final polyurethanes.

  1. 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


    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.

  2. Richness of Side-Chain Liquid-Crystal Polymers: From Isotropic Phase towards the Identification of Neglected Solid-Like Properties in Liquids


    Noirez , Laurence; Mendil-Jakani , Hakima; Baroni , Patrick; Wendorff , Joachim H.


    International audience; Very few studies concern the isotropic phase of Side-Chain Liquid-Crystalline Polymers (SCLCPs). However, the interest for the isotropic phase appears particularly obvious in flow experiments. Unforeseen shear-induced nematic phases are revealed away from the N-I transition temperature. The non-equilibrium nematic phase in the isotropic phase of SCLCP melts challenges the conventional timescales described in theoretical approaches and reveal very long timescales, negle...

  3. 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.


    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......-field optical microscopic scanning of the grating reveals, however, that the bulk of the film remains optically anisotropic. (C) 1996 American Institute of Physics....

  4. Pyroacm Resin: An Acetamidomethyl Derived Resin for Solid Phase Synthesis of Peptides through Side Chain Anchoring of C-Terminal Cysteine Residues. (United States)

    Juvekar, Vinayak; Gong, Young Dae


    The design, synthesis and utilization of an efficient acetamidomethyl derived resin for the peptide synthesis is presented using established Fmoc and Boc protocols via side chain anchoring. Cleavage of the target peptide from the resin is performed using carboxymethylsulfenyl chloride under mild conditions which gave in situ thiol-sulfenyl protection of the cysteine residues. The utility of the resin is successfully demonstrated through applications to the syntheses of model peptides and natural products Riparin 1.1 and Riparin 1.2.

  5. Influence of molecular weight on the phase behavior and structure formation of branched side-chain hairy-rod polyfluorene in bulk phase.

    NARCIS (Netherlands)

    Knaapila, M.; Stepanyan, R.; Torkkeli, M.; Lyons, B.P.; Ikonen, T.P.; Almasy, L.; Foreman, J.P.; Serimaa, R.; Guntner, R; Scherf, U.; Monkman, A.P.


    We report on an experimental study of the self-organization and phase behavior of hairy-rod π -conjugated branched side-chain polyfluorene, poly[9,9-bis(2-ethylhexyl)-fluorene-2,7-diyl]—i.e., poly[2,7–(9,9–bis(2–ethylhexyl)fluorene] (PF2∕6) —as a function of molecular weight (Mn) . The results have

  6. Side-chain amino-acid-based pH-responsive self-assembled block copolymers for drug delivery and gene transfer. (United States)

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


    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.

  7. 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


    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.

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

    KAUST Repository

    Yiu, Alan T.


    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.

  9. Photo-aligned blend films of azobenzene-containing polyimides with and without side-chains for inducing inclined alignment of liquid crystal molecules (United States)

    Usami, Kiyoaki; Sakamoto, Kenji


    We have succeeded in controlling the pretilt angle of liquid crystal (LC) molecules over the whole range of 0 to 90° by using photo-aligned blend films of two azobenzene-containing polyimides (Azo-PIs) with and without side-chains. The Azo-PIs were synthesized from pyromellitic dianhydride and a mixture of 4,4'-diaminoazobenzene and 4-(4'-propylbi(cyclohexan)-4-yl)phenyl 3,5-diaminobenzoate (PBCP-DABA). PBCP-DABA is a diamine to introduce a side-chain structure into the polyimide. Defect-free uniform LC alignment was obtained in the pretilt angle (θp) ranges of θp ≤ 11° and θp ≥ 78°. Previously, we reported that the pretilt angle can be controlled using pure photo-aligned films of Azo-PIs with different molar fractions of PBCP-DABA. For the pure photo-aligned films, the defect-free pretilt angle ranges were θp < 5° and θp ≥ 85°. These results suggest that the azimuthal anchoring strength of the blend Azo-PI film is stronger than that of the pure films of Azo-PIs with side-chains, at least for the pretilt angle range from 5 to 11°. We found that the defect-free pretilt angle range can be extended by using the blend Azo-PI films instead of the pure Azo-PI films.

  10. 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


    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.

  11. Double Hydrogen Bonding between Side Chain Carboxyl Groups in Aqueous Solutions of Poly (β-L-Malic Acid): Implication for the Evolutionary Origin of Nucleic Acids (United States)

    Francis, Brian R.; Watkins, Kevin; Kubelka, Jan


    The RNA world hypothesis holds that in the evolutionary events that led to the emergence of life RNA preceded proteins and DNA and is supported by the ability of RNA to act as both a genetic polymer and a catalyst. On the other hand, biosynthesis of nucleic acids requires a large number of enzymes and chemical synthesis of RNA under presumed prebiotic conditions is complicated and requires many sequential steps. These observations suggest that biosynthesis of RNA is the end product of a long evolutionary process. If so, what was the original polymer from which RNA and DNA evolved? In most syntheses of simpler RNA or DNA analogs, the D-ribose phosphate polymer backbone is altered and the purine and pyrimidine bases are retained for hydrogen bonding between complementary base pairs. However, the bases are themselves products of complex biosynthetic pathways and hence they too may have evolved from simpler polymer side chains that had the ability to form hydrogen bonds. We hypothesize that the earliest evolutionary predecessor of nucleic acids was the simple linear polyester, poly (β-D-malic acid), for which the carboxyl side chains could form double hydrogen bonds. In this study, we show that in accord with this hypothesis a closely related polyester, poly (β-L-malic acid), uses carboxyl side chains to form robust intramolecular double hydrogen bonds in moderately acidic solution. PMID:29061955

  12. Enzyme resistant feruloylated xylooligomer analogues from thermochemically treated corn fiber contain large side chains, ethyl glycosides and novel sites of acetylation. (United States)

    Appeldoorn, Maaike M; de Waard, Pieter; Kabel, Mirjam A; Gruppen, Harry; Schols, Henk A


    In order to use corn fiber as a source for bioethanol production the enzymatic hydrolysis of the complex glucuronoarabinoxylans present has to be improved. Several oligosaccharides present in the supernatant of mild acid pretreated and enzymatically saccharified corn fiber that resist the current available enzymes were (semi)purified for structural analysis by NMR or ESI-MS(n). The structural features of 21 recalcitrant oligosaccharides are presented. A common feature of almost all these oligosaccharides is that they contain (part of) an α-l-galactopyranosyl-(1→2)-β-d-xylopyranosyl-(1→2)-5-O-trans-feruloyl-l-arabinofuranose side chain attached to the O-3 position of the β-1-4 linked xylose backbone. Several of the identified oligosaccharides contained an ethyl group at the reducing end hypothesized to be formed during SSF. The ethyl glycosides found are far more complex than previously described structures. A new feature present in more than half of the oligosaccharides is an acetyl group attached to the O-2 position of the same xylose to which the oligomeric side chain was attached to the O-3 position. Finding enzymes attacking these large side chains and the dense substituted xylan backbone will boost the hydrolysis of corn fiber glucuronoxylan. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Identification of Oxygenated Fatty Acid as a Side Chain of Lipo-Alkaloids in Aconitum carmichaelii by UHPLC-Q-TOF-MS and a Database

    Directory of Open Access Journals (Sweden)

    Ying Liang


    Full Text Available Lipo-alkaloid is a kind of C19-norditerpenoid alkaloid usually found in Aconitum species. Structurally, they contain an aconitane skeleton and one or two fatty acid moieties of 3–25 carbon chains with 1–6 unsaturated degrees. Analysis of the lipo-alkaloids in roots of Aconitum carmichaelii resulted in the isolation of six known pure lipo-alkaloids (A1–A6 and a lipo-alkaloid mixture (A7. The mixture shared the same aconitane skeleton of 14-benzoylmesaconine, but their side chains were determined to be 9-hydroxy-octadecadienoic acid, 13-hydroxy-octadecadienoic acid and 10-hydroxy-octadecadienoic acid, respectively, by MS/MS analysis after alkaline hydrolysis. To our knowledge, this is the first time of the reporting of the oxygenated fatty acids as the side chains in naturally-occurring lipo-alkaloids. In order to identify more lipo-alkaloids, a compound database was established based on various combinations between the aconitane skeleton and the fatty acid chain, and then, the identification of lipo-alkaloids was conducted using the database, UHPLC-Q-TOF-MS and MS/MS. Finally, 148 lipo-alkaloids were identified from A. carmichaelii after intensive MS/MS analysis, including 93 potential new compounds and 38 compounds with oxygenated fatty acid moieties.

  14. Role of camalexin, indole glucosinolates, and side chain modification of glucosinolate-derived isothiocyanates in defense of Arabidopsis against Sclerotinia sclerotiorum. (United States)

    Stotz, Henrik U; Sawada, Yuji; Shimada, Yukihisa; Hirai, Masami Y; Sasaki, Eriko; Krischke, Markus; Brown, Paul D; Saito, Kazuki; Kamiya, Yuji


    Plant secondary metabolites are known to facilitate interactions with a variety of beneficial and detrimental organisms, yet the contribution of specific metabolites to interactions with fungal pathogens is poorly understood. Here we show that, with respect to aliphatic glucosinolate-derived isothiocyanates, toxicity against the pathogenic ascomycete Sclerotinia sclerotiorum depends on side chain structure. Genes associated with the formation of the secondary metabolites camalexin and glucosinolate were induced in Arabidopsis thaliana leaves challenged with the necrotrophic pathogen S. sclerotiorum. Unlike S. sclerotiorum, the closely related ascomycete Botrytis cinerea was not identified to induce genes associated with aliphatic glucosinolate biosynthesis in pathogen-challenged leaves. Mutant plant lines deficient in camalexin, indole, or aliphatic glucosinolate biosynthesis were hypersusceptible to S. sclerotiorum, among them the myb28 mutant, which has a regulatory defect resulting in decreased production of long-chained aliphatic glucosinolates. The antimicrobial activity of aliphatic glucosinolate-derived isothiocyanates was dependent on side chain elongation and modification, with 8-methylsulfinyloctyl isothiocyanate being most toxic to S. sclerotiorum. This information is important for microbial associations with cruciferous host plants and for metabolic engineering of pathogen defenses in cruciferous plants that produce short-chained aliphatic glucosinolates. © 2011 RIKEN (Growth Regulation Research Group). The Plant Journal © 2011 Blackwell Publishing Ltd.

  15. Rotational spectrum of tryptophan

    Energy Technology Data Exchange (ETDEWEB)

    Sanz, M. Eugenia, E-mail:; Cabezas, Carlos, E-mail:; Mata, Santiago, E-mail:; Alonso, Josè L., E-mail: [Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico Uva, Universidad de Valladolid, 47011 Valladolid (Spain)


    The rotational spectrum of the natural amino acid tryptophan has been observed for the first time using a combination of laser ablation, molecular beams, and Fourier transform microwave spectroscopy. Independent analysis of the rotational spectra of individual conformers has conducted to a definitive identification of two different conformers of tryptophan, with one of the observed conformers never reported before. The analysis of the {sup 14}N nuclear quadrupole coupling constants is of particular significance since it allows discrimination between structures, thus providing structural information on the orientation of the amino group. Both observed conformers are stabilized by an O–H···N hydrogen bond in the side chain and a N–H···π interaction forming a chain that reinforce the strength of hydrogen bonds through cooperative effects.





    ABSTRACT Patients irradiated for left-sided breast cancer have higher incidence of cardiovascular disease than those receiving irradiation for right-sided breast cancer. Most abnormalities were in the left anterior descending (LAD) coronary artery territory. We analyzed the relationships between preoperative examination results and irradiation dose to the LAD artery in patients with left-sided breast cancer. Seventy-one patients receiving breast radiotherapy were analyzed. The heart may rotat...

  17. Outer membrane phospholipase A in phospholipid bilayers: a model system for concerted computational and experimental investigations of amino acid side chain partitioning into lipid bilayers. (United States)

    Fleming, Patrick J; Freites, J Alfredo; Moon, C Preston; Tobias, Douglas J; Fleming, Karen G


    Understanding the forces that stabilize membrane proteins in their native states is one of the contemporary challenges of biophysics. To date, estimates of side chain partitioning free energies from water to the lipid environment show disparate values between experimental and computational measures. Resolving the disparities is particularly important for understanding the energetic contributions of polar and charged side chains to membrane protein function because of the roles these residue types play in many cellular functions. In general, computational free energy estimates of charged side chain partitioning into bilayers are much larger than experimental measurements. However, the lack of a protein-based experimental system that uses bilayers against which to vet these computational predictions has traditionally been a significant drawback. Moon & Fleming recently published a novel hydrophobicity scale that was derived experimentally by using a host-guest strategy to measure the side chain energetic perturbation due to mutation in the context of a native membrane protein inserted into a phospholipid bilayer. These values are still approximately an order of magnitude smaller than computational estimates derived from molecular dynamics calculations from several independent groups. Here we address this discrepancy by showing that the free energy differences between experiment and computation become much smaller if the appropriate comparisons are drawn, which suggests that the two fields may in fact be converging. In addition, we present an initial computational characterization of the Moon & Fleming experimental system used for the hydrophobicity scale: OmpLA in DLPC bilayers. The hydrophobicity scale used OmpLA position 210 as the guest site, and our preliminary results demonstrate that this position is buried in the center of the DLPC membrane, validating its usage in the experimental studies. We further showed that the introduction of charged Arg at position 210

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

    KAUST Repository

    Nam, Sungho


    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.

  19. Correlation between polymer architecture, mesoscale structure and photovoltaic performance in side-chain-modified PAE-PAV:fullerene bulk-heterojunction solar cells (United States)

    Rathgeber, S.; Kuehnlenz, F.; Hoppe, H.; Egbe, D. A. M.; Tuerk, S.; Perlich, J.; Gehrke, R.


    A poly(arylene-ethynylene)-alt-poly(arylene-vinylene) statistical copolymer carrying linear and branched alkoxy side chains along the conjugated backbone in a random manner, yields, compared to its regular substituted counterparts, an improved performance in polymer:fullerene bulk-heterojunction solar cells. Results obtained from GiWAXS experiments show that the improved performance of the statistical copolymer may be attributed to the following structural characteristics: 1) Well, ordered stacked domains that promote backbone planarization and thus improve the ππ-overlap. 2) Partly face-on alignment of domains relative to the electrodes for an improved active layer electrode charge transfer. Branched side chains seem to promote face-on domain orientation. Most likely they can minimize their unfavorable contact with the interface by just bringing the CH3 groups of the branches into direct contact with the surface so that favorable phenylene-substrate interaction can promote face-on orientation. 3) A more isotropic domain orientation throughout the active layer to ensure that the backbone alignment direction has components perpendicular and parallel to the electrodes in order to compromise between light absorption and efficient intra-chain charge transport.

  20. Palaeomagnetic Constrains on the Timing and the Geographical Distribution of Tectonic Rotations in the Betic Chain, Southern Spain. A Review (United States)

    Osete, M. L.; Villalain, J. J.; Pavon-Carrasco, F. J.; Palencia, A.


    The Betic Cordillera is the northern branch of the Betic-Rifean orogen, the westernmost segment of the Mediterranean Alpine orogenic system. Several palaeomagnetic studies have enhanced the important role that block rotations about vertical axes have played in the tectonic evolution of the region. In this work we present a review of published palaeomagnetic data. According with the rotational deformation, the Betics are divided into the central-western area and the eastern Betics. A sequence of rotations for the two regions is also proposed. In central and western Subbetics almost constant clockwise rotations of about 60 are documented in Jurassic limestones. The existence of a pervasive remagnetization of Jurassic limestones, which was coeval with the folding of the studied units and dated as post-Palaeogene, constrains the timing of tectonic rotations in western Subbetics. New palaeomagnetic data from Neogene sedimentary sequences in central Betics indicate that palaeomagnetic clockwise rotations continued after late Miocene. A similar pattern of 40 CW rotations occurred after 20-17 Ma was obtained from the study of the Ronda-Malaga peridotites (western Internal Betics). In eastern Subbetics a more heterogeneous pattern, including very high CW rotations has been observed. But recent rotational deformation in the Internal part of eastern Betics is CCW and related to the left-lateral strike-slip fault systems. Proposed kinematics models for the Betics are discussed under the light of the present available palaeomagnetic information.

  1. Acidic-basic properties of three alanine-based peptides containing acidic and basic side chains: comparison between theory and experiment. (United States)

    Makowska, Joanna; Bagińska, Katarzyna; Liwo, Adam; Chmurzyński, Lech; Scheraga, Harold A


    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.

  2. On the complex•OH/•O--induced free radical chemistry of arylalkylamines with special emphasis on the contribution of the alkylamine side chain. (United States)

    Szabó, László; Mile, Viktória; Tóth, Tünde; Balogh, György T; Földes, Tamás; Takács, Erzsébet; Wojnárovits, László


    A full account of the • OH-induced free radical chemistry of an arylalkylamine is given taking all the possible reaction pathways quantitatively into consideration. Such knowledge is indispensable when the alkylamine side chain plays a crucial role in biological activity. The fundamental reactions are investigated on the model compound N-methyl-3-phenypropylamine (MPPA), and extended to its biologically active analog, to the antidepressant fluoxetine (FLX). Pulse radiolysis techniques were applied including redox titration and transient spectral analysis supplemented with DFT calculations. The contribution of the amine moiety to the free radical-induced oxidation mechanism appeared to be appreciable. • O - was used to observe hydrogen atom abstraction events at pH 14 giving rise to the strongly reducing α-aminoalkyl radicals (∼38% of the radical yield) and to benzyl (∼4%), β-aminoalkyl (∼24%), and aminyl radicals (∼31%) of MPPA. One-electron transfer was also observed yielding aminium radicals with low efficiency (∼3%). In the • OH-induced oxidation protonated α-aminoalkyl (∼49%), β-aminoalkyl (∼27%), benzyl radicals (∼4%), and aminium radicals (∼5%) are initially generated on the side chain of MPPA at pH 6, whereas hydroxycyclohexadienyl radicals (∼15%) were also produced. These initial events are followed by complex protonation-deprotonation reactions establishing acid-base equilibria; however, these processes are limited by the transient nature of the radicals and the kinetics of the ongoing reactions. The contribution of the radicals from the side chain alkylamine substituent of FLX totals up to ∼54% of the initially available oxidant yield.

  3. Virulence Role of the GlcNAc Side Chain of the Lancefield Cell Wall Carbohydrate Antigen in Non-M1-Serotype Group A Streptococcus

    Directory of Open Access Journals (Sweden)

    Anna Henningham


    Full Text Available Classification of streptococci is based upon expression of unique cell wall carbohydrate antigens. All serotypes of group A Streptococcus (GAS; Streptococcus pyogenes, a leading cause of infection-related mortality worldwide, express the group A carbohydrate (GAC. GAC, the classical Lancefield antigen, is comprised of a polyrhamnose backbone with N-acetylglucosamine (GlcNAc side chains. The immunodominant GlcNAc epitope of GAC is the basis of all rapid diagnostic testing for GAS infection. We previously identified the 12-gene GAC biosynthesis gene cluster and determined that the glycosyltransferase GacI was required for addition of the GlcNAc side chain to the polyrhamnose core. Loss of the GAC GlcNAc epitope in serotype M1 GAS resulted in attenuated virulence in two animal infection models and increased GAS sensitivity to killing by whole human blood, serum, neutrophils, and antimicrobial peptides. Here, we report that the GAC biosynthesis gene cluster is ubiquitous among 520 GAS isolates from global sources, representing 105 GAS emm serotypes. Isogenic ΔgacI mutants were constructed in M2, M3, M4, M28, and M89 backgrounds and displayed an array of phenotypes in susceptibility to killing by whole human blood, baby rabbit serum, human platelet releasate, human neutrophils, and antimicrobial peptide LL-37. The contribution of the GlcNAc side chain to GAS survival in vivo also varied by strain, demonstrating that it is not a prerequisite for virulence in the murine infection model. Thus, the relative contribution of GAC to virulence in non-M1 serotypes appears to depend on the quorum of other virulence factors that each strain possesses.

  4. Improving the performance of P3HT-fullerene solar cells with side-chain-functionalized poly(thiophene) additives: a new paradigm for polymer design. (United States)

    Lobez, Jose M; Andrew, Trisha L; Bulović, Vladimir; Swager, Timothy M


    The motivation of this study is to determine if small amounts of designer additives placed at the polymer-fullerene interface in bulk heterojunction (BHJ) solar cells can influence their performance. A series of AB-alternating side-chain-functionalized poly(thiophene) analogues, P1-6, are designed to selectively localize at the interface between regioregular poly(3-hexylthiophene) (rr-P3HT) and PC(n)BM (n = 61, 71). The side chains of every other repeat unit in P1-6 contain various terminal aromatic moieties. BHJ solar cells containing ternary mixtures of rr-P3HT, PC(n)BM, and varying weight ratios of additives P1-6 are fabricated and studied. At low loadings, the presence of P1-6 consistently increases the short circuit current and decreases the series resistance of the corresponding devices, leading to an increase in power conversion efficiency (PCE) compared to reference P3HT/PC(61)BM cells. Higher additive loadings (>5 wt %) lead to detrimental nanoscale phase separation within the active layer blend and produce solar cells with high series resistances and low overall PCEs. Small-perturbation transient open circuit voltage decay measurements reveal that, at 0.25 wt % incorporation, additives P1-6 increase charge carrier lifetimes in P3HT/PC(61)BM solar cells. Pentafluorophenoxy-containing polymer P6 is the most effective side-chain-functionalized additive and yields a 28% increase in PCE when incorporated into a 75 nm thick rr-P3HT/PC(61)BM BHJ at a 0.25 wt % loading. Moreover, devices with 220 nm thick BHJs containing 0.25 wt % P6 display PCE values of up to 5.3% (30% PCE increase over a control device lacking P6). We propose that additives P1-6 selectively localize at the interface between rr-P3HT and PC(n)BM phases and that aromatic moieties at side-chain termini introduce a dipole at the polymer-fullerene interface, which decreases the rate of bimolecular recombination and, therefore, improves charge collection across the active layer.

  5. Design, synthesis, in silico and in vitro antimicrobial screenings of novel 1,2,4-triazoles carrying 1,2,3-triazole scaffold with lipophilic side chain tether


    Aouad, Mohamed Reda; Mayaba, Mariem Mohammed; Naqvi, Arshi; Bardaweel, Sanaa K.; Al-blewi, Fawzia Faleh; Messali, Mouslim; Rezki, Nadjet


    Background 1,2,4-Triazoles and 1,2,3-triazoles have gained significant importance in medicinal chemistry. Results This study describes a green, efficient and quick solvent free click synthesis of new 1,2,3-triazole-4,5-diesters carrying a lipophilic side chain via 1,3-dipolar cycloaddition of diethylacetylene dicarboxylate with different surfactant azides. Further structural modifications of the resulting 1,2,3-triazole diesters to their corresponding 1,2,4-triazole-3-thiones via multi-step s...

  6. 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


    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.

  7. High-performance all-polymer solar cells via side-chain engineering of the polymer acceptor: the importance of the polymer packing structure and the nanoscale blend morphology. (United States)

    Lee, Changyeon; Kang, Hyunbum; Lee, Wonho; Kim, Taesu; Kim, Ki-Hyun; Woo, Han Young; Wang, Cheng; Kim, Bumjoon J


    The effectiveness of side-chain engineering is demonstrated to produce highly efficient all-polymer solar cells (efficiency of 5.96%) using a series of naphthalene diimide-based polymer acceptors with controlled side chains. The dramatic changes in the polymer packing, blend morphology, and electron mobility of all-polymer solar cells elucidate clear trends in the photovoltaic performances. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Modeling the effects of structure and dynamics of the nitroxide side chain on the ESR spectra of spin-labeled proteins. (United States)

    Tombolato, Fabio; Ferrarini, Alberta; Freed, Jack H


    In the companion paper (J. Phys. Chem. B 2006, 110, jp0629487), a study of the conformational dynamics of methanethiosulfonate spin probes linked at a surface-exposed alpha-helix has been presented. Here, on the basis of this analysis, X-band ESR spectra of these spin labels are simulated within the framework of the Stochastic Liouville equation (SLE) methodology. Slow reorientations of the whole protein are superimposed on fast chain motions, which have been identified with conformational jumps and fluctuations in the minima of the chain torsional potential. Fast chain motions are introduced in the SLE for the protein reorientations through partially averaged magnetic tensors and relaxation times calculated according to the motional narrowing theory. The 72R1 and 72R2 mutants of T4 lysozyme, which bear the spin label at a solvent-exposed helix site, have been taken as test systems. For the side chain of the R2 spin label, only a few noninterconverting conformers are possible, whose mobility is limited to torsional fluctuations, yielding almost identical spectra, typical of slightly mobile nitroxides. In the case of R1, more complex spectra result from the simultaneous presence of constrained and mobile chain conformers, with relative weights that can depend on the local environment. The model provides an explanation for the experimentally observed dependence of the spectral line shapes on temperature, solvent, and pattern of substituents in the pyrroline ring. The relatively simple methodology presented here allows the introduction of realistic features of the spin probe dynamics into the simulation of ESR spectra of spin-labeled proteins; moreover, it provides suggestions for a proper account of such dynamics in more sophisticated approaches.

  9. Internal- and External-Rotation Peak Toque in Little League Baseball Players With Subacromial Impingement Syndrome: Improved by Closed Kinetic Chain Shoulder Training. (United States)

    Lee, Dong-Rour; Kim, Laurentius Jongsoon


    Many studies have explored closed kinetic chain (CKC) shoulder exercises (SEs) with a sling because they are safer and more effective than open-chain exercises, especially in early stages of treatment. However, the application of CKC SE in youth baseball players has rarely been attempted, although teenage baseball players also experience shoulder pain. To investigate the effects of CKC SE on the peak torque of shoulder internal rotation (IR) and external rotation (ER) in youth baseball players. Single-group pretest, posttest. Biomechanics laboratory. 23 Little League Baseball players with subacromial impingement syndrome. The CKC SE with a sling was CKC shoulder-flexion exercise, extension exercise, IR exercise, and ER exercise. This exercise regimen was conducted 2 or 3 times/wk for 8 wk. The peak torque of shoulder IR and ER was measured using an isokinetic dynamometer. Concentric shoulder rotation was performed, with 5 repetitions at an angular velocity of 60°/s and 15 at 180°/s. The IR and ER peak torque significantly increased at each angular velocity after the exercise program. In particular, the increase in IR and ER peak torque values was statistically significant at an angular velocity of 180°/s. CKC SE was effective in increasing shoulder IR and ER strength, demonstrating its potential benefits in the prevention and treatment of shoulder injury. In addition, increased IR peak torque appears to improve throwing velocity in baseball players.

  10. Symmetry Breaking in Side Chains Leading to Mixed Orientations and Improved Charge Transport in Isoindigo- alt -Bithiophene Based Polymer Thin Films

    Energy Technology Data Exchange (ETDEWEB)

    Xue, Guobiao [Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States; MOE Key; Zhao, Xikang [Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States; Qu, Ge [Department of Chemical & amp, Biomolecular; Xu, Tianbai [Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States; College; amp, Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China; Gumyusenge, Aristide [Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States; Zhang, Zhuorui [Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States; Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China; Zhao, Yan [Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States; Diao, Ying [Department of Chemical & amp, Biomolecular; Li, Hanying [MOE Key; Mei, Jianguo [Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States; Birck Nanotechnology Center, Purdue University, 1205 West State Street, West Lafayette, Indiana 47906, United States


    The selection of side chains is important in design of conjugated polymers. It not only affects their intrinsic physical properties, but also has an impact on thin film morphologies. Recent reports suggested that a face-on/edge-on bimodal orientation observed in polymer thin films may be responsible for a three-dimensional (3D) charge transport and leads to dramatically improved mobility in donor–acceptor based conjugated polymers. To achieve a bimodal orientation in thin films has been seldom explored from the aspect of molecular design. Here, we demonstrate a design strategy involving the use of asymmetric side chains that enables an isoindigo-based polymer to adopt a distinct bimodal orientation, confirmed by the grazing incidence X-ray diffraction. As a result, the polymer presents an average high mobility of 3.8 ± 0.7 cm2 V–1 s–1 with a maximum value of 5.1 cm2 V–1 s–1, in comparison with 0.47 and 0.51 cm2 V–1 s–1 obtained from the two reference polymers. This study exemplifies a new strategy to develop the next generation polymers through understanding the property-structure relationship.

  11. 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


    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.

  12. 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


    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

  13. 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


    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...

  14. 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


    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

  15. 15N-edited Three-Dimensional NOESY-HMQC with Water Flipback: Enhancement of Weak Labile 1H Resonances of Protein Side Chains Contacting DNA (United States)

    Gruschus, James M.; Ferretti, James A.


    Two pulse sequences are described that employ a modified water flipback technique to enhance the signal intensity of weak side chain resonances at the protein-DNA interface of the vnd/NK-2 homeodomain/DNA complex in an15N-edited three-dimensional NOESY-HMQC spectrum. The pulse sequences presented employ water flipback pulses at the beginning of the NOESY mixing time, optimizing the direct NOE transfer of magnetization from the water to the protein by maximizing thez-component of the water magnetization. In one of the pulse sequences, radiation damping during the the indirect1H and15N evolution times is suppressed. A modified version of the WATERGATE water suppression technique is employed during the HMQC portion of the experiment. The signal enhancement is demonstrated for the resonances of the side chain amide of Asn51, an invariant homeodomain residue whose contact with the DNA is critical for binding. An ancillary advantage of the experiment is the ability to observe NOE transfer of magnetization from water. The information present in the water resonance plane of the three-dimensional spectrum is illustrated in a comparison with the corresponding HMQC spectrum of the protein/DNA complex.

  16. In vivo cough suppressive activity of pectic polysaccharide with arabinogalactan type II side chains of Piper nigrum fruits and its synergistic effect with piperine. (United States)

    Khawas, Sadhana; Nosáľová, Gabriela; Majee, Sujay Kumar; Ghosh, Kanika; Raja, Washim; Sivová, Veronika; Ray, Bimalendu


    Piper nigrum L. fruits are not only a prized spice, but also highly valued therapeutic agent that heals many ailments including asthma, cold and respiratory problems. Herein, we have investigated structural features and in vivo antitussive activity of three fractions isolated from Piper nigrum fruits. The water extract (PN-WE) upon fractionation with EtOH yielded two fractions: a soluble fraction (PN-eSf) and a precipitated (PN-ePf) one. The existence of a pectic polysaccharide with arabinogalactan type II side chains (147kDa) in PN-ePf and piperine in PN-eSf were revealed. Moreover, oligosaccharides providing fine structural details of side chains were generated from PN-ePf and then characterized. The parental water extract (PN-WE) that contained both pectic polysaccharide and piperine, after oral administration (50mgkg -1 body weight) to guinea pigs, showed antitussive activity comparable to codeine phosphate (10mgkg -1 body weight). The EtOH precipitated fraction (PN-ePf) containing pectic polysaccharide showed comparatively higher antitussive activity than EtOH soluble fraction (PN-eSf) that contained piperine, but their potencies are lower than the parental water extract. Significantly, the specific airway smooth muscle reactivity of all three fractions remained unchanged. Finally, pectic polysaccharide-piperine combination in parental extract synergistically enhances antitussive effect in guinea pigs. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Pretilt angle control of liquid crystal molecules by photoaligned films of azobenzene-containing polyimide with a different content of side-chain (United States)

    Usami, Kiyoaki; Sakamoto, Kenji; Yokota, Junichiro; Uehara, Yoichi; Ushioda, Sukekatsu


    We have investigated the pretilt angle of liquid crystal (LC) molecules induced by photoaligned films of a series of polyimides. The polyimides were random copolymers synthesized from pyromellitic dianhydride and a mixture of 4,4'-diaminoazobenzene and 4-[4'-propylbi(cyclohexan)-4-yl]phenyl 3,5-diaminobenzoate (PBCP-DABA). PBCP-DABA is a diamine to introduce a side-chain structure into polyimide. We found that the pretilt angle of LC molecules can be controlled from 0° to 90° by varying the molar fraction (x) of PBCP-DABA from 0 to 0.5. Defect-free uniform LC alignment was observed for x ≤0.125 and x ≥0.3, but threadlike textures appeared for 0.15≤x≤0.25. Since the interaction between the polyimide backbone structure and the LC molecule may be blocked by relatively dense side-chains, the appearance of threadlike texture is tentatively attributed to weak azimuthal anchoring strength of the photoaligned polyimide films with x ≥0.15.

  18. Context-dependent effects on the hydrophilicity/hydrophobicity of side-chains during reversed-phase high-performance liquid chromatography: Implications for prediction of peptide retention behaviour. (United States)

    Mant, C T; Hodges, R S


    The present study set out to investigate whether observed relative hydrophilicity/hydrophobicity values of positively charged side-chains (with Lys and Arg as representative side-chains) or hydrophobic side-chains (with Ile as the representative side-chain) were context-dependent, i.e., did such measured values vary depending on characteristics of the peptides within which such side-chains are substituted (overall peptide hydrophobicity, number of positive charges) and/or properties of the mobile phase (anionic counterions of varying hydrophobicity and concentration)? Reversed-phase high-performance liquid chromatography (RP-HPLC) was applied to two series of four synthetic peptide analogues (+1, +2, +3 and +4 net charge), the only difference between the two peptide series being the substitution of one hydrophobic Ile residue for a Gly residue, in the presence of anionic ion-pairing reagents of varying hydrophobicity (HCOOH approximately H3PO4 < TFA < PFPA < HFBA) and concentration (2-50 mM). RP-HPLC of these peptide series revealed that the relative hydrophilicity of Lys and Arg side-chains in the peptides increased with peptide hydrophobicity. In addition the relative hydrophobicity of Ile decreased dramatically with an increase in the number of positive charges in the peptide, this hydrophobicity decrease being of greater magnitude as the hydrophobicity of the anionic ion-pairing reagent increased. These results have significant implications in the prediction of peptide retention times for proteomic applications.

  19. Richness of Side-Chain Liquid-Crystal Polymers: From Isotropic Phase towards the Identification of Neglected Solid-Like Properties in Liquids

    Directory of Open Access Journals (Sweden)

    Joachim H. Wendorff


    Full Text Available Very few studies concern the isotropic phase of Side-Chain Liquid-Crystalline Polymers (SCLCPs. However, the interest for the isotropic phase appears particularly obvious in flow experiments. Unforeseen shear-induced nematic phases are revealed away from the N-I transition temperature. The non-equilibrium nematic phase in the isotropic phase of SCLCP melts challenges the conventional timescales described in theoretical approaches and reveal very long timescales, neglected until now. This spectacular behavior is the starter of the present survey that reveals long range solid-like interactions up to the sub-millimetre scale. We address the question of the origin of this solid-like property by probing more particularly the non-equilibrium behavior of a polyacrylate substituted by a nitrobiphenyl group (PANO2. The comparison with a polybutylacrylate chain of the same degree of polymerization evidences that the solid-like response is exacerbated in SCLCPs. We conclude that the liquid crystal moieties interplay as efficient elastic connectors. Finally, we show that the “solid” character can be evidenced away from the glass transition temperature in glass formers and for the first time, in purely alkane chains above their crystallization temperature. We thus have probed collective elastic effects contained not only in the isotropic phase of SCLCPs, but also more generically in the liquid state of ordinary melts and of ordinary liquids.

  20. Optimal design of ethanol supply chains considering carbon trading effects and multiple technologies for side-product exploitation. (United States)

    Ortiz-Gutiérrez, R A; Giarola, S; Bezzo, F


    This work proposes a spatially explicit mixed integer linear programming modelling framework representing the dynamic evolution of a bioethanol supply chain (SC) under increasing biofuel demand and greenhouse gas (GHG) emission savings over time. Key features of the proposed framework comprise: (i) the incorporation of available set-aside rural surfaces for energy crop cultivation; (ii) the acknowledgement ofan economic value to the overall GHG emissions through the introduction of an Emission Trading System. Multiple technological options are assessed to exploit the co-product Distiller's Dried Grains with Solubles either as animal fodder (standard usage) or as fuel for heat and power generation or as raw material for biogas production (and hence heat and power). Bioethanol production in Northern Italy is chosen as a demonstrative case study.

  1. Effects of Odd–Even Side Chain Length of Alkyl-Substituted Diphenylbithiophenes on First Monolayer Thin Film Packing Structure

    KAUST Repository

    Akkerman, Hylke B.


    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.

  2. A Hamiltonian Replica Exchange Approach and Its Application to the Study of Side-Chain Type and Neighbor Effects on Peptide Backbone Conformations. (United States)

    Xu, Chao; Wang, Jun; Liu, Haiyan


    We presented a Hamiltonian replica exchange approach and applied it to investigate the effects of various factors on the conformational equilibrium of peptide backbone. In different replicas, biasing potentials of varying strengths are applied to all backbone (φ,ψ) torsional angle pairs to overcome sampling barriers. A general form of constructing biasing potentials based on a reference free energy surface is employed to minimize sampling in physically irrelevant parts of the conformational space. An extension of the weighted histogram analysis formulation allows for conformational free energy surfaces to be computed using all replicas, including those with biased Hamiltonians. This approach can significantly reduce the statistical uncertainties in computed free energies. For the peptide systems considered, it allows for effects of the order of 0.5-1 kJ/mol to be quantified using explicit solvent simulations. We applied this approach to capped peptides of 2-5 peptide units containing Ala, Phe, or Val in explicit water solvent and focused on how the conformational equilibrium of a single pair of backbone angles are influenced by changing the residue types of the same and neighboring residues as well as conformations of neighboring residues. For the effects of changing side-chain types of the same residue, our results consistently showed increased preference of β for Phe and Val relative to Ala. As for neighbor effects, our results not only indicated that they can be as large as the effects of changing the side-chain type of the same residue but also led to several new insights. We found that for the N-terminal neighbors, their conformations seem to have large effects. Relative to the β conformer of an N-terminal neighbor, its α conformer stabilizes the β conformer of its next Ala disregarding the residue type of the neighbor. For C-terminal neighbors, their chemical identities seem to play more important roles. Val as the C-terminal neighbor significantly

  3. The role of water and K + ion in the charge transfer between PO4- groups of DNA and the lysine + and arginine + side chains of histone proteins (United States)

    Bende, A.; Bogár, F.; Ladik, J.


    We have calculated the charge transfer (CT) between the PO4- group of DNA and the lysine (Lys) and arginine (Arg) positive side chains of histones in presence of water and K + ions. The calculations were performed at the HF + MP2 level, using the TZVP basis set. The calculations were corrected for basis set superposition error and besides Mulliken's population analysis we have introduced the - for charged systems more reliable - natural population analysis. The results show that the bare PO4--Lys and the PO4--Arg interactions become weaker, mainly, due to the presence of the K + ion. We have found 0.067 e CT for Lys and 0.050 e for Arg.

  4. Circulating N-Linked Glycoprotein Side-Chain Biomarker, Rosuvastatin Therapy, and Incident Cardiovascular Disease: An Analysis From the JUPITER Trial. (United States)

    Akinkuolie, Akintunde O; Glynn, Robert J; Padmanabhan, Latha; Ridker, Paul M; Mora, Samia


    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: Unique identifier: NCT00239681. © 2016 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

  5. New potent antibacterials against Gram-positive multiresistant pathogens: effects of side chain modification and chirality in linezolid-like 1,2,4-oxadiazoles. (United States)

    Fortuna, Cosimo G; Berardozzi, Roberto; Bonaccorso, Carmela; Caltabiano, Gianluigi; Di Bari, Lorenzo; Goracci, Laura; Guarcello, Annalisa; Pace, Andrea; Palumbo Piccionello, Antonio; Pescitelli, Gennaro; Pierro, Paola; Lonati, Elena; Bulbarelli, Alessandra; Cocuzza, Clementina E A; Musumarra, Giuseppe; Musumeci, Rosario


    The effects of side chain modification and chirality in linezolid-like 1,2,4-oxadiazoles have been studied to design new potent antibacterials against Gram-positive multidrug-resistant pathogens. The adopted strategy involved a molecular modelling approach, the synthesis and biological evaluation of new designed compounds, enantiomers separation and absolute configuration assignment. Experimental determination of the antibacterial activity of the designed (S)-1-((3-(4-(3-methyl-1,2,4-oxadiazol-5-yl)phenyl)-oxazolidin-2-one-5-yl)methyl)-3-methylthiourea and (S)-1-((3-(3-fluoro-4-(3-methyl-1,2,4-oxadiazol-5-yl)phenyl)-oxazolidin-2-one-5-yl)methyl)-3-methylthiourea against multidrug resistant linezolid bacterial strains was higher than that of linezolid. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. 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


    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

  7. Functionalized PHB granules provide the basis for the efficient side-chain cleavage of cholesterol and analogs in recombinant Bacillus megaterium. (United States)

    Gerber, Adrian; Kleser, Michael; Biedendieck, Rebekka; Bernhardt, Rita; Hannemann, Frank


    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

  8. A novel branched side-chain-type sulfonated polyimide membrane with flexible sulfoalkyl pendants and trifluoromethyl groups for vanadium redox flow batteries (United States)

    Li, Jinchao; Liu, Suqin; He, Zhen; Zhou, Zhi


    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.

  9. Characterizing hydrophobicity of amino acid side chains in a protein environment via measuring contact angle of a water nanodroplet on planar peptide network. (United States)

    Zhu, Chongqin; Gao, Yurui; Li, Hui; Meng, Sheng; Li, Lei; Francisco, Joseph S; Zeng, Xiao Cheng


    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.

  10. 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


    . V genes from the Jkappa-proximal duplication unit of the kappa locus were almost exclusively used. A total of 65% of the sequences could be assigned to four or five genes: A27 (humkv325), L6 (Vg), L2 (humkv328), and A3 and/or A19. N additions and P nucleotides were quite common and found in 32......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...... agreement with those of previous repertoire studies using potentially V-gene-biased techniques. Thus, it is clear that restricted V-gene usage, common N and P additions, and extended CDR3 regions are normal features and not, as has been claimed, characteristics of pathological autoantibodies....

  11. 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. (United States)

    Anderson, Kurtis M; Nguyen, Dan; Esadze, Alexandre; Zandrashvili, Levani; Gorenstein, David G; Iwahara, Junji


    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 NH3 (+) 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.

  12. 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


    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

  13. 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:, E-mail: [University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (United States)


    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.

  14. Side chain modified 5-deazafolate and 5-deazatetrahydrofolate analogues as mammalian folylpolyglutamate synthetase and glycinamide ribonucleotide formyltransferase inhibitors: synthesis and in vitro biological evaluation. (United States)

    Rosowsky, A; Forsch, R A; Reich, V E; Freisheim, J H; Moran, R G


    5-Deazafolate and 5-deazatetrahydrofolate (DATHF) analogues with the glutamic acid side chain replaced by homocysteic acid (HCysA), 2-amino-4-phosphonobutanoic acid (APBA), and ornithine (Orn) were synthesized as part of a larger program directed toward inhibitors of folylpolyglutamate synthetase (FPGS) as probes of the FPGS active site and as potential therapeutic agents. The tetrahydro compounds were also of interest as non-polyglutamatable inhibitors of the purine biosynthetic enzyme glycinamide ribonucleotide formyltransferase (GARFT). Reductive coupling of N2-acetamido-6-formylpyrido[2,3-d]pyrimidin-4(3H)-one with 4-aminobenzoic acid, followed by N10-formylation, mixed anhydride condensation of the resultant N2-acetyl-N10-formyl-5- deazapteroic acid with L-homocysteic acid, and removal of the N2-acetyl and N10-formyl groups with NaOH, afforded N-(5-deazapteroyl)-L-homocysteic acid (5-dPteHCysA). Mixed anhydride condensation of N2-acetyl-N10-formyl- 5-deazapteroic acid with methyl D,L-2-amino-4-(diethoxyphosphinyl)butanoic acid, followed by consecutive treatment with Me3SiBr and NaOH, yielded D,L-2-[(5-deazapteroyl)amino]-4-phosphonobutanoic acid (5-dPteAPBA). Treatment with NaOH alone led to retention of one ethyl ester group on the phosphonate moiety. Catalytic hydrogenation of N2-acetyl-N10-formyl-5-deazapteroic acid followed by mixed anhydride condensation with methyl L-homocysteate and deprotection with NaOH afforded N-(5,6,7,8-tetrahydro-5-deazapteroyl)-L-homocysteic acid (5-dH4PteHCysA). Similar chemistry starting from methyl D,L-2-amino-4-(diethoxyphosphinyl)butanoic acid and methyl N delta-(benzyloxycarbonyl)-L-ornithinate yielded D,L-2-[(5-deaza-5,6,7,8-tetrahydropteroyl)amino]-4-phosphonobut ano ic acid (5-dH4Pte-APBA) and N alpha-(5-deaza-5,6,7,8-tetrahydropteroyl)-L-ornithine (5-dH4PteOrn), respectively. The 5-deazafolate analogues were inhibitors of mouse liver FPGS, and the DATHF analogues inhibited both mouse FPGS and mouse leukemic cell GARFT

  15. Amino Acid Functionalization of Doped Single-Walled Carbon Nanotubes: Effects of Dopants and Side Chains as Well as Zwitterionic Stabilizations. (United States)

    Jiang, Lisha; Zhu, Chang; Fu, Yujie; Yang, Gang


    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.

  16. Backbone and side-chain 1H, 15N, and 13C resonance assignments of a novel Staphylococcal inhibitor of myeloperoxidase. (United States)

    Ploscariu, Nicoleta T; Herrera, Alvaro I; Jayanthi, Srinivas; Suresh Kumar, Thallapuranam K; Geisbrecht, Brian V; Prakash, Om


    The bacterium Staphylococcus aureus produces an array of anti-inflammatory molecules that prevent the innate immune system from recognizing it as a pathogen and clearing it from the host. In the acute phase of inflammation, our immune system relies on neutrophils to clear invading bacteria. Recently, novel classes of secreted proteins from S. aureus, including the Extracellular Adherence Protein (EAP) family (Stapels et al., Proc Natl Acad Sci USA 111:13187-13192, 2014) and the Staphylococcal Peroxidase Inhibitor (SPIN), (unpublished work) have been identified as highly selective inhibitors acting on Neutrophil Serine Proteases (NSPs) and myeloperoxidase (MPO) respectively. SPIN is a protein found only in Staphylococci, with no sequence homology to any known proteins. Solution NMR structural studies of SPIN are therefore expected to provide a deeper understanding of its interaction with MPO. In this study, we report the backbone and side-chain 1 H, 15 N, and 13 C resonance assignments of SPIN. Furthermore, using the chemical shifts of these resonances, we predicted the secondary structure of SPIN in solution via the TALOS-N server. The assignment data has been deposited in the BMRB data bank under Accession No. 27069.

  17. Effect of semiconductor polymer backbone structures and side-chain parameters on the facile separation of semiconducting single-walled carbon nanotubes from as-synthesized mixtures (United States)

    Lee, Dennis T.; Chung, Jong Won; Park, Geonhee; Kim, Yun-Tae; Lee, Chang Young; Cho, Yeonchoo; Yoo, Pil J.; Han, Jae-Hee; Shin, Hyeon-Jin; Kim, Woo-Jae


    Semiconducting single-walled carbon nanotubes (SWNTs) show promise as core materials for next-generation solar cells and nanoelectronic devices. However, most commercial SWNT production methods generate mixtures of metallic SWNTs (m-SWNTs) and semiconducting SWNT (sc-SWNTs). Therefore, sc-SWNTs must be separated from their original mixtures before use. In this study, we investigated a polymer-based, noncovalent sc-SWNT separation approach, which is simple to perform and does not disrupt the electrical properties of the SWNTs, thus improving the performance of the corresponding sc-SWNT-based applications. By systematically investigating the effect that different structural features of the semiconductor polymer have on the separation of sc-SWNTs, we discovered that the length and configuration of the alkyl side chains and the rigidity of the backbone structure exert significant effects on the efficiency of sc-SWNT separation. We also found that electron transfer between the semiconductor polymers and sc-SWNTs is strongly affected by their energy-level alignment, which can be tailored by controlling the donor-acceptor configuration in the polymer backbone structures. Among the polymers investigated, the highly planar P8T2Z-C12 semiconductor polymer showed the best sc-SWNT separation efficiency and unprecedentedly strong electronic interaction with the sc-SWNTs, which is important for improving their performance in applications.

  18. An Investigation of Atomic Structures Derived from X-ray Crystallography and Cryo-Electron Microscopy Using Distal Blocks of Side-Chains. (United States)

    Chen, Lin; He, Jing; Sazzed, Salim; Walker, Rayshawn


    Cryo-electron microscopy (cryo-EM) is a structure determination method for large molecular complexes. As more and more atomic structures are determined using this technique, it is becoming possible to perform statistical characterization of side-chain conformations. Two data sets were involved to characterize block lengths for each of the 18 types of amino acids. One set contains 9131 structures resolved using X-ray crystallography from density maps with better than or equal to 1.5 Å resolutions, and the other contains 237 protein structures derived from cryo-EM density maps with 2-4 Å resolutions. The results show that the normalized probability density function of block lengths is similar between the X-ray data set and the cryo-EM data set for most of the residue types, but differences were observed for ARG, GLU, ILE, LYS, PHE, TRP, and TYR for which conformations with certain shorter block lengths are more likely to be observed in the cryo-EM set with 2-4 Å resolutions.

  19. Supramolecular Phase-Selective Gelation by Peptides Bearing Side-Chain Azobenzenes: Effect of Ultrasound and Potential for Dye Removal and Oil Spill Remediation (United States)

    Bachl, Jürgen; Oehm, Stefan; Mayr, Judith; Cativiela, Carlos; Marrero-Tellado, José Juan; Díaz Díaz, David


    Phase selective gelation (PSG) of organic phases from their non-miscible mixtures with water was achieved using tetrapeptides bearing a side-chain azobenzene moiety. The presence of the chromophore allowed PSG at the same concentration as the minimum gelation concentration (MGC) necessary to obtain the gels in pure organic phases. Remarkably, the presence of the water phase during PSG did not impact the thermal, mechanical, and morphological properties of the corresponding organogels. In the case of miscible oil/water mixtures, the entire mixture was gelled, resulting in the formation of quasi-hydrogels. Importantly, PSG could be triggered at room temperature by ultrasound treatment of the mixture or by adding ultrasound-aided concentrated solution of the peptide in an oil-phase to a mixture of the same oil and water. Moreover, the PSG was not affected by the presence of salts or impurities existing in water from natural sources. The process could be scaled-up, and the oil phases (e.g., aromatic solvents, gasoline, diesel fuel) recovered almost quantitatively after a simple distillation process, which also allowed the recovery and reuse of the gelator. Finally, these peptidic gelators could be used to quantitatively remove toxic dyes from aqueous solutions. PMID:26006247

  20. 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.

  1. The Penicillium chrysogenum aclA gene encodes a broad-substrate-specificity acyl-coenzyme A ligase involved in activation of adipic acid, a side-chain precursor for cephem antibiotics

    NARCIS (Netherlands)

    Koetsier, Martijn J.; Gombert, Andreas K.; Fekken, Susan; Bovenberg, Roel A. L.; Van den Berg, Marco A.; Kiel, Jan A. K. W.; Jekel, Peter A.; Janssen, Dick B.; Pronk, Jack T.; Van der Klei, Ida J.; Daran, Jean-Marc

    Activation of the cephalosporin side-chain precursor to the corresponding CoA-thioester is an essential step for its incorporation into the P-lactam backbone. To identify an acyl-CoA ligase involved in activation of adipate, we searched in the genome database of Penicillium chrysogenum for putative

  2. Molecular cloning of cytochrome P450 side-chain cleavage and changes in its mRNA expression during gonadal development of brown hagfish, Paramyxine atami. (United States)

    Nishiyama, Maki; Uchida, Katsuhisa; Abe, Nozomi; Nozaki, Masumi


    Since hagfishes are considered the most primitive vertebrate known, extant or extinct, studies on their reproduction are indispensable for understanding phylogenetic aspects of vertebrate reproduction. However, little information is available on the endocrine regulation of the gonadal function in the hagfish. Based on EST analysis of the testis of the brown hagfish (Paramyxine atami), P450 side chain cleavage (CYP11A), which is the first and essential enzyme for steroidogenesis in jawed vertebrates, was cloned. The deduced amino acid sequence of hagfish CYP11A shows high identity to other animal forms especially in two functional domains, adrenodoxin binding domain and heme-binding domain. In the phylogenetic analysis, hagfish CYP11A forms a clade with the vertebrate CYP11A. Following the real-time PCR analysis, CYP11A mRNA expression levels were clearly correlated to the developmental stages of gonads in both sexes of the brown hagfish. By in situ hybridization, CYP11A mRNA signals were found in the theca cells of the ovarian follicles and Leydig cells and the tubule-boundary cells of the testis. These molecular and histological evidences are suggesting that CYP11A plays functional roles as a steroidogenic enzyme in gonadal development. Moreover, native GTH purified from hagfish pituitary stimulated the transcriptional levels of CYP11A in the organ-cultured testis in vitro, clearly suggesting that the steroidogenic activity of the hagfish is under the control of the pituitary GTH. It is suggested that vertebrates, during their early evolution, have established the pituitary-gonadal reproductive system. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Autoantibodies against Cytochrome P450 Side-Chain Cleavage Enzyme in Dogs (Canis lupus familiaris) Affected with Hypoadrenocorticism (Addison’s Disease) (United States)

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


    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. PMID:26618927

  4. Localization and functional activity of cytochrome P450 side chain cleavage enzyme (CYP11A1) in the adult rat kidney. (United States)

    Pagotto, Melina A; Roldán, María L; Pagotto, Romina M; Lugano, María C; Pisani, Gerardo B; Rogic, Gastón; Molinas, Sara M; Trumper, Laura; Pignataro, Omar P; Monasterolo, Liliana Alicia


    Cumulative evidence demonstrated effective downstream metabolism of pregnenolone in renal tissue. The aim of this study was to evaluate the expression and functional activity of cytochrome P450 side chain cleavage enzyme (CYP11A1), which converts cholesterol into pregnenolone, in adult rat kidney. Immunohistochemical labeling for CYP11A1 was observed in renal cortex and medulla, on structures identified as distal convoluted tubule and thick ascending limb of Henle's loop, respectively. Immunoblotting analysis corroborated the renal expression of the protein in inner mitochondrial membrane fractions. The incubation of isolated mitochondria with the membrane-permeant cholesterol analogue 22R-hydroxycholesterol resulted in efficient formation of pregnenolone, the immediate precursor for the synthesis of all the steroid hormones. The low progesterone production rate observed in these experiments suggested a poor activity of 3β-hydroxysteroid dehydrogenase enzyme in renal mitochondria. The steroidogenic acute regulatory protein (StAR), involved in the mitochondrial import of cholesterol, was detected in renal tissue at both mRNA and protein level. Immunostaining for StAR showed similar distribution to that observed for CYP11A1. The expression of StAR and CYP11A1 was found to be higher in medulla than in cortex. This enhanced expression of steroidogenesis-related proteins correlated with a greater pregnenolone synthesis rate and higher steroid hormones tissular content measured in medulla. In conclusion, we have established the expression and localization of StAR and CYP11A1 protein, the ability of synthesizing pregnenolone and a region-specific content of sex hormones in the adult rat kidney. These data clearly show that the kidney is a steroid hormones synthesizing organ. It is proposed that the existence in the kidney of complete steroidogenic machinery would respond to a physiological significance. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  5. The Integrated Adjustment of Chlorine Substitution and Two-Dimensional Side Chain of Low Band Gap Polymers in Organic Solar Cells.

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Zhen; Chen, Hui; Wang, Huan; Mo, Daize; Liu, Longzhu; Chao, Pengjie; Zhu, Yulin; Liu, Chuanjun; Chen, Wei; He, Feng


    A series of conjugated T2 polymers (PBBF1-T2 and PBBCl1-T2), and T3 polymers (PBBF1-T3, PBBCl1-T3 and PBBCl2-T3) were synthesized using chlorinated/fluorinated benzothiadiazole (BT) and the twodimensional benzo[1,2-b:4,5-b’]dithiophene (BDT) units as the building blocks. When compared to the fluorinated polymer, the performance of the polymer photovoltaic devices showed that these chlorinated polymers gave extended optical absorption spectrum, and lower highest occupied molecular orbital (HOMO) energy levels. The introduction of chlorine atoms increases the twist angle between the polymer backbones, and led to a lower HOMO energy level and resulted in the increase of open circuit voltage (Voc) up to 0.84 V in PBBCl2-T3 based devices with a two chlorine substitution. However, the device based on PBBCl1-T3 with only one chlorine atom exhibited the best power conversion efficiency (PCE) which was as high as 6.87% with a Voc of 0.73 V, and this was about 10% higher than that of its fluorinated analogs. This result indicated that the introduction of chlorine atoms into polymers is not only a simple route to synthesize a large amount of material and which avoids the tedious synthesis steps in widely used fluorinated polymers, but it is also a feasible and effective strategy to fine tune the energy level of polymer solar cell with optimized PCE. Furthermore, it is worth noting that the introduction of longer π-conjugation side chains could minimize the influence of chlorine substitution by reducing the twist angle between the polymer backbones, which would reduce the gap of Voc between the chlorinated polymers and their fluorinated analogs.

  6. Very high-density lipoprotein and vitellin as carriers of novel biliverdins IXα with a farnesyl side-chain presumably derived from heme A in Spodoptera littoralis. (United States)

    Kayser, Hartmut; Nimtz, Manfred; Ringler, Philippe; Müller, Shirley A


    Bilins in complex with specific proteins play key roles in many forms of life. Biliproteins have also been isolated from insects; however, structural details are rare and possible functions largely unknown. Recently, we identified a high-molecular weight biliprotein from a moth, Cerura vinula, as an arylphorin-type hexameric storage protein linked to a novel farnesyl biliverdin IXα; its unusual structure suggests formation by cleavage of mitochondrial heme A. In the present study of another moth, Spodoptera littoralis, we isolated two different biliproteins. These proteins were identified as a very high-density lipoprotein (VHDL) and as vitellin, respectively, by mass spectrometric sequencing. Both proteins are associated with three different farnesyl biliverdins IXα: the one bilin isolated from C. vinula and two new structurally closely related bilins, supposed to be intermediates of heme A degradation. The different bilin composition of the two biliproteins suggests that the presumed oxidations at the farnesyl side-chain take place mainly during egg development. The egg bilins are supposedly transferred from hemolymph VHDL to vitellin in the female. Both biliproteins show strong induced circular dichroism activity compatible with a predominance of the M-conformation of the bilins. This conformation is opposite to that of the arylphorin-type biliprotein from C. vinula. Electron microscopy of the VHDL-type biliprotein from S. littoralis provided a preliminary view of its structure as a homodimer and confirmed the biochemically determined molecular mass of ∼350 kDa. Further, images of S. littoralis hexamerins revealed a 2 × 3 construction identical to that known from the hexamerin from C. vinula. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Observation of the side chain O-methylation of glutamic acid or aspartic acid containing model peptides by electrospray ionization-mass spectrometry. (United States)

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


    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.

  8. Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid-protein interactions, side chain transfer free energies and model proteins

    International Nuclear Information System (INIS)

    Tieleman, D Peter; MacCallum, Justin L; Ash, Walter L; Kandt, Christian; Xu Zhitao; Monticelli, Luca


    We have reparameterized the dihedral parameters in a commonly used united-atom lipid force field so that they can be used with the all-atom OPLS force field for proteins implemented in the molecular dynamics simulation software GROMACS. Simulations with this new combination give stable trajectories and sensible behaviour of both lipids and protein. We have calculated the free energy of transfer of amino acid side chains between water and 'lipid-cyclohexane', made of lipid force field methylene groups, as a hydrophobic mimic of the membrane interior, for both the OPLS-AA and a modified OPLS-AA force field which gives better hydration free energies under simulation conditions close to those preferred for the lipid force field. The average error is 4.3 kJ mol -1 for water-'lipid-cyclohexane' compared to 3.2 kJ mol -1 for OPLS-AA cyclohexane and 2.4 kJ mol -1 for the modified OPLS-AA water-'lipid-cyclohexane'. We have also investigated the effect of different methods to combine parameters between the united-atom lipid force field and the united-atom protein force field ffgmx. In a widely used combination, the strength of interactions between hydrocarbon lipid tails and proteins is significantly overestimated, causing a decrease in the area per lipid and an increase in lipid ordering. Using straight combination rules improves the results. Combined, we suggest that using OPLS-AA together with the united-atom lipid force field implemented in GROMACS is a reasonable approach to membrane protein simulations. We also suggest that using partial volume information and free energies of transfer may help to improve the parameterization of lipid-protein interactions and point out the need for accurate experimental data to validate and improve force field descriptions of such interactions

  9. Cardiac counterclockwise rotation is a risk factor for high-dose irradiation to the left anterior descending coronary artery in patients with left-sided breast cancer who receiving adjuvant radiotherapy after breast-conserving surgery. (United States)

    Tanaka, Hidekazu; Hayashi, Shinya; Hoshi, Hiroaki


    Patients irradiated for left-sided breast cancer have higher incidence of cardiovascular disease than those receiving irradiation for right-sided breast cancer. Most abnormalities were in the left anterior descending (LAD) coronary artery territory. We analyzed the relationships between preoperative examination results and irradiation dose to the LAD artery in patients with left-sided breast cancer. Seventy-one patients receiving breast radiotherapy were analyzed. The heart may rotate around longitudinal axis, showing either clockwise or counterclockwise rotation (CCWR). On electrocardiography, the transition zone (TZ) was judged in precordial leads. CCWR was considered to be present if TZ was at or to the right of V3. The prescribed dose was 50 Gy in 25 fractions. The maximum (Dmax) and mean (Dmean) doses to the LAD artery and the volumes of the LAD artery receiving at least 20 Gy, 30 Gy and 40 Gy (V20Gy, V30Gy and V40Gy, respectively) were significantly higher in CCWR than in the non-CCWR patients. On multivariate analysis, TZ was significantly associated with Dmax, Dmean, V20Gy, V30Gy, and V40Gy. CCWR is a risk factor for high-dose irradiation to the LAD artery. Electrocardiography is useful for evaluating the cardiovascular risk of high-dose irradiation to the LAD artery.

  10. Influence of molecular weight on the phase behavior and structure formation of branched side-chain hairy-rod polyfluorene in bulk phase. (United States)

    Knaapila, M; Stepanyan, R; Torkkeli, M; Lyons, B P; Ikonen, T P; Almásy, L; Foreman, J P; Serimaa, R; Güntner, R; Scherf, U; Monkman, A P


    We report on an experimental study of the self-organization and phase behavior of hairy-rod pi -conjugated branched side-chain polyfluorene, poly[9,9-bis(2-ethylhexyl)-fluorene-2,7-diyl]-i.e., poly[2,7-(9,9-bis(2-ethylhexyl)fluorene] (PF2/6) -as a function of molecular weight (M(n)) . The results have been compared to those of phenomenological theory. Samples for which M(n) =3-147 kg/mol were used. First, the stiffness of PF2/6 , the assumption of the theory, has been probed by small-angle neutron scattering in solution. Thermogravimetry has been used to show that PF2/6 is thermally stable over the conditions studied. Second, the existence of nematic and hexagonal phases has been phenomenologically identified for lower and higher M(n) (LMW, M(n) M(*)(n) ) regimes, respectively, based on free-energy argument of nematic and hexagonal hairy rods and found to correspond to the experimental x-ray diffraction (XRD) results for PF2/6 . By using the lattice parameters of PF2/6 as an experimental input, the nematic-hexagonal transition has been predicted in the vicinity of glassification temperature (T(g)) of PF2/6 . Then, by taking the orientation parts of the free energies into account the nematic-hexagonal transition has been calculated as a function of temperature and M(n) and a phase diagram has been formed. Below T(g) of 80 degrees C only (frozen) nematic phase is observed for M(n) M(*)(n) . The nematic-hexagonal transition upon heating is observed for the HMW regime depending weakly on M(n) , being at 140-165 degrees C for M(n) > M(*)(n). Third, the phase behavior and structure formation as a function of M(n) have been probed using powder and fiber XRD and differential scanning calorimetry and reasonable semiquantitative agreement with theory has been found for M(n) >or=3 kg/mol. Fourth, structural characteristics are widely discussed. The nematic phase of LMW materials has been observed to be denser than high-temperature nematic phase of HMW compounds. The hexagonal

  11. Property Enhancement Effects of Side-Chain-Type Naphthalene-Based Sulfonated Poly(arylene ether ketone) on Nafion Composite Membranes for Direct Methanol Fuel Cells. (United States)

    Wang, Baolong; Hong, Lihua; Li, Yunfeng; Zhao, Liang; Zhao, Chengji; Na, Hui


    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.

  12. 2-(1H-Imidazol-4-yl)ethanamine and 2-(1H-pyrazol-1-yl)ethanamine side chain variants of the IGF-1R inhibitor BMS-536924. (United States)

    Saulnier, Mark G; Frennesson, David B; Wittman, Mark D; Zimmermann, Kurt; Velaparthi, Upender; Langley, David R; Struzynski, Charles; Sang, Xiaopeng; Carboni, Joan; Li, Aixin; Greer, Ann; Yang, Zheng; Balimane, Praveen; Gottardis, Marco; Attar, Ricardo; Vyas, Dolatrai


    A series of IGF-1R inhibitors is disclosed, wherein the (m-chlorophenyl)ethanol side chain of BMS-536924 (1) is replaced with a series of 2-(1H-imidazol-4-yl)ethanamine and 2-(1H-pyrazol-1-yl)ethanamine side chains. Some analogs show improved IGF-1R potency and oral exposure. Analogs from both series, 16a and 17f, show in vivo activity comparable to 1 in our constitutively activated IGF-1R Sal tumor model. This may be the due to the improved protein binding in human and mouse serum for imidazole 16a and the excellent oral exposure of pyrazole 17f.

  13. Strategy for O-Alkylation of Serine and Threonine from Serinyl and Threoninyl Acetic Acids by Photoinduced Decarboxylative Radical Reactions: Connection between Serine/Threonine and Carbohydrates/Amino Acids at the Side Chain. (United States)

    Yamamoto, Takashi; Iwasaki, Tomoya; Morita, Toshio; Yoshimi, Yasuharu


    O-Alkylations of serine and threonine derivatives at the hydroxy group were achieved using photoinduced decarboxylative radical reactions of serinyl and threoninyl acetic acids with an organic photocatalyst without racemization under mild conditions. Photoinduced decarboxylative radical additions of serinyl and threoninyl acetic acids to electron-deficient alkenes provided linked serine and threonine with carbohydrates and amino acids at the side chain. In addition, O-methylations containing deuterium and O-benzylation of serine were performed under similar photochemical conditions.

  14. 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


    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.

  15. 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.


    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

  16. 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


    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.

  17. Disorder and order in unfolded and disordered peptides and proteins: a view derived from tripeptide conformational analysis. II. Tripeptides with short side chains populating asx and β-type like turn conformations. (United States)

    Rybka, Karin; Toal, Siobhan E; Verbaro, Daniel J; Mathieu, Daniel; Schwalbe, Harald; Schweitzer-Stenner, Reinhard


    In the preceding paper, we found that ensembles of tripeptides with long or bulky chains can include up to 20% of various turns. Here, we determine the structural and thermodynamic characteristics of GxG peptides with short polar and/or ionizable central residues (D, N, C), whose conformational distributions exhibit higher than average percentage (>20%) of turn conformations. To probe the side-chain conformations of these peptides, we determined the (3)J(H(α),H(β)) coupling constants and derived the population of three rotamers with χ1 -angles of -60°, 180° and 60°, which were correlated with residue propensities by DFT-calculations. For protonated GDG, the rotamer distribution provides additional evidence for asx-turns. A comparison of vibrational spectra and NMR coupling constants of protonated GDG, ionized GDG, and the protonated aspartic acid dipeptide revealed that side chain protonation increases the pPII content at the expense of turn populations. The charged terminal groups, however, have negligible influence on the conformational properties of the central residue. Like protonated GDG, cationic GCG samples asx-turns to a significant extent. The temperature dependence of the UVCD spectra and (3)J(H(N)H(α)) constants suggest that the turn populations of GDG and GNG are practically temperature-independent, indicating enthalpic and entropic stabilization. The temperature-independent J-coupling and UVCD spectra of GNG require a three-state model. Our results indicate that short side chains with hydrogen bonding capability in GxG segments of proteins may serve as hinge regions for establishing compact structures of unfolded proteins and peptides. Copyright © 2012 Wiley Periodicals, Inc.

  18. High-grade bursal-side partial rotator cuff tears: comparison of mid- and long-term results following arthroscopic repair after conversion to a full-thickness tear. (United States)

    Aydin, Nuri; Karaismailoglu, Bedri


    Partial-thickness rotator cuff tears (PTRCTs) are one of the leading causes of shoulder dysfunction. Successful results have been reported with different treatment techniques, but the long-term consequences of these procedures are not yet clearly known. The purposes of this study were to evaluate and compare the mid- and long-term clinical outcomes of arthroscopically repaired bursal-side PTRCTs after conversion to full-thickness tears and identify the possible effects of age, gender, and hand dominance on clinical outcomes. Twenty-nine patients who had undergone arthroscopic repair of a significant bursal-side PTRCT were functionally evaluated. The repair was made after conversion to a full-thickness tear. The average patient age was 55.2 years (range 35-69 years, SD ±7.6 years). Clinical outcomes were evaluated at 2 and 5 years after surgery. Constant Shoulder Score (CSS) and Visual Analogue Scale for Pain (VAS pain) were used as outcome measures. The average CSS improved from 38.9 preoperatively to 89.2 and 87.8 at 2 and 5 years after surgery, respectively (p functional outcomes and VAS pain scores at 2 and 5 years after surgery compared with the preoperative period. The patients who underwent surgery from their non-dominant extremity showed a significantly higher CSS increase relative to those who underwent surgery on the dominant extremity (p = 0.022). Arthroscopic repair of high-grade bursal-side PTRCTs after conversion to full-thickness tears is a reliable surgical technique with good functional outcomes and pain relief both at mid- and long-term follow-ups. Surgery on the non-dominant side may be related to better functional outcomes.

  19. Side Effects (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.

  20. Variation of the Side Chain Branch Position Leads to Vastly Improved Molecular Weight and OPV Performance in 4,8-dialkoxybenzo[1,2-b:4,5-b′]dithiophene/2,1,3-benzothiadiazole Copolymers

    Directory of Open Access Journals (Sweden)

    Robert C. Coffin


    Full Text Available Through manipulation of the solubilizing side chains, we were able to dramatically improve the molecular weight (Mw of 4,8-dialkoxybenzo[1,2-b:4,5-b′]dithiophene (BDT/2,1,3-benzothiadiazole (BT copolymers. When dodecyl side chains (P1 are employed at the 4- and 8-positions of the BDT unit, we obtain a chloroform-soluble copolymer fraction with Mw of 6.3 kg/mol. Surprisingly, by moving to the commonly employed 2-ethylhexyl branch (P2, Mw decreases to 3.4 kg/mol. This is despite numerous reports that this side chain increases solubility and Mw. By moving the ethyl branch in one position relative to the polymer backbone (1-ethylhexyl, P3, Mw is dramatically increased to 68.8 kg/mol. As a result of this Mw increase, the shape of the absorption profile is dramatically altered, with λmax = 637 nm compared with 598 nm for P1 and 579 nm for P2. The hole mobility as determined by thin film transistor (TFT measurements is improved from ~1×10−6 cm2/Vs for P1 and P2 to 7×10−4 cm2/Vs for P3, while solar cell power conversion efficiency in increased to 2.91% for P3 relative to 0.31% and 0.19% for P1 and P2, respectively.

  1. ¹H, ¹³C and ¹⁵N backbone and side-chain resonance assignments of the N-terminal ubiquitin-binding domains of the human deubiquitinase Usp28. (United States)

    Wen, Yi; Cui, Rong; Zhang, Huaqun; Zhang, Naixia


    Deubiquitinases (DUBs) reversibly remove ubiquitin tags from polypeptides and play crucial regulatory roles in multiple cellular processes. Ubiquitin-specific protease 28 (Usp28), a member of the DUB family, exerts its deubiquitination function on key protein molecules in a couple of cancer-associated pathways, likely acting as an oncogenic factor in vivo. The N-terminal ubiquitin-binding domains (UBDs) of Usp28 are potentially required for the full catalytic capacity of Usp28 toward ubiquitin chains. Here we report the expression, purification and (1)H, (13)C and (15)N backbone and side-chain resonance assignments of the N-terminal UBDs of Usp28. The BMRB accession number is 19077.

  2. Backbone and side-chain ¹H, ¹⁵N, and ¹³C resonance assignments of the microtubule-binding domain of yeast cytoplasmic dynein in the high and low-affinity states. (United States)

    Takarada, Osamu; Nishida, Noritaka; Kikkawa, Masahide; Shimada, Ichio


    Cytoplasmic dynein is a motor protein that walks toward the minus end of microtubules (MTs) by utilizing the energy of ATP hydrolysis. The heavy chain of cytoplasmic dynein contains the microtubule-binding domain (MTBD). Switching of MTBD between high and low affinity states for MTs is crucial for processive movement of cytoplasmic dynein. Previous biochemical studies demonstrated that the affinity of MTBD is regulated by the AAA+ family ATPase domain, which is separated by 15 nm long coiled-coil helix. In order to elucidate the structural basis of the affinity switching mechanism of MTBD, we designed two MTBD constructs, termed MTBD-High and MTBD-Low, which are locked in high and low affinity state for MTs, respectively, by introducing a disulfide bond between the coiled-coil helix. Here, we established the backbone and side-chain assignments of MTBD-High and MTBD-Low for further structural analyses.

  3. Methylobacterium extorquens AM1 produces a novel type of acyl-homoserine lactone with a double unsaturated side chain under methylotrophic growth conditions. (United States)

    Nieto Penalver, Carlos G; Morin, Danièle; Cantet, Franck; Saurel, Olivier; Milon, Alain; Vorholt, Julia A


    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.

  4. Accomplishment of Multifunctional π-Conjugated Polymers by Regulating the Degree of Side-Chain Fluorination for Efficient Dopant-Free Ambient-Stable Perovskite Solar Cells and Organic Solar Cells. (United States)

    Kranthiraja, Kakaraparthi; Park, Sang Ho; Kim, Hyunji; Gunasekar, Kumarasamy; Han, Gibok; Kim, Bumjoon J; Kim, Chang Su; Kim, Soohyun; Lee, Hyunjung; Nishikubo, Ryosuke; Saeki, Akinori; Jin, Sung-Ho; Song, Myungkwan


    We present an efficient approach to develop a series of multifunctional π-conjugated polymers (P1-P3) by controlling the degree of fluorination (0F, 2F, and 4F) on the side chain linked to the benzodithiophene unit of the π-conjugated polymer. The most promising changes were noticed in optical, electrochemical, and morphological properties upon varying the degree of fluorine atoms on the side chain. The properly aligned energy levels with respect to the perovskite and PCBM prompted us to use them in perovskite solar cells (PSCs) as hole-transporting materials (HTMs) and in bulk heterojunction organic solar cells (BHJ OSCs) as photoactive donors. Interestingly, P2 (2F) and P3 (4F) showed an enhanced power conversion efficiency (PCE) of 14.94%, 10.35% compared to P1 (0F) (9.80%) in dopant-free PSCs. Similarly, P2 (2F) and P3 (4F) also showed improved PCE of 7.93% and 7.43%, respectively, compared to P1 (0F) (PCE of 4.35%) in BHJ OSCs. The high photvoltaic performance of the P2 and P3 based photovotaic devices over P1 are well correlated with their energy level alignment, charge transporting, morphological and packing properties, and hole transfer yields. In addition, the P1-P3 based dopant-free PSCs and BHJ OSCs showed an excellent ambient stability up to 30 days without a significant drop in their initial performance.

  5. 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)


    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.

  6. 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


    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...... spacer are preferentially oriented perpendicular to the laser light polarization. The extent of orientation increases with increasing spacer length. On the other hand, in the shorter adipates only the chromophore and the spacer are likewise oriented. Rapid-scan FTIR analysis performed on...

  7. Cation-pi interactions with a model for the side chain of tryptophan: structures and absolute binding energies of alkali metal cation-indole complexes. (United States)

    Ruan, Chunhai; Yang, Zhibo; Hallowita, Nuwan; Rodgers, M T


    Threshold collision-induced dissociation techniques are employed to determine bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Li+, Na+, K+, Rb+, and Cs+, with indole, C8H7N. The primary and lowest energy dissociation pathway in all cases is endothermic loss of an intact indole ligand. Sequential loss of a second indole ligand is observed at elevated energies for the bis-complexes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31G* geometries. The agreement between theory and experiment is very good for all complexes except Li+ (C8H7N), where theory underestimates the strength of the binding. The trends in the BDEs of these alkali metal cation-indole complexes are compared with the analogous benzene and naphthalene complexes to examine the influence of the extended pi network and heteroatom on the strength of the cation-pi interaction. The Na+ and K+ binding affinities of benzene, phenol, and indole are also compared to those of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan to elucidate the factors that contribute to the binding in complexes to the aromatic amino acids. The nature of the binding and trends in the BDEs of cation-pi complexes between alkali metal cations and benzene, phenol, and indole are examined to help understand nature's preference for engaging tryptophan over phenylalanine and tyrosine in cation-pi interactions in biological systems.

  8. Copolymerization of ethylene with polar monomers: chain propagation and side reactions. A DFT theoretical study using zwitterionic Ni(II) and Pd(II) catalysts. (United States)

    Szabo, Miklos J; Galea, Natasha M; Michalak, Artur; Yang, Sheng-Yong; Groux, Laurent F; Piers, Warren E; Ziegler, Tom


    Calculations utilizing anionic substituted derivates of the cationic N(wedge)N--Ni(II) and Pd(II) diimine Brookhart complex have been carried out on the barriers of ethylene and acrylonitrile insertion into a M- methyl, propyl and CH(CN)Et bond for M = Ni, Pd. The possibility of side reactions such as chelate formation with the polar functionality and oligomerization of the active species after acrylonitrile insertion are explored. The diimine ring system N--N = -NR' 'CR(1)CR(2)NR' ' with R' ' = 2,6-C(6)H(3)(i-Pr)(2) and R(1),R(2) = Me was functionalized by adding one or two anionic groups (BF(3)(-), etc.) in place of i-Pr on the aryl rings or by replacing one Me diimine backbone group (R(1)) with BH(3)(-). The objective of this investigation is computationally to design catalysts for ethylene/acrylonitrile copolymerization that have activities that are comparable to that of the cationic Ni(II) diimine or at least the Pd(II) diimine Brookhart system for ethylene homopolymerization. Complexes that might meet this objective are discussed.

  9. Quantitative assessment of retropulsion of the hip, excessive hip external rotation, and excessive lateral shift of the trunk over the unaffected side in hemiplegia using three-dimensional treadmill gait analysis. (United States)

    Tanikawa, Hiroki; Ohtsuka, Kei; Mukaino, Masahiko; Inagaki, Keisuke; Matsuda, Fumihiro; Teranishi, Toshio; Kanada, Yoshikiyo; Kagaya, Hitoshi; Saitoh, Eiichi


    Gait assessment is important to determine the most effective strategy to regain gait function during stroke rehabilitation. To understand the mechanisms that cause abnormal gait patterns, it is useful to objectively identify and quantify the abnormal gait patterns. Objective assessment also helps evaluate the efficacy of treatments and can be used to provide suggestions for treatment. To evaluate the validity of quantitative indices for retropulsion of the hip, excessive hip external rotation, and excessive lateral shift of the trunk over the unaffected side in hemiplegic patients. Forty-six healthy control subjects and 112 hemiplegic patients participated. From the 112 patients, 50 patients were selected into each abnormal gait pattern with some overlap. Participants were instructed to walk on a treadmill and were recorded using a three-dimensional motion analysis system. An index to quantify each of the three abnormal gait patterns was calculated from the three-dimensional coordinate data. The index values of patients were compared with those of healthy subjects and with the results of observational gait assessment by three physical therapists with expertise in gait analysis. Strong correlation was observed between the index value and the median observational rating for all three abnormal gait patterns (-0.56 to -0.74). Most of the patients with an abnormal gait pattern had a higher index value than the healthy subjects. The proposed indices are useful for clinical gait analysis. Our results encourage a more detailed analysis of hemiplegic gait using a motion analysis system.

  10. Three-Component Aminoalkylations Yielding Dihydronaphthoxazine-Based Sirtuin Inhibitors: Scaffold Modification and Exploration of Space for Polar Side-Chains. (United States)

    Vojacek, Steffen; Beese, Katja; Alhalabi, Zayan; Swyter, Sören; Bodtke, Anja; Schulzke, Carola; Jung, Manfred; Sippl, Wolfgang; Link, Andreas


    Nonpolar derivatives of heterocyclic aromatic screening hits like the non-selective sirtuin inhibitor splitomicin tend to be poorly soluble in biological fluids. Unlike sp 3 -rich natural products, flat aromatic compounds are prone to stacking and often difficult to optimize into leads with activity in cellular systems. The aim of this work was to identify anchor points for the introduction of sp 3 -rich fragments with polar functional groups into the newly discovered active (IC 50  = 5 μM) but nonpolar scaffold 1,2-dihydro-3H-naphth[1,2-e][1,3]oxazine-3-thione by a molecular modeling approach. Docking studies were conducted with structural data from crystallized human SIRT2 enzyme. Subsequent evaluation of the in silico hypotheses through synthesis and biological evaluation of the designed structures was accomplished with the aim to discover new SIRT2 inhibitors with improved aqueous solubility. Derivatives of 8-bromo-1,2-dihydro-3H-naphth[1,2-e][1,3]oxazine-3-thione N-alkylated with a hydrophilic morpholino-alkyl chain at the thiocarbamate group intended for binding in the acetyl-lysine pocket of the enzyme appeared to be promising. Both the sulfur of the thiocarbamate and the bromo substituent were assumed to result in favorable hydrophobic interactions and the basic morpholino-nitrogen was predicted to build a hydrogen bond with the backbone Ile196. While the brominated scaffold showed moderately improved activity (IC 50  = 1.8 μM), none of the new compounds displayed submicromolar activity. Synthesis and characterization of the new compounds are reported and the possible reasons for the outcome are discussed. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. ¹H, ¹³C, and ¹⁵N backbone and side-chain chemical shift assignment of the toxin Doc in the unbound state. (United States)

    De Gieter, Steven; Loris, Remy; van Nuland, Nico A J; Garcia-Pino, Abel


    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.

  12. 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. (United States)

    Shimizu, Satoko; Yokoyama, Tomoya; Akiyama, Takuya; Matsumoto, Yuji


    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.

  13. ¹H, ¹³C and ¹⁵N backbone and side-chain resonance assignments of the N-terminal ubiquitin-binding domains of USP25. (United States)

    Shi, Li; Wen, Yi; Zhang, Naixia


    Ubiquitin Specific Protease 25 (USP25), a member of the deubiquitinase family, is involved in several disease-related signal pathways including myogenesis, immunity and protein degradation. It specially catalyzes the hydrolysis of the K48-linked and K63-linked polyubiquitin chains. USP25 contains one ubiquitin-associated domain and two ubiquitin-interacting motifs (UIMs) in its N-terminal region, which interact with ubiquitin and play a role in substrate recognition. Besides, it has been shown that the catalysis activity of USP25 is either impaired by sumoylation or enhanced by ubiquitination within its UIM. To elucidate the structural basis of the cross-regulation of USP25 function by non-covalent binding and covalent modifications of ubiquitin and SUMO2/3, a systematic structural biology study of USP25 is required. Here, we report the (1)H, (13)C and (15)N backbone and side-chain resonance assignments of the N-terminal ubiquitin binding domains (UBDs) of USP25 with BMRB accession number of 19111, which is the first step of the systematic structural biology study of the enzyme.

  14. Comparing Demand Side Management approaches

    NARCIS (Netherlands)

    Molderink, Albert; Bakker, Vincent; Hurink, Johann L.; Smit, Gerardus Johannes Maria


    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

  15. Piriformis electromyography activity during prone and side-lying hip joint movement. (United States)

    Morimoto, Yasuhiro; Oshikawa, Tomoki; Imai, Atsushi; Okubo, Yu; Kaneoka, Koji


    [Purpose] To measure electromyographic activity of the piriformis using fine-wire electrodes during 7 hip movements. [Subjects and Methods] Eleven healthy men, without severe low back pain or lower limb injury, participated in this study. Fine-wire electrodes were inserted into the piriformis and surface electrodes were attached to the muscles in the hip region and the trunk muscles on the dominant arm side. Electromyographic signal amplitude was measured during 7 hip movements: side-lying external rotation in hip neutral position, side-lying abduction in hip neutral position, side-lying abduction in hip external rotation, side-lying abduction in hip internal rotation, prone extension in hip neutral position, prone extension in hip external rotation, and prone extension in hip internal rotation. Repeated-measures one-way analysis of variance was used to examine electromyographic activity in each of the 7 hip movements. [Results] Piriformis electromyographic activity was highest during prone hip extension in external rotation. Both the superior and inferior portions of the gluteus maximus were also highly activated during prone hip extension in external rotation. [Conclusion] Prone hip extension in external rotation induced high electromyographic activity in the piriformis and superior and inferior gluteus maximus muscles.


    International Nuclear Information System (INIS)



    During the summer of 2002, eight superconducting helical spin rotators were installed into RHIC in order to control the polarization directions independently at the STAR and PHENIX experiments. Without the rotators, the orientation of polarization at the interaction points would only be vertical. With four rotators around each of the two experiments, we can rotate either or both beams from vertical into the horizontal plane through the interaction region and then back to vertical on the other side. This allows independent control for each beam with vertical, longitudinal, or radial polarization at the experiment. In this paper, we present results from the first run using the new spin rotators at PHENIX

  17. Spin chains and string theory. (United States)

    Kruczenski, Martin


    Recently, an important test of the anti de Sitter/conformal field theory correspondence has been done using rotating strings with two angular momenta. We show that such a test can be described more generally as the agreement between two actions: one a low energy description of a spin chain appearing in the field theory side, and the other a limit of the string action in AdS5xS5. This gives a map between the mean value of the spin in the boundary theory and the position of the string in the bulk, and shows how a string action can emerge from a gauge theory in the large-N limit.

  18. 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. (United States)

    Xayarath, Bobbi; Yother, Janet


    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.

  19. Rotational seismology (United States)

    Lee, William H K.


    Rotational seismology is an emerging study of all aspects of rotational motions induced by earthquakes, explosions, and ambient vibrations. It is of interest to several disciplines, including seismology, earthquake engineering, geodesy, and earth-based detection of Einstein’s gravitation waves.Rotational effects of seismic waves, together with rotations caused by soil–structure interaction, have been observed for centuries (e.g., rotated chimneys, monuments, and tombstones). Figure 1a shows the rotated monument to George Inglis observed after the 1897 Great Shillong earthquake. This monument had the form of an obelisk rising over 19 metres high from a 4 metre base. During the earthquake, the top part broke off and the remnant of some 6 metres rotated about 15° relative to the base. The study of rotational seismology began only recently when sensitive rotational sensors became available due to advances in aeronautical and astronomical instrumentations.

  20. The Penicillium chrysogenum aclA gene encodes a broad-substrate-specificity acyl-coenzyme A ligase involved in activation of adipic acid, a side-chain precursor for cephem antibiotics. (United States)

    Koetsier, Martijn J; Gombert, Andreas K; Fekken, Susan; Bovenberg, Roel A L; van den Berg, Marco A; Kiel, Jan A K W; Jekel, Peter A; Janssen, Dick B; Pronk, Jack T; van der Klei, Ida J; Daran, Jean-Marc


    Activation of the cephalosporin side-chain precursor to the corresponding CoA-thioester is an essential step for its incorporation into the beta-lactam backbone. To identify an acyl-CoA ligase involved in activation of adipate, we searched in the genome database of Penicillium chrysogenum for putative structural genes encoding acyl-CoA ligases. Chemostat-based transcriptome analysis was used to identify the one presenting the highest expression level when cells were grown in the presence of adipate. Deletion of the gene renamed aclA, led to a 32% decreased specific rate of adipate consumption and a threefold reduction of adipoyl-6-aminopenicillanic acid levels, but did not affect penicillin V production. After overexpression in Escherichia coli, the purified protein was shown to have a broad substrate range including adipate. Finally, protein-fusion with cyan-fluorescent protein showed co-localization with microbody-borne acyl-transferase. Identification and functional characterization of aclA may aid in developing future metabolic engineering strategies for improving the production of different cephalosporins.

  1. ¹H, ¹³C, and ¹⁵N backbone and side chain resonance assignments of the C-terminal DNA binding and dimerization domain of v-Myc. (United States)

    Kızılsavaş, Gönül; Saxena, Saurabh; Żerko, Szymon; Koźmiński, Wiktor; Bister, Klaus; Konrat, Robert


    The oncogenic transcription factor Myc is one of the most interesting members of the basic-helix-loop-helix-zipper (bHLHZip) protein family. Deregulation of Myc via gene amplification, chromosomal translocation or other mechanisms lead to tumorigenesis including Burkitt lymphoma, multiple myeloma, and many other malignancies. The oncogene myc is a highly potent transforming gene and capable to transform various cell types in vivo and in vitro. Its oncogenic activity initialized by deregulated expression leads to a shift of the equilibrium in the Myc/Max/Mad network towards Myc/Max complexes. The Myc/Max heterodimerization is a prerequisite for transcriptional functionality of Myc. Primarily, we are focusing on the apo-state of the C-terminal domain of v-Myc, the retroviral homolog of human c-Myc. Based on multi-dimensional NMR measurements v-Myc appears to be neither a fully structured nor a completely unstructured protein. The bHLHZip domain of v-Myc does not exist as a random coil but exhibits partially pre-formed α-helical regions in its apo-state. In order to elucidate the structural propensities of Myc in more detail, the backbone and side-chain assignments obtained here for apo-Myc are a crucial prerequisite for further NMR measurements.

  2. Bioresolution production of (2R,3S)-ethyl-3-phenylglycidate for chemoenzymatic synthesis of the taxol C-13 side chain by Galactomyces geotrichum ZJUTZQ200, a new epoxide-hydrolase-producing strain. (United States)

    Wei, Chun; Ling, Jinlong; Shen, Honglei; Zhu, Qing


    A newly isolated Galactomyces geotrichum ZJUTZQ200 strain containing an epoxide hydrolase was used to resolve racemic ethyl 3-phenylglycidate (rac-EPG) for producing (2R,3S)-ethyl-3-phenylglycidate ((2R,3S)-EPG). G. geotrichum ZJUTZQ200 was verified to be able to afford high enantioselectivity in whole cell catalyzed synthesis of this chiral phenylglycidate synthon. After the optimization of the enzymatic production and bioresolution conditions, (2R,3S)-EPG was afforded with high enantioselectivity (e.e.S > 99%, E > 49) after a 8 h reaction. The co-solvents, pH buffer solutions and substrate/cell ratio were found to have significant influences on the bioresolution properties of G. geotrichum ZJUTZQ200. Based on the bioresolution product (2R,3S)-EPG, taxol's side chain ethyl (2R,3S)-3-benzoylamino-2-hydroxy-3-phenylpropionate was successfully synthesized by a chemoenzymatic route with high enantioselectivity (e.e.S > 95%).

  3. Bioresolution Production of (2R,3S-Ethyl-3-phenylglycidate for Chemoenzymatic Synthesis of the Taxol C-13 Side Chain by Galactomyces geotrichum ZJUTZQ200, a New Epoxide-Hydrolase-Producing Strain

    Directory of Open Access Journals (Sweden)

    Chun Wei


    Full Text Available A newly isolated Galactomyces geotrichum ZJUTZQ200 strain containing an epoxide hydrolase was used to resolve racemic ethyl 3-phenylglycidate (rac-EPG for producing (2R,3S-ethyl-3-phenylglycidate ((2R,3S-EPG. G. geotrichum ZJUTZQ200 was verified to be able to afford high enantioselectivity in whole cell catalyzed synthesis of this chiral phenylglycidate synthon. After the optimization of the enzymatic production and bioresolution conditions, (2R,3S-EPG was afforded with high enantioselectivity (e.e.S > 99%, E > 49 after a 8 h reaction. The co-solvents, pH buffer solutions and substrate/cell ratio were found to have significant influences on the bioresolution properties of G. geotrichum ZJUTZQ200. Based on the bioresolution product (2R,3S-EPG, taxol’s side chain ethyl (2R,3S-3-benzoylamino-2-hydroxy-3-phenylpropionate was successfully synthesized by a chemoenzymatic route with high enantioselectivity (e.e.S > 95%.

  4. Steroidogenic impairment due to reduced ovarian transcription of cytochrome P450 side-chain-cleavage (P450scc) and steroidogenic acute regulatory protein (StAR) during experimental nephrotic syndrome. (United States)

    Peña-Rico, Miguel; Guadalupe Ortiz-López, María; Camacho-Castillo, Luz; Cárdenas, Mario; Pedraza-Chaverri, José; Menjívar, Marta


    The nephrotic syndrome is a renal disease characterized by proteinuria, hypoproteinemia, edema and hyperlipidemia. It has been reported that female nephrotic rats are characterized by loss of the oestrus cycle, follicle atresia, low gonadotropin and steroid concentrations; particularly, undetectable estradiol levels. Therefore, to determine the mechanisms involved in the ovarian steroidogenesis impairment, in this present study we evaluated the ovarian expression of the essential steroidogenesis components: cytochrome P450 side cholesterol chain cleavage enzyme (P450scc) and steroidogenic acute regulatory protein (StAR). The experiments were conducted in the rat experimental model of nephrosis induced by puromycin aminonucleoside (PAN) and in control groups. The evaluation of the expression of P450scc and StAR mRNA were performed during the acute phase of nephrosis as well as after the exogenous administration of 1 or 4 doses of human chorionic gonadotrophin (hCG), or a daily dose of FSH or FSH+hCG for 10 days. In addition, serum hormone concentrations, intra-ovarian steroid content, and the reproductive capacity were determined. The results revealed a decreased expression of mRNA of P450scc enzyme and StAR during nephrosis, and eventhough they increased after gonadotropins treatment, they did not conduce to a normal cycling rat period or fertility recovery. This study demonstrates that the mechanism by which ovarian steroid biosynthesis is altered during acute nephrosis involves damage at the P450scc and StAR mRNA synthesis and processing.

  5. 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 (United States)

    Liu, Dong; Peng, Jinhua; Li, Zhuoyao; Liu, Bin; Wang, Lei


    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.

  6. Global rotation

    International Nuclear Information System (INIS)

    Rosquist, K.


    Global rotation in cosmological models is defined on an observational basis. A theorem is proved saying that, for rigid motion, the global rotation is equal to the ordinary local vorticity. The global rotation is calculated in the space-time homogeneous class III models, with Godel's model as a special case. It is shown that, with the exception of Godel's model, the rotation in these models becomes infinite for finite affine parameter values. In some directions the rotation changes sign and becomes infinite in a direction opposite to the local vorticity. The points of infinite rotation are identified as conjugate points along the null geodesics. The physical interpretation of the infinite rotation is discussed, and a comparison with the behaviour of the area distance at conjugate points is given. (author)

  7. (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. (United States)

    Kumar, Dinesh; Arora, Ashish


    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.

  8. 1H, 13C, 15N backbone and side chain NMR resonance assignments of the N-terminal NEAr Iron transporter domain 1 (NEAT 1) of the hemoglobin receptor IsdB of Staphylococcus aureus (United States)

    Fonner, Brittany A.; Tripet, Brian P.; Lui, Mengyao; Zhu, Hui; Lei, Benfang; Copié, Valérie


    Staphylococcus aureus is an opportunistic pathogen that causes skin and severe infections in mammals. Critical to S. aureus growth is its ability to scavenge iron from host cells. To this effect, S. aureus has evolved a sophisticated pathway to acquire heme from hemoglobin (Hb) as a preferred iron source. The pathway is comprised of nine iron-regulated surface determinant (Isd) proteins involved in heme capture, transport, and degradation. A key protein of the heme acquisition pathway is the surface-anchored hemoglobin receptor protein IsdB, which is comprised of two NEAr transporter (NEAT) domains that act in concert to bind Hb and extract heme for subsequent transfer to downstream acquisition pathway proteins. Despite significant advances in the structural knowledge of other Isd proteins, the structural mechanisms and molecular basis of the IsdB-mediated heme acquisition process are not well understood. In order to provide more insights into the mode of function of IsdB, we have initiated NMR structural studies of the first NEAT domain of IsdB (IsdBN1). Herein, we report the near complete 1H, 13C and 15N resonance assignments of backbone and side chain atoms, and the secondary structural topology of the 148-residue IsdB NEAT 1 domain. The NMR results are consistent with the presence of eight β-strands and one α-helix characteristic of an immunoglobulin-like fold observed in other NEAT domain family proteins. This work provides a solid framework to obtain atomic-level insights toward understanding how IsdB mediates IsdB-Hb protein-protein interactions critical for heme capture and transfer. PMID:23686822

  9. 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.


    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

  10. An Improved Triangular Element With Drilling Rotations

    DEFF Research Database (Denmark)

    Damkilde, Lars; Grønne, Mikael


    A new plane element with rotational degrees in the corner nodes is presented. The element has 12 degrees of freedom and the only difference from the well-known Linear Strain Triangular (LST) element is that the displacements perpendicular to the element sides in the mid-side nodes are replaced...... by rotations in the corner nodes. Compared to Allman's plane element which was the first succesfull implementation of drilling rotations the proposed element has extra displacements in the mid-side nodes parallel to the element sides. The performance should therefore be better and closer to the LST-element...

  11. Structure of molecules and internal rotation

    CERN Document Server

    Mizushima, San-Ichiro


    Structure of Molecules and Internal Rotation reviews early studies on dihalogenoethanes. This book is organized into two parts encompassing 8 chapters that evaluate the Raman effect in ethane derivatives, the energy difference between rotational isomers, and the infrared absorption of ethane derivatives. Some of the topics covered in the book are the potential barrier to internal rotation; nature of the hindering potential; entropy difference between the rotational isomers; internal rotation in butane, pentane, and hexane; and internal rotation in long chain n-paraffins. Other chapters deal wi

  12. Rotating Wavepackets (United States)

    Lekner, John


    Any free-particle wavepacket solution of Schrodinger's equation can be converted by differentiations to wavepackets rotating about the original direction of motion. The angular momentum component along the motion associated with this rotation is an integral multiple of [h-bar]. It is an "intrinsic" angular momentum: independent of origin and…

  13. The rotator

    DEFF Research Database (Denmark)

    Jensen, Eva B. Vedel; Gundersen, Hans Jørgen Gottlieb


    The mean particle volume can be stereologically estimated using the nucleator principle. In the present paper, we discuss another principle for estimating mean particle volume, namely the rotator. The vertical rotator has already been previously described and is supplemented in the present paper ...

  14. Rotational elasticity (United States)

    Vassiliev, Dmitri


    We consider an infinite three-dimensional elastic continuum whose material points experience no displacements, only rotations. This framework is a special case of the Cosserat theory of elasticity. Rotations of material points are described mathematically by attaching to each geometric point an orthonormal basis that gives a field of orthonormal bases called the coframe. As the dynamical variables (unknowns) of our theory, we choose the coframe and a density. We write down the general dynamic variational functional for our rotational theory of elasticity, assuming our material to be physically linear but the kinematic model geometrically nonlinear. Allowing geometric nonlinearity is natural when dealing with rotations because rotations in dimension three are inherently nonlinear (rotations about different axes do not commute) and because there is no reason to exclude from our study large rotations such as full turns. The main result of the talk is an explicit construction of a class of time-dependent solutions that we call plane wave solutions; these are travelling waves of rotations. The existence of such explicit closed-form solutions is a non-trivial fact given that our system of Euler-Lagrange equations is highly nonlinear. We also consider a special case of our rotational theory of elasticity which in the stationary setting (harmonic time dependence and arbitrary dependence on spatial coordinates) turns out to be equivalent to a pair of massless Dirac equations. The talk is based on the paper [1]. [1] C.G.Boehmer, R.J.Downes and D.Vassiliev, Rotational elasticity, Quarterly Journal of Mechanics and Applied Mathematics, 2011, vol. 64, p. 415-439. The paper is a heavily revised version of preprint

  15. Electrophilic heteroaromatic substitutions. 8. Studies on the mechanism of the -side-chain aminomethylation and hydrogen/deuterium isotope exchange reactions of -methylpyrroles. [Ethyl 1,3,4,5-tetramethylpyrrole-2-carboxylate and Ethyl 4-bromo-1,3,5-trimethylpyrrole-2-carboxylate

    Energy Technology Data Exchange (ETDEWEB)

    Curulli, A.; Sleiter, G.


    A kinetic investigation of the acid-mediated -side-chain (dimethylamino)alkylation and hydrogen/deuterium isotope exchange reactions of ethyl 1,3,4,5-tetramethylpyrrole-2-carboxylate and ethyl 4-bromo-1,3,5-trimethylpyrrole-2-carboxylate in aqueous acetonitrile has been carried out. The effect of a number of variables, such as nature and concentration of the catalyzing acid, amount of water in the reaction medium, and concentration and type of the electrophile, on the reaction rate indicates that both processes are subject to general acid catalysis and that their limiting step is electrophilic attack on an -methylenepyrroline. The influence on the rate of the Mannich reaction of the nuclear substituent adjacent to the side chain undergoing attack is also discussed. The conditional dissociation constants of acetic and formic acid in 95% aqueous acetonitrile have been measured. 13 references, 2 tables.

  16. Molecular design of boronic acid-functionalized squarylium cyanine dyes for multiple discriminant analysis of sialic acid in biological samples: selectivity toward monosaccharides controlled by different alkyl side chain lengths. (United States)

    Ouchi, Kazuki; Colyer, Christa L; Sebaiy, Mahmoud; Zhou, Jin; Maeda, Takeshi; Nakazumi, Hiroyuki; Shibukawa, Masami; Saito, Shingo


    We designed a new series of boronic acid-functionalized squarylium cyanine dyes (SQ-BA) with different lengths of alkyl chain residues, suitable for multiple discriminant analysis (MDA) of sialic acid (Neu5Ac) in biological samples. The SQ-BA dyes form aggregates based on hydrophobic interactions, which result in quenched fluorescence in aqueous solutions. When the boronic acid binds with saccharides, the fluorescence intensity increases as a result of dissociation to the emissive monomeric complex. We inferred that different dye aggregate structures (H-aggregates and J-aggregates) were induced depending on the alkyl chain length, so that monosaccharides would be recognized in different ways (especially, multipoint interaction with J-aggregates). A distinctive emission enhancement of SQ-BA dyes with shorter-alkyl-chains in the presence of Neu5Ac was observed (2.4-fold fluorescence enhancement; with formation constant 10(1.7) M(-1)), with no such enhancement for SQ-BA dyes with longer-alkyl-chain. In addition, various enhancement factors for other monosaccharides were observed depending on the alkyl chain length. Detailed thermodynamic and NMR studies of the SQ-BA complexes revealed the unique recognition mechanism: the dye aggregate with a shorter-alkyl-chain causes the slipped parallel structure and forms a stable 2:1 complex with Neu5Ac, as distinct from longer-alkyl-chain dyes, which form a 1:1 monomeric complex. MDA using the four SQ-BA dyes was performed for human urine samples, resulting in the successful discrimination between normal and abnormal Neu5Ac levels characteristic of disease. Thus, we successfully controlled various responses to similar monosaccharides with a novel approach that chemically modified not the boronic acid moiety itself but the length of the alkyl chain residue attached to the dye in order to generate specificity.

  17. Competing hydrogen bonding in methoxyphenols: The rotational spectrum of o-vanillin (United States)

    Cocinero, Emilio J.; Lesarri, Alberto; Écija, Patricia; Basterretxea, Francisco; Fernández, José A.; Castaño, Fernando


    The conformational preferences of o-vanillin have been investigated in a supersonic jet expansion using Fourier transform microwave (FT-MW) spectroscopy. Three molecular conformations were derived from the rotational spectrum. The two most stable structures are characterized by a moderate O sbnd H···O dbnd C hydrogen bond between the aldehyde and the hydroxyl groups, with the methoxy side chain either in plane (global minimum a- cis-trans) or out of plane (a- cis-gauche) with respect to the aromatic ring. In the third conformer the aldehyde group is rotated by ca. 180°, forming a O sbnd H···O hydrogen bond between the methoxy and hydroxyl groups (s- trans-trans). Rotational parameters and relative populations are provided for the three conformations, which are compared with the results of ab initio (MP2) and density-functional (B3LYP, M05-2X) theoretical predictions.

  18. Rotational Spectra of Adrenaline and Noradrenaline (United States)

    Cortijo, V.; López, J. C.; Alonso, J. L.


    The emergence of Laser Ablation Molecular Beam Fourier Transform Microwave (LA-MB-FTMW) spectroscopy has rendered accessible the gas-phase study of solid biomolecules with high melting points. Among the biomolecules to benefit from this technique, neurotransmitters have received special attention due to the lack of experimental information and their biological relevance. As a continuation of the we present the study of adrenaline and noradrenaline. The comparison between the experimental rotational and ^{14}N nuclear quadrupole coupling constants and those calculated ab initio provide a definitive test for molecular structures and confirm unambiguously the identification of four conformers of adrenaline and three conformers of noradrenaline. Their relative population in the jet has been evaluated by relative intensity measurements of selected rotational transitions. The most abundant conformer in both neurotransmitters present an extended AG configuration with a O-H\\cdotsN hydrogen bond in the side chain. J.L. Alonso, M.E. Sanz, J.C. López and V. Cortijo, J. Am. Chem. Soc. (in press), 2009

  19. Rotating preventers

    International Nuclear Information System (INIS)

    Tangedahl, M.J.; Stone, C.R.


    This paper reports that recent changes in the oil and gas industry and ongoing developments in horizontal and underbalanced drilling necessitated development of a better rotating head. A new device called the rotating blowout preventer (RBOP) was developed by Seal-Tech. It is designed to replace the conventional rotating control head on top of BOP stacks and allows drilling operations to continue even on live (underbalanced) wells. Its low wear characteristics and high working pressure (1,500 psi) allow drilling rig crews to drill safely in slightly underbalanced conditions or handle severe well control problems during the time required to actuate other BOPs in the stack. Drilling with a RBOP allows wellbores to be completely closed in tat the drill floor rather than open as with conventional BOPs

  20. The Spatiale Rotator

    DEFF Research Database (Denmark)

    Rasmusson, Allan


    it is embedded and sectioned. This has the unfortunate side effect that all information about positioning within the object is lost for blocks and sections. For complex tissue, like the mammalian brain, this information is of utmost importance to ensure measurements are performed in the correct region......The inherent demand for unbiasedness for some stereological estimators imposes a demand of not only positional uniform randomness but also isotropic randomness, i.e. directional uniform randomness. In order to comply with isotropy, one must perform a random rotation of the object of interest before...... is obeyed by randomizing the orientation of the virtual probe itself within the thick section. Overall, the benefit is that positional information is kept for any block and section of the specimen. As the Spatial Rotator is a 3D probe, data must be gathered from sections thicker than 25 micro meters to form...

  1. Chain Posets


    Johnson, Ian T.


    A chain poset, by definition, consists of chains of ordered elements in a poset. We study the chain posets associated to two posets: the Boolean algebra and the poset of isotropic flags. We prove that, in both cases, the chain posets satisfy the strong Sperner property and are rank-log concave.

  2. Vortex chain formation in regions of ion concentration polarization. (United States)

    Hanasoge, Srinivas; Diez, Francisco J


    The local vortical flow generated inside an ion concentration polarization (ICP) region is evaluated experimentally. The ICP is induced by a patterned nanoporous self-assembling membrane integrated inside a single microchannel. A bottom-view image of the depletion region near the membrane revealed a primary vortex which results from the electric field amplification. A unique perspective of the flow is obtained by imaging the microchannel from its side. This visualization shows for the first time the formation of a chain of three vortices all rotating in the same direction in the depletion region. While observation of multiple vortices has been previously reported, it was in reference to counter rotating vortex pairs and not to the same direction of rotating vortex chain formation. A physical model is proposed which considers a two dimensionally varying concentration profile in the depletion region to account for the formation of multiple vortices rotating in the same direction. The fast rotating primary vortex changes the local concentration in regions adjacent to it, as the advection time scale is much higher than the diffusion time scale. Near the membrane, it moves the low concentration electrolyte from the bottom wall upwards into a higher concentration region. Away from the membrane, it moves the high concentration electrolyte from the middle of the channel downwards into a low concentration region. These local changes in the wall concentration result in a varying slip velocity capable of inducing a secondary vortex. Similarly, this secondary vortex can induce a tertiary one. A numerical simulation is performed using the proposed varying slip velocity model which showed excellent agreement with the experimental observations.

  3. 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▿


    Xayarath, Bobbi; Yother, Janet


    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 ...

  4. Snakes and spin rotators

    International Nuclear Information System (INIS)

    Lee, S.Y.


    The generalized snake configuration offers advantages of either shorter total snake length and smaller orbit displacement in the compact configuration or the multi-functions in the split configuration. We found that the compact configuration can save about 10% of the total length of a snake. On other hand, the spilt snake configuration can be used both as a snake and as a spin rotator for the helicity state. Using the orbit compensation dipoles, the spilt snake configuration can be located at any distance on both sides of the interaction point of a collider provided that there is no net dipole rotation between two halves of the snake. The generalized configuration is then applied to the partial snake excitation. Simple formula have been obtained to understand the behavior of the partial snake. Similar principle can also be applied to the spin rotators. We also estimate the possible snake imperfections are due to various construction errors of the dipole magnets. Accuracy of field error of better than 10 -4 will be significant. 2 refs., 5 figs

  5. Medications and Side Effects (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 ...


    NARCIS (Netherlands)


    New observations of H I rotation curves at the Very Large Array have uncovered two galaxies with rotation curves declining between 1 and 3 optical radii. The velocity decrease is large, more than 50 km s-1 (approximately 25% of the maximum rotation velocity), and is present on both sides of the

  7. Sympathetic chain Schwannoma

    International Nuclear Information System (INIS)

    Al-Mashat, Faisal M.


    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)

  8. Rotational scanography

    International Nuclear Information System (INIS)

    Moore, R.; Amplatz, K.


    With rotational scanography contrast and resolution of X-ray images are improved. The technique bases on the principle of a narrow X-ray passing along an object, thus exposing the whole film. The X-ray is limited by a primary shield next to the X-ray tube. A second shield between object and film prevents that scattered rays spoil the film. The X-ray tube is turned around a horizontal axis, whilst the shield is shifted so that the irradiation intensity remains constant and the smallest projected focal size is obtained. This technique permits to enlarge the X-ray images by 3 or 6 times its size. Thus, films up to a length of 96 cm can be exposed. Main advantages of rotary scanography are reduced exposure to radiation of patient and applicant, improved contrast and resolution of the X-ray image, and a larger play of exposure for the X-ray technique. Disadvantages are a longer exposure time and the consequently increased demands on X-ray generator and treatment head. When a multi-slit shield is used, the patient must be cooperative in order to prevent movement artifacts. This imaging technique is highly sensitive to artifacts, particularly if the tube voltage provides large fluctuations. Supplementary units are necessary. The significance of the rotational scanography is that it permits the reduction of the radiation dose, whilst contrast and resolution of the images are improved. This can be illustrated by X-ray images of a CT-phantom and of pelvic, hand and gastrointenstinal phantoms. (orig./MG) [de

  9. Glenohumeral internal rotation deficit in table tennis players. (United States)

    Kamonseki, Danilo Harudy; Cedin, Luísa; Habechian, Fernanda Assis Paes; Piccolomo, Guigliano Franco; Camargo, Paula Rezende


    Table tennis requires rapid and extreme movements that may result in shoulder adaptations, such as glenohumeral internal rotation deficit, which is a risk factor for several injuries. This study compared range of motion of internal and external rotation and total rotation motion of glenohumeral joint between dominant and non-dominant shoulders of table tennis players. This is a cross-sectional observational study. Twenty healthy male table tennis players that were enrolled in an official table tennis league took part in this study (mean age: 22.9 ± 12.9 years, time of sports practice: 6.2 ± 7.12 years). Measurements of passive glenohumeral external rotation and internal rotation were taken with the individuals in the supine and sidelying positions. Total rotation motion was calculated by summing external and internal rotations. The dominant side showed decreased internal rotation when compared to non-dominant side in both supine (mean difference: 14.9°, p = 0.02) and sidelying positions (mean difference: 16.3°, p = 0.01). No significant difference (p > 0.05) was found for external rotation and total rotation motion between dominant and non-dominant shoulders. The findings indicate that table tennis players exhibit glenohumeral internal rotation deficit of dominant shoulder.

  10. Heavy Chain Diseases (United States)

    ... heavy chain produced: Alpha Gamma Mu Alpha Heavy Chain Disease Alpha heavy chain disease (IgA heavy chain ... disease or lead to a remission. Gamma Heavy Chain Disease Gamma heavy chain disease (IgG heavy chain ...

  11. Quaternary ammonium room-temperature ionic liquid including an oxygen atom in side chain/lithium salt binary electrolytes: ionic conductivity and 1H, 7Li, and 19F NMR studies on diffusion coefficients and local motions. (United States)

    Hayamizu, Kikuko; Tsuzuki, Seiji; Seki, Shiro; Ohno, Yasutaka; Miyashiro, Hajime; Kobayashi, Yo


    A room-temperature ionic liquid (RTIL) of a quaternary ammonium cation having an ether chain, N,N-diethyl-N-methyl-N-(2-methoxyethyl)ammonium bis(trifluoromethylsulfonyl)amide (DEME-TFSA), is a candidate for use as an electrolyte of lithium secondary batteries. In this study, the electrochemical ionic conductivity, sigma, of the neat DEME-TFSA and DEME-TFSA-Li doped with five different concentrations of lithium salt (LiTFSA) was measured and correlated with NMR measurements of the diffusion coefficients D and the spin-lattice relaxation times T1 of the individual components DEME (1H), TFSA (19F), and lithium ion (7Li). The ion conduction of charged ions can be activated with less thermal energy than ion diffusion which contains a contribution from paired ions in DEME-TFSA. In the doped DEME-TFSA-Li samples, the sigma and D values decreased with increasing salt concentration, and within the same sample generally DLisalt concentration at low temperatures. Since plots of the temperature dependence of T1 of the 1H and 7Li resonances showed T1 minima, the correlation times tauc(H) and tauc(Li) were calculated for reorientational motions of DEME and the lithium jump, respectively. At the same temperature, tauc(Li) is longer than tauc(H), suggesting that the molecular motion of DEME occurs more rapidly than the lithium jump. Combining the DLi and tauc(Li), averaged distances for the lithium jump were estimated.

  12. Side Effects (Management) (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 ...

  13. Markov chains

    CERN Document Server

    Revuz, D


    This is the revised and augmented edition of a now classic book which is an introduction to sub-Markovian kernels on general measurable spaces and their associated homogeneous Markov chains. The first part, an expository text on the foundations of the subject, is intended for post-graduate students. A study of potential theory, the basic classification of chains according to their asymptotic behaviour and the celebrated Chacon-Ornstein theorem are examined in detail. The second part of the book is at a more advanced level and includes a treatment of random walks on general locally compact abelian groups. Further chapters develop renewal theory, an introduction to Martin boundary and the study of chains recurrent in the Harris sense. Finally, the last chapter deals with the construction of chains starting from a kernel satisfying some kind of maximum principle.

  14. The Simulation of DFIG Grid Side Converter

    Directory of Open Access Journals (Sweden)

    LU Yan-Ling


    Full Text Available Firstly,DFIG basic structure of grid side converter was analyzed according to basic principles of voltage converter, and a mathematical model of grid side converter was established in the three-phase stationary coordinate system and the two-phase rotating coordinate system respectively. Then use the grid voltage oriented vector control strategy based On dq coordinate model of the grid side converter and its essential principles and realization scheme were introduced. Finally,SVPWM,Park,control systems and other power electronics model were built in matlab/simulink,converter was simulated based On vector control strategy under rectifier state and inverter state respectively. The simulation results show that the control strategy has a good dynamic response,and by choosing the appropriate inductance,capacitance,the network side current will reach stable state quickly with smooth waveform and small harmonic,while the DC voltage will reach stable value quickly with small overshoot.

  15. Rotating Cavitation Supression Project (United States)

    National Aeronautics and Space Administration — FTT proposes development of a rotating cavitation (RC) suppressor for liquid rocket engine turbopump inducers. Cavitation instabilities, such as rotating cavitation,...

  16. The low-temperature inflection observed in neutron scattering measurements of proteins is due to methyl rotation: direct evidence using isotope labeling and molecular dynamics simulations. (United States)

    Wood, Kathleen; Tobias, Douglas J; Kessler, Brigitte; Gabel, Frank; Oesterhelt, Dieter; Mulder, Frans A A; Zaccai, Giuseppe; Weik, Martin


    There is increasing interest in the contribution of methyl groups to the overall dynamics measured by neutron scattering experiments of proteins. In particular an inflection observed in atomic mean square displacements measured as a function of temperature on high resolution spectrometers (approximately 1 microeV) was explained by the onset of methyl group rotations. By specifically labeling a non-methyl-containing side-chain in a native protein system, the purple membrane, and performing neutron scattering measurements, we here provide direct experimental evidence that the observed inflection is indeed due to methyl group rotations. Molecular dynamics simulations reproduce the experimental data, and their analysis suggests that the apparent transition is due to methyl group rotation entering the finite instrumental resolution of the spectrometer. Methyl group correlation times measured by solid state NMR in the purple membrane, taken from previous work, support the interpretation.

  17. CHAIN 2

    International Nuclear Information System (INIS)

    Bailey, D.


    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

  18. The effect of chain flexibility and chain mobility on radiation crosslinking reactions of polymers

    International Nuclear Information System (INIS)

    Sun Jiazhen


    Flexibility of polymer chains is an important factor to effects of radiation crosslinking of the polymer. Polymers with flexible chains are easier to be crosslinked, with lower dose of gelation, than polymers with more rigid chains. And it is known that most polymers with abnormal rigidity can be radiation-crosslinked only at high temperatures when the molecular chains get enough mobility. The flexibility of polymer chains also influences the relationship between degree of degradation and radiation dose. A chain flexibility factor β has been introduced to modify the Charlesby-Pinner equation of sol-fraction and radiation dose. The new relationship equation applies to a wider range of polymers in radiation crosslinking. Studies also show that for flexible polymers with lower T g and molecular internal rotating factor, mechanism of radiation crosslinking is mainly in H type, whereas for rigid polymers with higher T g and molecular internal rotating factor, mechanism of radiation crosslinking is mainly in T type

  19. Hardwood siding performance. (United States)

    Glenn A. Cooper


    A 6-year exposure test of three styles of siding made from nine hardwoods and given three treatments showed that full-length yellow-poplar vertical tongue-and-groove siding dip-treated in a water-repellent preservative performed best.

  20. Single-sided NMR

    CERN Document Server

    Casanova, Federico; Blümich, Bernhard


    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.

  1. The effect of problems on supply chain wide efficiency

    Directory of Open Access Journals (Sweden)

    Micheline J. Naude


    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.

  2. Rotational discontinuities and the structure of the magnetopause

    International Nuclear Information System (INIS)

    Swift, D.W.; Lee, L.C.


    Symmetric and asymmetric rotational discontinuities are studied by means of a one-dimensional computer simulation and by single-particle trajectory calculations. The numerical simulations show the symmetric rotation to be stable for both ion and electron senses of rotation with a thickness of the order of a few ion gyroradii when the rotation angle of the tangential field is 180 0 or less. Larger rotation angles tend to be unstable. In an expansive discontinuity, when the magnetic field on the downstream side of the discontinuity is larger, an expanding transition layer separating the high-field from a low-field region develops on the downstream side, and a symmetric rotational discontinuity forms at the upstream edge. The implication of these results for magnetopause structure and energy flow through the magnetopause is described

  3. HER-2 peptides p776 and F7, N-terminal-linked with Ii-Key tetramer (LRMK) help the proliferation of E75-TCR+ cells: The dependency of help on the side chains of LRMK-extended peptide pointed towards the T cell receptor. (United States)

    Li, Yufeng; Ishiyama, Satoshi; Matsueda, Satoko; Tsuda, Naotake; Ioannides, Constantin G


    The objective of this study was to determine whether peptides consisting of the Ii-Key peptide LRMK linked to the N-terminal ends of HER-2 peptides would stimulate the expansion of antigen-specific E75-TCR+CD8+ cells. The peptides tested were N-acetylated and linked to an alpha-amide at the C-terminus; some of the peptides contained epsilon-aminovaleric acid (Ava) between the LRMK and the HER-2 peptide. Of the seven LRMK-HER-2 peptides tested to date, three effectively induced IFN-gamma production by peripheral blood mononuclear cells (PBMCs) from healthy donors and women with ductal carcinoma in situ. A fusion peptide, LRMK-Ava-HER-2(777-789), was more immunogenic than the natural HER-2(777-789) antigen, G89, with regard to IFN-gamma production. In combination with the CD8-activating peptide E75 [HER-2(369-377)] LRMK-p776 and LRMK-Ava-F7 induced the proliferation of E75-TCR(Med+Hi) CD8+ cells to a greater extent than did 1,000 or 5,000 nM of E75 alone, respectively. The induction effects were strongest at 600 nM for LRMK-p776 and 3,000 nM for LRMK-Ava-F7. At 3,000 nM, LRMK-p776 was cytotoxic to PBMCs. LRMK-p776 and F7 had a similar specificity and preferences for binding HLA-DR molecules. The molecular modeling of HLA-DR:LRMK-p776 and HLA-DR:LRMK-Ava-F7 complexes revealed the side chains of the peptides, which pointed towards the T-cell receptor. Differences in side chain orientation introduced by various N-terminal extensions of MHC class II-bound peptides should be important for directing CD4+ cells to stimulate CD8+ cells or for eliminating regulatory T cells in cancer immunotherapy.

  4. Moving Segmentation Up the Supply-Chain: Supply Chain Segmentation and Artificial Neural Networks


    Erevelles, Sunil; Fukawa, Nobuyuki


    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...

  5. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    γ-Al2O3 catalyst, Transition metals. INTRODUCTION. Today, automobile prevails across the globe as the most popular and necessary mode of transportation in our daily lives. About 50 million cars are produced every year, and over 700.

  6. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    heptyl- isocoumarin) (1), a metabolite of natural lichens, has been described. Reaction of 3,5- dimethoxyhomophthalic anhydride (2) with octanoyl chloride in the presence of 1,1,3,3- tetramethylguanidine (TMG) and triethyl amine afforded the 6 ...

  7. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    complexes, we studied the structural changes occurring in the ligand upon complexation with. IR, NMR, and UV-visible spectroscopic techniques. EXPERIMENTAL. Potentiometric titrations. ... glass electrode and calomel electrode. The following solutions were titrated potentiometrically against standard carbonate free 0.1 M ...

  8. Propargyloxycarbonyl as a protecting group for the side chains of ...

    Indian Academy of Sciences (India)


    obtained was isolated by filtration. The crystalline solid was washed with isopropyl alcohol (25 mL × 2), ether (25 mL × 4) and dried under vacuum to get brick red crystals of ammonium tetrathiomolybdate. (13⋅4–14⋅2 g, 92%). A solution of benzyltriethylammonium chloride. (23⋅31 g, 102⋅5 mmol) in distilled water (60 mL).

  9. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    with water, dried over potassium carbonate and concentrated. The residue is distilled to give the amine 2. For mixtures of products the concentrated organic phases was distilled bulb-to-bulb into a liquid nitrogen cooled receiver and separation is made by preparative GLC (30% SE 30 on chromosorb W columns).

  10. Microwave heating in peptide side chain modification via cysteine alkylation. (United States)

    Calce, Enrica; De Luca, Stefania


    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.

  11. Propargyloxycarbonyl as a protecting group for the side chains of ...

    Indian Academy of Sciences (India)


    100–200 mesh) using a solution of ethyl acetate. (10–20%) in petroleum ether as eluent. 2.4a Boc–Ser(Poc)–OMe, 4a: Colourless oil;. Yield: 90%; [α]D: +34 (c = 1, MeOH); FTIR (Neat):. 3289 (br), 2130 (w), 1754 (s), 1713 (s); δH. (300 MHz, CDCl3): 5⋅39 (bd, J = 7⋅8 Hz, 1H), 4⋅73. (d, J = 1⋅8 Hz, 2H), 4⋅52–4⋅60 (m, 2H), ...

  12. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    allow the modification of the organic substituent R to manipulate the biodistribution of the radiopharmaceutical. In addition ... spectra were all obtained in acetonitrile, and data are given as λmax/nm with extinction coefficients (in units .... To a volume of 25 cm3 of ethanol was added a mass of 89 mg (94 µmol) of complex 2 ...

  13. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    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 ...

  14. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    between 8 and 8.5) to. 6.1. KEY WORDS: ... INTRODUCTION. In the last three decades the CysF9[93]β sulfhydryl group of haemoglobin has been employed as ... Male guinea pigs were purchased from the local market at Ibadan. Haemoglobin was ...

  15. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    dideoxyuridine (CS-. 87) are active inhibitors of HIV-1 replication, the causative agents of AIDS. We report Abinitio,. DFT results of two AZT conformers; A-AZT and CS-87 by different basis sets and on structural and electronic properties. It is shown ...

  16. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    ornamental minerals analysed for minor and trace elements with the neutron activation analysis technique are discussed. The samples of interest were the Biriniwa tin pyrite, which the local indigenous used to paint their huts and the ornamental lead ...

  17. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    to those of paraoxon which is the dominant intermediate oxidative product of parathion. Earlier studies [2] showed that interaction of organophosphate pesticides with soils depend on the soil type. Metal ion catalysis for the hydrolysis of organophosphates has been the subject of previous. ______. *Corresponding author.

  18. 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, ...

  19. Pendant triazole ring assisted mesogen containing side chain liquid ...

    Indian Academy of Sciences (India)

    grammer. Samples were made by placing small quantity of materials between two thin glass cover slips, and the anisotropic behaviour observed by heating and/or cooling at the rates of 5°C/min. The photographs were taken with a Nikon FM10 camera and exposed on a Konica film. 3. Results and discussion. 3.1 Synthesis.

  20. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    Cu couple;. Simmons-Smith reaction. INTRODUCTION. Considerable information is available on the synthesis of various kinds of cyclopropanes via carbene [1-4] or carbenoid [5-8] addition to olefins. However, only a few of these studies report.

  1. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    pyridylazo)-5-diethylaminophenol (5-Br-PADAP) as an analytical reagent. The sorption is quantitative in the pH range 7.0-9.5, whereas quantitative desorption occurs instantaneously with. 2 M HCl and selected trace elements have been determined using flame atomic absorption spectrometry. The linearity is maintained ...

  2. Pendant triazole ring assisted mesogen containing side chain liquid ...

    Indian Academy of Sciences (India)

    Two series of click chemistry assisted alkoxymethyl-1H-[1,2,3]-triazol-1-yl containing sidechain liquid-crystalline polymethacrylates were synthesized by free radical polymerization technique. Mesogen was linked to backbone through various spacer units. Monomers and polymers were characterized by FT-IR, 1H and ...

  3. Functional photochromic methylhydrosiloxane-based side chain liquid crystalline polymers

    Czech Academy of Sciences Publication Activity Database

    Tóth-Katona, T.; Cigl, Martin; Fodor-Csorba, K.; Hamplová, Věra; Jánossy, I.; Kašpar, Miroslav; Vojtylová, Terézia; Hampl, F.; Bubnov, Alexej


    Roč. 215, č. 8 (2014), s. 742-752 ISSN 1022-1352 R&D Projects: GA ČR GA13-14133S; GA MŠk 7AMB13PL038 Grant - others:AVČR(CZ) M100101204 Institutional support: RVO:68378271 Keywords : azo-polymers * nematics * polysiloxanes * self-assembly Subject RIV: JJ - Other Materials Impact factor: 2.616, year: 2014

  4. Novel Polymers Containing Metal Ligands in the Side Chain (United States)


    great promise. In addition, interest in magnetic materials for giant- magnetoresistance devices, magnetic sensors, and more are highly sought after. (a...nanoparticles within the phase-separated domains were responsible for the RTF properties of the nanostructured BCPs. Monomer Synthesis. The same strained

  5. new polythiophenes with oligo(oxyethylene) side chains

    African Journals Online (AJOL)


    Color. H2L (C10H12N2O3). 57.55 (57.68) 5.79 (5.81) 13.46 (13.45). 89. 199 White. A [{Cu(HL)(H2O)}2].2BF4. 31.92 (31.98) 3.42 (3.49) 7.42 (7.46). 69. -. Green. B [{Cu(L)}2].5/2H2O. 44.54 (44.53) 3.75 (3.74) 10.36 (10.38) ... a Td symmetry for the BF4. - anion which plays a counter ion role. The bands of moderate intensity ...

  6. One-electron oxidation of 2-(4-methoxyphenyl)-2-methylpropanoic and 1-(4-methoxyphenyl)cyclopropanecarboxylic acids in aqueous solution. the involvement of radical cations and the influence of structural effects and pH on the side-chain fragmentation reactivity. (United States)

    Bietti, Massimo; Capone, Alberto


    A product and time-resolved kinetic study on the one-electron oxidation of 2-(4-methoxyphenyl)-2-methylpropanoic acid (2), 1-(4-methoxyphenyl)cyclopropanecarboxylic acid (3), and of the corresponding methyl esters (substrates 4 and 5, respectively) has been carried out in aqueous solution. With 2, no direct evidence for the formation of an intermediate radical cation 2*+ but only of the decarboxylated 4-methoxycumyl radical has been obtained, indicating either that 2*+ is not formed or that its decarboxylation is too fast to allow detection under the experimental conditions employed (k > 1 x 10(7) s(-1)). With 3, oxidation leads to the formation of the corresponding radical cation 3*+ or radical zwitterion -3*+ depending on pH. At pH 1.0 and 6.7, 3*+ and -3*+ have been observed to undergo decarboxylation as the exclusive side-chain fragmentation pathway with rate constants k = 4.6 x 10(3) and 2.3 x 10(4) s(-1), respectively. With methyl esters 4 and 5, direct evidence for the formation of the corresponding radical cations 4*+ and 5*+ has been obtained. Both radical cations have been observed to display a very low reactivity and an upper limit for their decay rate constants has been determined as k or=10, with the latter process that becomes the major fragmentation pathway around pH 12.

  7. Photoorientation of a liquid crystalline polyester with azobenzene side groups

    DEFF Research Database (Denmark)

    Zebger, I; Rutloh, M; Hoffmann, U


    The photoorientation process in a polyester with 4-cyano-4'-alkoxyazobenzene side group and long methylene spacers in the side and the main-chain was studied as a function of irradiation with linearly polarized light of 488 nm under systematic variation of the power density and temperature....... This model polymer is characterized by liquid crystallinity (g 24 S-X 26 S-A 34 n 47 i) and a strong aggregation tendency. The photoorientation is cooperative, i.e., the orientation of the photochromic side group induces the alignment of the ester unit (which is a part of the main-chain) and both methylene...... 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...

  8. Side Effects: Appetite Loss (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.

  9. Side Effects: Fatigue (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.

  10. Side Effects: Sleep Problems (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.

  11. Side Effects: Pain (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.

  12. Side Effects: Diarrhea (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.

  13. Side Effects: Anemia (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.

  14. On Averaging Rotations

    DEFF Research Database (Denmark)

    Gramkow, Claus


    In this article two common approaches to averaging rotations are compared to a more advanced approach based on a Riemannian metric. Very offten the barycenter of the quaternions or matrices that represent the rotations are used as an estimate of the mean. These methods neglect that rotations belong...... approximations to the Riemannian metric, and that the subsequent corrections are inherient in the least squares estimation. Keywords: averaging rotations, Riemannian metric, matrix, quaternion...

  15. Parameterization of rotational spectra

    International Nuclear Information System (INIS)

    Zhou Chunmei; Liu Tong


    The rotational spectra of the strongly deformed nuclei with low rotational frequencies and weak band mixture are analyzed. The strongly deformed nuclei are commonly encountered in the rare-earth region (e. g., 150 220). A lot of rotational band knowledge are presented

  16. [Psychoanalysis and Side Effect]. (United States)

    Shirahase, Joichiro


    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

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

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Across the world, in search of greater value, businesses have moved their operations online, resulting in an ... wherein buyers and sellers transact goods, services and information using an electronic trad- ing platform. .... ponent suppliers, OEMs and logistics service providers in different geographical locations, interacting ...

  18. Microseismic sources of rotational type (United States)

    Pasternak, Elena; Dyskin, Arcady; He, Junxian


    Traditionally the sources of seismic and microseismic events are related to shear fractures. The analysis of the seismic moment tensors of the sources associated with rock fracturing and hydraulic fracturing in the laboratory experiments and in-situ reveals that while there exist tensile and compressive sources, the shear sources prevail. The appearance of multiple shear sources, accompanied rock fracturing contradicts the results of the direct experiments suggesting that the rock as well as other materials not exhibiting clear plastic flow fail in tension. This contradiction is conventionally resolved by assuming the presence of multiple pre-existing shear fractures (faults or microfaults) whose sudden sliding provides microseismic events of shear type. We consider alternative mechanisms associated with bending of links between rotating particles and fragments of geomaterial and bending of bridges connecting opposite sides of hydraulic fractures. In both cases the fracturing is caused by the action of moments (or moment stresses) leading to bending, while at microscale the failure is associated with tensile microstresses leading to formation of tensile microcracks. In other words, at microscale the moment-related failure is failure in tension, as routinely observed in materials even in compression. It is easy to demonstrate that from a distance the sources of rotational type are equivalent to a standard double couple, similar to the one associated with shear fracturing. In other words what is currently interpreted as shear microseismic sources can in fact be rotational sources. This calls for new methods of detecting and interpreting microseismic sources; some possible methods are discussed.

  19. Rotating Stars in Relativity

    Directory of Open Access Journals (Sweden)

    Stergioulas Nikolaos


    Full Text Available Rotating relativistic stars have been studied extensively in recent years, both theoretically and observationally, because of the information they might yield about the equation of state of matter at extremely high densities and because they are considered to be promising sources of gravitational waves. The latest theoretical understanding of rotating stars in relativity is reviewed in this updated article. The sections on the equilibrium properties and on the nonaxisymmetric instabilities in f-modes and r-modes have been updated and several new sections have been added on analytic solutions for the exterior spacetime, rotating stars in LMXBs, rotating strange stars, and on rotating stars in numerical relativity.

  20. Visualizing molecular unidirectional rotation (United States)

    Lin, Kang; Song, Qiying; Gong, Xiaochun; Ji, Qinying; Pan, Haifeng; Ding, Jingxin; Zeng, Heping; Wu, Jian


    We directly visualize the spatiotemporal evolution of a unidirectional rotating molecular rotational wave packet. Excited by two time-delayed polarization-skewed ultrashort laser pulses, the cigar- or disk-shaped rotational wave packet is impulsively kicked to unidirectionally rotate as a quantum rotor which afterwards disperses and exhibits field-free revivals. The rich dynamics can be coherently controlled by varying the timing or polarization of the excitation laser pulses. The numerical simulations very well reproduce the experimental observations and intuitively revivify the thoroughgoing evolution of the molecular rotational wave packet of unidirectional spin.

  1. EBR-II rotating plug seal maintenance

    International Nuclear Information System (INIS)

    Allen, K.J.


    The EBR-II rotating plug seals require frequent cleaning and maintenance to keep the plugs from sticking during fuel handling. Time consuming cleaning on the cover gas and air sides of the dip ring seal is required to remove oxidation and sodium reaction products that accumulate and stop plug rotation. Despite severely limited access, effective seal cleaning techniques have removed 11 800 lb (5 352 kg) of deposits from the seals since 1964. Temperature control modifications and repairs have also required major maintenance work. Suggested seal design recommendations could significantly reduce maintenance on future similar seals

  2. Controlled sample orientation and rotation in an acoustic levitator (United States)

    Barmatz, Martin B. (Inventor); Gaspar, Mark S. (Inventor); Trinh, Eugene H. (Inventor)


    A system is described for use with acoustic levitators, which can prevent rotation of a levitated object or control its orientation and/or rotation. The acoustic field is made nonsymmetrical about the axis of the levitator, to produce an orienting torque that resists sample rotation. In one system, a perturbating reflector is located on one side of the axis of the levitator, at a location near the levitated object. In another system, the main reflector surface towards which incoming acoustic waves are directed is nonsymmetrically curved about the axis of the levitator. The levitated object can be reoriented or rotated in a controlled manner by repositioning the reflector producing the nonsymmetry.

  3. Regulation by retinoids of luteinizing hormone/chorionic gonadotropin receptor, cholesterol side-chain cleavage cytochrome P-450, 3 beta-hydroxysteroid dehydrogenase/delta (5-4)-isomerase and 17 alpha-hydroxylase/C17-20 lyase cytochrome P-450 messenger ribonucleic acid levels in the K9 mouse Leydig cell line. (United States)

    Lefèvre, A; Rogier, E; Astraudo, C; Duquenne, C; Finaz, C


    Vitamin A is a potent regulator of testicular function. We have reported that retinol (R) and retinoic acid (RA) induced a down regulation of luteinizing hormone/human chorionic gonadotropin (LH/CG) binding sites in K9 Leydig cells. In the present study we evaluated the effect of R and RA on LH/CG receptors, cholesterol side-chain cleavage cytochrome P-450 (P-450 scc), 17 alpha-hydroxylase/C17-20 lyase (P-450 17 alpha) and 3 beta-hydroxysteroid dehydrogenase (3 beta HSD) mRNA levels in K9 mouse Leydig cells. To validate K9 cells as a model for studying Leydig cell steroidogenesis at the molecular level, we first investigated the effect of hCG on mRNA levels of the steroidogenic enzymes. P-450 scc, 3 beta HSD and P-450 17 alpha were expressed constitutively. The addition of 10 ng/ml hCG enhanced mRNA levels for the three genes within 2 h. Maximal accumulation of P-450 scc, P-450 17 alpha and 3 beta HSD mRNA in treated cells represents a 2.5-, 8.5- and 4-fold increase over control values, respectively. P-450 17 alpha expression reached a maximum by 4 h and then declined rapidly to return to control value by 24 h. The pattern of LH/CG receptor mRNAs in K9 cells was very similar to that of MA10 Leydig cells and showed six transcripts of 1.1, 1.6, 1.9, 2.6, 4.2 and 7.0 kb. Treatment of cells with R or RA resulted in a time- and dose-dependent decrease in all six species.(ABSTRACT TRUNCATED AT 250 WORDS)

  4. ¹H, ¹³C, ¹⁵N backbone and side chain NMR resonance assignments of the N-terminal NEAr iron transporter domain 1 (NEAT 1) of the hemoglobin receptor IsdB of Staphylococcus aureus. (United States)

    Fonner, Brittany A; Tripet, Brian P; Lui, Mengyao; Zhu, Hui; Lei, Benfang; Copié, Valérie


    Staphylococcus aureus is an opportunistic pathogen that causes skin and severe infections in mammals. Critical to S. aureus growth is its ability to scavenge iron from host cells. To this effect, S. aureus has evolved a sophisticated pathway to acquire heme from hemoglobin (Hb) as a preferred iron source. The pathway is comprised of nine iron-regulated surface determinant (Isd) proteins involved in heme capture, transport, and degradation. A key protein of the heme acquisition pathway is the surface-anchored hemoglobin receptor protein IsdB, which is comprised of two NEAr transporter (NEAT) domains that act in concert to bind Hb and extract heme for subsequent transfer to downstream acquisition pathway proteins. Despite significant advances in the structural knowledge of other Isd proteins, the structural mechanisms and molecular basis of the IsdB-mediated heme acquisition process are not well understood. In order to provide more insights into the mode of function of IsdB, we have initiated NMR structural studies of the first NEAT domain of IsdB (IsdB(N1)). Herein, we report the near complete (1)H, (13)C and (15)N resonance assignments of backbone and side chain atoms, and the secondary structural topology of the 148-residue IsdB NEAT 1 domain. The NMR results are consistent with the presence of eight β-strands and one α-helix characteristic of an immunoglobulin-like fold observed in other NEAT domain family proteins. This work provides a solid framework to obtain atomic-level insights toward understanding how IsdB mediates IsdB-Hb protein-protein interactions critical for heme capture and transfer.

  5. Four Sided Seal Tester (United States)


    The Center for Advanced Food Technology School of Enviromental and Biological Sciences New Brunswick, NJ 08903 FTR 216 Defense Logistics Agency...specification for four sided seal tester as function of confinement plate distance” The following modifications were issued :  Jul 18, 2007 0013/01

  6. Forskningens personlige side

    DEFF Research Database (Denmark)

    Hansen, Finn Thorbjørn


    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...

  7. Supply chain reaction

    International Nuclear Information System (INIS)

    Snieckus, Darius


    '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

  8. Humanitarian relief supply chain

    Indian Academy of Sciences (India)

    This paper models a humanitarian relief chain that includes a relief goods supply chain and an evacuation chain in case of a natural disaster. Optimum network flow is studied for both the chains by considering three conflicting objectives, namely demand satisfaction in relief chain, demand satisfaction in evacuation chain ...

  9. Composition of Muscle Fiber Types in Rat Rotator Cuff Muscles. (United States)

    Rui, Yongjun; Pan, Feng; Mi, Jingyi


    The rat is a suitable model to study human rotator cuff pathology owing to the similarities in morphological anatomy structure. However, few studies have reported the composition muscle fiber types of rotator cuff muscles in the rat. In this study, the myosin heavy chain (MyHC) isoforms were stained by immunofluorescence to show the muscle fiber types composition and distribution in rotator cuff muscles of the rat. It was found that rotator cuff muscles in the rat were of mixed fiber type composition. The majority of rotator cuff fibers labeled positively for MyHCII. Moreover, the rat rotator cuff muscles contained hybrid fibers. So, compared with human rotator cuff muscles composed partly of slow-twitch fibers, the majority of fast-twitch fibers in rat rotator cuff muscles should be considered when the rat model study focus on the pathological process of rotator cuff muscles after injury. Gaining greater insight into muscle fiber types in rotator cuff muscles of the rat may contribute to elucidate the mechanism of pathological change in rotator cuff muscles-related diseases. Anat Rec, 299:1397-1401, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  10. Rotations with Rodrigues' vector

    International Nuclear Information System (INIS)

    Pina, E


    The rotational dynamics was studied from the point of view of Rodrigues' vector. This vector is defined here by its connection with other forms of parametrization of the rotation matrix. The rotation matrix was expressed in terms of this vector. The angular velocity was computed using the components of Rodrigues' vector as coordinates. It appears to be a fundamental matrix that is used to express the components of the angular velocity, the rotation matrix and the angular momentum vector. The Hamiltonian formalism of rotational dynamics in terms of this vector uses the same matrix. The quantization of the rotational dynamics is performed with simple rules if one uses Rodrigues' vector and similar formal expressions for the quantum operators that mimic the Hamiltonian classical dynamics.

  11. Optimizing Circular Side-Resonators to Reduce Computer Fan Noise

    NARCIS (Netherlands)

    Nijhof, M.J.J.; Beltman, W.M.


    One of the main noise sources in computers are the cooling fans. Tonal noise at the rotational frequency of the fan, the blade passing frequency (BPF) and its higher harmonics are important in fan noise. So called 'side-resonators' integrated in the duct of an in-duct axial fan cause an impedance

  12. Chain reaction

    International Nuclear Information System (INIS)

    Balogh, Brian.


    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)

  13. 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...... – years where parts of the U.S. Army and intelligence community set up a rampant torture regime all across the world. Yet, the connection between a so-called “dark side,” “working” this “dark side,” and the torture that followed is not a given, but, instead, a consequence of a set of very specific legal......, political, and personal choices in the early years after 9/11. This dissertation is an investigation into how the notion of a “dark side” took form, and of how and why the specific make-up of this“dark side” ended up creating a torture regime which already today seems almost unreal. The dissertation's first...

  14. Controlling inertial focussing using rotational motion. (United States)

    Prohm, Christopher; Zöller, Nikolas; Stark, Holger


    In inertial microfluidics lift forces cause a particle to migrate across streamlines to specific positions in the cross section of a microchannel. We control the rotational motion of a particle and demonstrate that this allows to manipulate the lift-force profile and thereby the particle's equilibrium positions. We perform two-dimensional simulation studies using the method of multi-particle collision dynamics. Particles with unconstrained rotational motion occupy stable equilibrium positions in both halfs of the channel while the center is unstable. When an external torque is applied to the particle, two equilibrium positions annihilate by passing a saddle-node bifurcation and only one stable fixpoint remains so that all particles move to one side of the channel. In contrast, non-rotating particles accumulate in the center and are pushed into one half of the channel when the angular velocity is fixed to a non-zero value.

  15. The spatial rotator

    DEFF Research Database (Denmark)

    Rasmusson, Allan; Hahn, Ute; Larsen, Jytte Overgaard


    This paper presents a new local volume estimator, the spatial rotator, which is based on measurements on a virtual 3D probe, using computer assisted microscopy. The basic design of the probe builds upon the rotator principle which requires only a few manual intersection markings, thus making...

  16. Units of rotational information (United States)

    Yang, Yuxiang; Chiribella, Giulio; Hu, Qinheping


    Entanglement in angular momentum degrees of freedom is a precious resource for quantum metrology and control. Here we study the conversions of this resource, focusing on Bell pairs of spin-J particles, where one particle is used to probe unknown rotations and the other particle is used as reference. When a large number of pairs are given, we show that every rotated spin-J Bell state can be reversibly converted into an equivalent number of rotated spin one-half Bell states, at a rate determined by the quantum Fisher information. This result provides the foundation for the definition of an elementary unit of information about rotations in space, which we call the Cartesian refbit. In the finite copy scenario, we design machines that approximately break down Bell states of higher spins into Cartesian refbits, as well as machines that approximately implement the inverse process. In addition, we establish a quantitative link between the conversion of Bell states and the simulation of unitary gates, showing that the fidelity of probabilistic state conversion provides upper and lower bounds on the fidelity of deterministic gate simulation. The result holds not only for rotation gates, but also to all sets of gates that form finite-dimensional representations of compact groups. For rotation gates, we show how rotations on a system of given spin can simulate rotations on a system of different spin.

  17. Deconstructing Mental Rotation

    DEFF Research Database (Denmark)

    Larsen, Axel


    A random walk model of the classical mental rotation task is explored in two experiments. By assuming that a mental rotation is repeated until sufficient evidence for a match/mismatch is obtained, the model accounts for the approximately linearly increasing reaction times (RTs) on positive trials...

  18. Einstein -coefficients for rotational transitions in the ring-chain ...

    Indian Academy of Sciences (India)

    1994). [5] S Chandra and Rashmi, Astron. Astrophys. Suppl. 131, 137 (1998). [6] S Chandra, D A Varshalovich and W H Kegel, Pramana - J. Phys. 25, 557 (1995). [7] S Chandra, Indian J. Phys. 76В, 649 (2002). Pramana - J. Phys., Vol. 62, No.

  19. The rotating universe

    International Nuclear Information System (INIS)

    Ruben, G.; Treder, H.J.


    For a long time the question whether the universe rotates or not is discussed. Aspects of Huygens, Newton, Mach and other important historical scientists in this field are reported. The investigations of the mathematician Kurt Groedel in order to prove the rotation of the universe are illustrated. Kurt Groedel has shown that Einstein's gravitational equations of general relativity theory and the cosmological postulate of global homogeneity of cosmic matter (that is the Copernical principle) are not contradictionary to a rotating universe. Abberation measurements, position determination by means of radiointerferometry and methods for the determination of the rotation of the universe from the isotropy of the background radiation are presented. From these experiments it can be concluded that the universe seems not to rotate as already Einstein expected

  20. Rotation sensor switch

    International Nuclear Information System (INIS)

    Sevec, J.B.


    A protective device to provide a warning if a piece of rotating machinery slows or stops is comprised of a pair of hinged weights disposed to rotate on a rotating shaft of the equipment. When the equipment is rotating, the weights remain in a plane essentially perpendicular to the shaft and constitute part of an electrical circuit that is open. When the shaft slows or stops, the weights are attracted to a pair of concentric electrically conducting disks disposed in a plane perpendicular to the shaft and parallel to the plane of the weights when rotating. A disk magnet attracts the weights to the electrically conducting plates and maintains the electrical contact at the plates to complete an electrical circuit that can then provide an alarm signal

  1. Rotating stars in relativity. (United States)

    Paschalidis, Vasileios; Stergioulas, Nikolaos


    Rotating relativistic stars have been studied extensively in recent years, both theoretically and observationally, because of the information they might yield about the equation of state of matter at extremely high densities and because they are considered to be promising sources of gravitational waves. The latest theoretical understanding of rotating stars in relativity is reviewed in this updated article. The sections on equilibrium properties and on nonaxisymmetric oscillations and instabilities in f -modes and r -modes have been updated. Several new sections have been added on equilibria in modified theories of gravity, approximate universal relationships, the one-arm spiral instability, on analytic solutions for the exterior spacetime, rotating stars in LMXBs, rotating strange stars, and on rotating stars in numerical relativity including both hydrodynamic and magnetohydrodynamic studies of these objects.

  2. Tuning the NLO properties of polymethineimine chains by chemical substitution

    International Nuclear Information System (INIS)

    Medved’, Miroslav; Jacquemin, Denis


    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

  3. Broadcasting with side information


    Alon, Noga; Hasidim, Avinatan; Lubetzky, Eyal; Stav, Uri; Weinstein, Amit


    A sender holds a word x consisting of n blocks x_i, each of t bits, and wishes to broadcast a codeword to m receivers, R_1,...,R_m. Each receiver R_i is interested in one block, and has prior side information consisting of some subset of the other blocks. Let \\beta_t be the minimum number of bits that has to be transmitted when each block is of length t, and let \\beta be the limit \\beta = \\lim_{t \\to \\infty} \\beta_t/t. In words, \\beta is the average communication cost per bit in each block (f...

  4. Midplane Faraday Rotation: A densitometer for BPX

    International Nuclear Information System (INIS)

    Jobes, F.C.; Mansfield, D.K.


    The density in a high field, high density tokamak such as BPX can be determined by measuring the Faraday rotation of a 10.6 μm laser directed tangent to the toroidal field. If there is a horizontal array of such beams, then n e (R) can be readily obtained with a simple Abel version about the center line of the tokamak. For BPX operated at full field and density, the rotation angle would be quite large -- about 75 degrees per pass. A layout in which a single laser beam is fanned out in the horizontal midplane of the tokamak, with a set of retroreflectors on the far side of the vacuum vessel, would provide good spatial resolution, depending only upon the number of reflectors. With this proposed layout, only one window would be needed. Because the rotation angle is never more than 1 ''fringe,'' the data is always good, and it is also a continuous measurement in time. Faraday rotation is dependent only upon the plasma itself, and thus is not sensitive to vibration of the optical components. Simulations of the expected results show that BPX would be well served even at low densities by a Midplane Faraday Rotation densitometer of ∼64 channels. Both TFTR and PBX-M would be suitable test beds for the BPX system

  5. Rotatable seal assembly. [Patent application; rotating targets (United States)

    Logan, C.M.; Garibaldi, J.L.


    An assembly is provided for rotatably supporting a rotor on a stator so that vacuum chambers in the rotor and stator remain in communication while the chambers are sealed from ambient air, which enables the use of a ball bearing or the like to support most of the weight of the rotor. The apparatus includes a seal device mounted on the rotor to rotate therewith, but shiftable in position on the rotor while being sealed to the rotor as by an O-ring. The seal device has a flat face that is biased towards a flat face on the stator, and pressurized air is pumped between the faces to prevent contact between them while spacing them a small distance apart to avoid the inflow of large amounts of air between the faces and into the vacuum chambers.

  6. A rotating quantum vacuum

    Energy Technology Data Exchange (ETDEWEB)

    Lorenci, V.A. de; Svaiter, N.F. [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil)


    It was investigated which mapping has to be used to compare measurements made in a rotating frame to those made in an inertial frame. Using a non-Galilean coordinate transformation, the creation-annihilation operators of a massive scalar field in the rotating frame are not the same as those of an inertial observer. This leads to a new vacuum state(a rotating vacuum) which is a superposition of positive and negative frequency Minkowski particles. Polarization effects in circular accelerators in the proper frame of the electron making a connection with the inertial frame point of view were analysed. 65 refs.

  7. Basic tests of a rotation seismograph; Kaiten jishinkei no kaihatsu

    Energy Technology Data Exchange (ETDEWEB)

    Matsubayashi, H.; Kawamura, S.; Watanabe, F.; Hirai, Y.; Kasahara, K. [Nippon Geophysical Prospecting Co. Ltd., Tokyo (Japan)


    For the purpose of developing a rotational seismograph capable of measuring the rotational component of seismic waves, vibratory gyroscopes were installed in the ground for the measurement of vibration of the ground, and the measurements were compared with the values obtained from tests using conventional velocity type seismographs. In the experiment, the plank was hammered on the east side and west side. The seismographs were arranged in two ways: one wherein they were installed at 7 spots at intervals of 1m toward the south beginning at a position 3m south of the vibration source with their rotation axes oriented vertical, with velocity type seismographs provided at the same spots; and the other wherein three rotational seismographs were installed 3m south of the vibration source with their rotation axes respectively oriented vertical, in the direction of N-S, and in the direction of E-W, with a velocity type seismograph provided at the same spot. It was found as the result that the rotational seismograph has a flat band on the lower frequency side and that it may be applied to elastic wave observation across a wide band. Accordingly, it is expected that it will be applied to exploration that uses the SH wave, to structural assessment that uses the Love wave, and to collecting knowledge about the features of natural earthquakes. 2 refs., 8 figs.

  8. On Averaging Rotations

    DEFF Research Database (Denmark)

    Gramkow, Claus


    In this paper two common approaches to averaging rotations are compared to a more advanced approach based on a Riemannian metric. Very often the barycenter of the quaternions or matrices that represent the rotations are used as an estimate of the mean. These methods neglect that rotations belong...... to a non-linear manifold and re-normalization or orthogonalization must be applied to obtain proper rotations. These latter steps have been viewed as ad hoc corrections for the errors introduced by assuming a vector space. The article shows that the two approximative methods can be derived from natural...... approximations to the Riemannian metric, and that the subsequent corrections are inherent in the least squares estimation....

  9. Robot Grasps Rotating Object (United States)

    Wilcox, Brian H.; Tso, Kam S.; Litwin, Todd E.; Hayati, Samad A.; Bon, Bruce B.


    Experimental robotic system semiautomatically grasps rotating object, stops rotation, and pulls object to rest in fixture. Based on combination of advanced techniques for sensing and control, constructed to test concepts for robotic recapture of spinning artificial satellites. Potential terrestrial applications for technology developed with help of system includes tracking and grasping of industrial parts on conveyor belts, tracking of vehicles and animals, and soft grasping of moving objects in general.

  10. Rotating universe models

    International Nuclear Information System (INIS)

    Tozini, A.V.


    A review is made of some properties of the rotating Universe models. Godel's model is identified as a generalized filted model. Some properties of new solutions of the Einstein's equations, which are rotating non-stationary Universe models, are presented and analyzed. These models have the Godel's model as a particular case. Non-stationary cosmological models are found which are a generalization of the Godel's metrics in an analogous way in which Friedmann is to the Einstein's model. (L.C.) [pt

  11. Electromagnetic rotational actuation.

    Energy Technology Data Exchange (ETDEWEB)

    Hogan, Alexander Lee


    There are many applications that need a meso-scale rotational actuator. These applications have been left by the wayside because of the lack of actuation at this scale. Sandia National Laboratories has many unique fabrication technologies that could be used to create an electromagnetic actuator at this scale. There are also many designs to be explored. In this internship exploration of the designs and fabrications technologies to find an inexpensive design that can be used for prototyping the electromagnetic rotational actuator.

  12. Probiotics: Safety and Side Effects (United States)

    ... turn JavaScript on. Feature: Probiotics Safety and Side Effects Past Issues / Winter 2016 Table of Contents What the Science Says About the Safety and Side Effects of Probiotics Whether probiotics are likely to be ...

  13. HIV Medicines and Side Effects (United States)

    ... Apps skip to content Side Effects of HIV Medicines Home Understanding HIV/AIDS Fact Sheets HIV Medicines ... p.m. ET) Send us an email HIV Medicines and Side Effects Last Reviewed: October 9, 2017 ...

  14. Using demand-side management to decrease transformer ageing

    NARCIS (Netherlands)

    van der Klauw, Thijs; Gerards, Marco Egbertus Theodorus; Hurink, Johann L.


    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

  15. Running away from side effects

    DEFF Research Database (Denmark)

    Casla, S; Hojman, P; Márquez-Rodas, I


    The number of breast cancer survivors increases every year, thanks to the development of new treatments and screening techniques. However, patients present with numerous side effects that may affect their quality of life. Exercise has been demonstrated to reduce some of these side effects, but in...... of how to design exercise interventions in patients with different side effects....

  16. Side-View Face Recognition

    NARCIS (Netherlands)

    Santemiz, P.; Spreeuwers, Lieuwe Jan; Veldhuis, Raymond N.J.


    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

  17. Magnetosome chain superstructure in uncultured magnetotactic bacteria

    International Nuclear Information System (INIS)

    Abraçado, Leida G; Farina, Marcos; Abreu, Fernanda; Keim, Carolina N; Lins, Ulysses; Campos, Andrea P C


    Magnetotactic bacteria produce magnetosomes, which are magnetic particles enveloped by biological membranes, in a highly controlled mineralization process. Magnetosomes are used to navigate in magnetic fields by a phenomenon called magnetotaxis. Two levels of organization and control are recognized in magnetosomes. First, magnetotactic bacteria create a spatially distinct environment within vesicles defined by their membranes. In the vesicles, the bacteria control the size, composition and purity of the mineral content of the magnetic particles. Unique crystal morphologies are produced in magnetosomes as a consequence of this bacterial control. Second, magnetotactic bacteria organize the magnetosomes in chains within the cell body. It has been shown in a particular case that the chains are positioned within the cell body in specific locations defined by filamentous cytoskeleton elements. Here, we describe an additional level of organization of the magnetosome chains in uncultured magnetotactic cocci found in marine and freshwater sediments. Electron microscopy analysis of the magnetosome chains using a goniometer showed that the magnetic crystals in both types of bacteria are not oriented at random along the crystal chain. Instead, the magnetosomes have specific orientations relative to the other magnetosomes in the chain. Each crystal is rotated either 60°, 180° or 300° relative to their neighbors along the chain axis, causing the overlapping of the (1 1 1) and (1-bar 1-bar 1-bar) capping faces of neighboring crystals. We suggest that genetic determinants that are not present or active in bacteria with magnetosomes randomly rotated within a chain must be present in bacteria that organize magnetosomes so precisely. This particular organization may also be used as an indicative biosignature of magnetosomes in the study of magnetofossils in the cases where this symmetry is observed

  18. Vortex suppression in the wake of counter rotating cylinders (United States)

    Dewey, Peter; Smits, Alexander J.


    Digital particle image velocimetry is used to study the flow past a pair of counter rotating cylinders placed side-by-side normal to the freestream flow direction. The Reynolds numbers based on cylinder diameter is varied from 100 to 200 and gap-to-diameter ratios of 1, 3 and 5 are considered. An unsteady wake consisting of a pair of von K'arm'an vortex streets is present in the flow field when the cylinders are rotated below a critical value. Above this critical value, counter rotation of the cylinders suppresses vortex formation. The critical rotational speed varies only slightly with Reynolds number but exhibits a strong dependence on the gap-to-diameter ratio. As the gap-to-diameter ratio increases, the critical rotational speed approaches values expected to suppress vortex formation for a single rotating cylinder, indicating that the wakes of the cylinder pair have more interaction for small gap-to-diameter ratios. At sufficiently high rotational speeds the streamlines around the cylinder pair resemble a doublet potential flow. The experiments were inspired by the computations performed by Andy Chan and Antony Jameson at Stanford University.

  19. Rotating superconductor magnet for producing rotating lobed magnetic field lines (United States)

    Hilal, Sadek K.; Sampson, William B.; Leonard, Edward F.


    This invention provides a rotating superconductor magnet for producing a rotating lobed magnetic field, comprising a cryostat; a superconducting magnet in the cryostat having a collar for producing a lobed magnetic field having oppositely directed adjacent field lines; rotatable support means for selectively rotating the superconductor magnet; and means for energizing the superconductor magnet.

  20. Chains and identity

    NARCIS (Netherlands)

    Grijpink, J.H.A.M.


    This article is available in English and DutchGuidelines are presented to cope with identity problems in chains. A chain is a collaboration of a great number of autonomous organisations and professionals to tackle a dominant chain problem. In many chains identity fraud is an aspect of the dominant