WorldWideScience

Sample records for acid molecular switches

  1. Monitoring Gene Expression In Vivo with Nucleic Acid Molecular Switches

    David C. Ward; Patricia Bray-Ward

    2005-01-26

    The overall objectives of this project were (1) to develop allosteric ribozymes capable of acting as molecular switches for monitoring the levels of both wild-type and mutant mRNA species in living cells and whole animals and (2) to develop highly efficient reagents to deliver nucleic acid molecular switches into living cells, tissues and animals with the ultimate goal of expression profiling specific mRNAs of diagnostic or prognostic value within tumors in animals. During the past year, we have moved our laboratory to Nevada and in the moving process we have lost electronic and paper copies of prior progress reports concerning the construction and biological properties of the molecular switches. Since there was minimal progress during the last year on molecular switches, we are relying on past project reports to provide a summary of our data on this facet of the grant. Here we are summarizing the work done on the delivery reagents and their application to inducing mutations in living cells, which will include work done during the no cost extension.

  2. Molecular Rotors as Switches

    Kang L. Wang

    2012-08-01

    Full Text Available The use of a functional molecular unit acting as a state variable provides an attractive alternative for the next generations of nanoscale electronics. It may help overcome the limits of conventional MOSFETd due to their potential scalability, low-cost, low variability, and highly integratable characteristics as well as the capability to exploit bottom-up self-assembly processes. This bottom-up construction and the operation of nanoscale machines/devices, in which the molecular motion can be controlled to perform functions, have been studied for their functionalities. Being triggered by external stimuli such as light, electricity or chemical reagents, these devices have shown various functions including those of diodes, rectifiers, memories, resonant tunnel junctions and single settable molecular switches that can be electronically configured for logic gates. Molecule-specific electronic switching has also been reported for several of these device structures, including nanopores containing oligo(phenylene ethynylene monolayers, and planar junctions incorporating rotaxane and catenane monolayers for the construction and operation of complex molecular machines. A specific electrically driven surface mounted molecular rotor is described in detail in this review. The rotor is comprised of a monolayer of redox-active ligated copper compounds sandwiched between a gold electrode and a highly-doped P+ Si. This electrically driven sandwich-type monolayer molecular rotor device showed an on/off ratio of approximately 104, a read window of about 2.5 V, and a retention time of greater than 104 s. The rotation speed of this type of molecular rotor has been reported to be in the picosecond timescale, which provides a potential of high switching speed applications. Current-voltage spectroscopy (I-V revealed a temperature-dependent negative differential resistance (NDR associated with the device. The analysis of the device

  3. Molecular current switch

    Nešpůrek, Stanislav; Sworakowski, J.

    Brno : Faculty of Chemistry, Brno University of Technology, 2002 - (Schauer, F.), s. 89-96 ISBN 80-214-2265-3. [Seminar on Physics and Chemistry of Molecular Systems /7./. Brno (CZ), 13.12.2001] R&D Projects: GA AV ČR IAA1050901; GA ČR GA202/01/0518 Institutional research plan: CEZ:AV0Z4050913 Keywords : current switch * local states * dipolar species Subject RIV: BM - Solid Matter Physics ; Magnetism

  4. A Novel Molecular Switch

    Daber, Robert; Lewis, Mitchell

    2009-01-01

    Transcriptional regulation is a fundamental process for regulating the flux of all metabolic pathways. For the last several decades, the lac operon has served as a valuable model for studying transcription. More recently, the switch that controls the operon has also been successfully adapted to function in mammalian cells. Here we describe how, using directed evolution, we have created a novel switch that recognizes an asymmetric operator sequence. The new switch has a repressor with altered ...

  5. The Smallest Molecular Switch

    Emberly, Eldon G.; Kirczenow, George

    2003-01-01

    Ab-initio total energy calculations reveal benzene-dithiolate (BDT) molecules on a gold surface, contacted by a monoatomic gold STM tip to have two classes of low energy conformations with differing symmetries. Lateral motion of the tip or excitation of the molecule cause it to change from one conformation class to the other and to switch between a strongly and a weakly conducting state. Thus, surprisingly, despite their apparent simplicity these Au/BDT/Au nanowires are shown to be electrical...

  6. Switching in molecular systems

    Nešpůrek, Stanislav; Wang, Geng; Sworakowski, J.

    Lanškroun : IMAPS, Brno University of Technology, 2004 - (Šikula, J.), s. 215-220 ISBN 80-239-2835-X. [European Microelectronics and Packaging Symposium /3./. Prague (CZ), 16.06.2004-18.06.2004] R&D Projects: GA MŠk OC D14.30 Institutional research plan: CEZ:AV0Z4050913 Keywords : poly[3,4-(ethylenedioxy)thiophene] * electrical conductivity * charge carrier transport Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders

  7. An acidic loop and cognate phosphorylation sites define a molecular switch that modulates ubiquitin charging activity in Cdc34-like enzymes.

    Elena Papaleo

    2011-05-01

    Full Text Available E2 ubiquitin-conjugating enzymes are crucial mediators of protein ubiquitination, which strongly influence the ultimate fate of the target substrates. Recently, it has been shown that the activity of several enzymes of the ubiquitination pathway is finely tuned by phosphorylation, an ubiquitous mechanism for cellular regulation, which modulates protein conformation. In this contribution, we provide the first rationale, at the molecular level, of the regulatory mechanism mediated by casein kinase 2 (CK2 phosphorylation of E2 Cdc34-like enzymes. In particular, we identify two co-evolving signature elements in one of the larger families of E2 enzymes: an acidic insertion in β4α2 loop in the proximity of the catalytic cysteine and two conserved key serine residues within the catalytic domain, which are phosphorylated by CK2. Our investigations, using yeast Cdc34 as a model, through 2.5 µs molecular dynamics simulations and biochemical assays, define these two elements as an important phosphorylation-controlled switch that modulates opening and closing of the catalytic cleft. The mechanism relies on electrostatic repulsions between a conserved serine phosphorylated by CK2 and the acidic residues of the β4α2 loop, promoting E2 ubiquitin charging activity. Our investigation identifies a new and unexpected pivotal role for the acidic loop, providing the first evidence that this loop is crucial not only for downstream events related to ubiquitin chain assembly, but is also mandatory for the modulation of an upstream crucial step of the ubiquitin pathway: the ubiquitin charging in the E2 catalytic cleft.

  8. MNAzymes, a Versatile New Class of Nucleic Acid Enzymes That Can Function as Biosensors and Molecular Switches

    Mokany, Elisa; Bone, Simon M.; Young, Paul E; Doan, Tram B.; Todd, Alison V.

    2009-01-01

    To increase the versatility and utility of nucleic acid enzymes, we developed multicomponent complexes, known as MNAzymes, which produce amplified “output” signals in response to specific “input” signals. Multiple oligonucleotide partzymes assemble into active MNAzymes only in the presence of an input assembly facilitator such as a target nucleic acid. Once formed, MNAzymes catalytically modify a generic substrate, generating an amplified output signal that heralds the presence of the target ...

  9. Remotely Controlled Isomer Selective Molecular Switching.

    Schendel, Verena; Borca, Bogdana; Pentegov, Ivan; Michnowicz, Tomasz; Kraft, Ulrike; Klauk, Hagen; Wahl, Peter; Schlickum, Uta; Kern, Klaus

    2016-01-13

    Nonlocal addressing-the "remote control"-of molecular switches promises more efficient processing for information technology, where fast speed of switching is essential. The surface state of the (111) facets of noble metals, a confined two-dimensional electron gas, provides a medium that enables transport of signals over large distances and hence can be used to address an entire ensemble of molecules simultaneously with a single stimulus. In this study we employ this characteristic to trigger a conformational switch in anthradithiophene (ADT) molecules by injection of hot carriers from a scanning tunneling microscope (STM) tip into the surface state of Cu(111). The carriers propagate laterally and trigger the switch in molecules at distances as far as 100 nm from the tip location. The switching process is shown to be long-ranged, fully reversible, and isomer selective, discriminating between cis and trans diastereomers, enabling maximum control. PMID:26619213

  10. Self-consistent theory of molecular switching

    Pistolesi, F; Blanter, Ya. M.; Martin, I.

    2008-01-01

    International audience We study the model of a molecular switch comprised of a molecule with a soft vibrational degree of freedom coupled to metallic leads. In the presence of strong electron-ion interaction, different charge states of the molecule correspond to substantially different ionic configurations, which can lead to very slow switching between energetically close configurations (Franck-Condon blockade). Application of transport voltage, however, can drive the molecule far out of t...

  11. Light-driven molecular current switch

    Nešpůrek, Stanislav; Toman, Petr; Sworakowski, J.; Lipinski, J.

    Seoul: Yonsei University, 2002, s. 279-291. ISBN 89-88706-43-9. [Multilateral Symposium between the Korean Academy of Science and Technology and the Foreign Academies. Seoul (KR), 08.05.2002-10.05.2002] R&D Projects: GA AV ČR IAA1050901 Institutional research plan: CEZ:AV0Z4050913 Keywords : molecular switch * molecular electronics * charge transport Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders

  12. A nanoplasmonic switch based on molecular machines

    Zheng, Yue Bing

    2009-06-01

    We aim to develop a molecular-machine-driven nanoplasmonic switch for its use in future nanophotonic integrated circuits (ICs) that have applications in optical communication, information processing, biological and chemical sensing. Experimental data show that an Au nanodisk array, coated with rotaxane molecular machines, switches its localized surface plasmon resonances (LSPR) reversibly when it is exposed to chemical oxidants and reductants. Conversely, bare Au nanodisks and disks coated with mechanically inert control compounds, do not display the same switching behavior. Along with calculations based on time-dependent density functional theory (TDDFT), these observations suggest that the nanoscale movements within surface-bound "molecular machines" can be used as the active components in plasmonic devices. ©2009 IEEE.

  13. 8-Quinolineboronic acid as a potential phosphorescent molecular switch for the determination of alpha-fetoprotein variant for the prediction of primary hepatocellular carcinoma

    8-Quinolineboronic acid phosphorescent molecular switch (8-QBA-PMS) in the 'off' state emitted weak room temperature phosphorescence (RTP) of 8-QBA on the acetylcellulose membrane (ACM) with the perturbation of Pb2+. When 8-QBA-PMS was used to label concanavalin agglutinin (Con A) to form 8-QBA-PMS-Con A based on the reaction between -OH of 8-QBA-PMS and -COOH of Con A, 8-QBA-PMS turned 'on' automatically due to its structure change, and RTP of the system increased 2.7 times. Besides, -NH2 of 8-QBA-PMS-Con A could carry out affinity adsorption (AA) reaction with the -COOH of alpha-fetoprotein variant (AFP-V) to form the product Con A-AFP-V-Con A-8-QBA-PMS containing -NH-CO- bond, causing the RTP of the system to further increase. Moreover, the amount of AFP-V was linear to the ΔIp of the system in the range of 0.012-2.40 (fg spot-1). Thus, a new affinity sensitive adsorption solid substrate room temperature phosphorimetry using 8-QBA-PMS as labelling reagent (8-QBA-PMS-AASSRTP) for the determination of AFP-V was proposed with the detection limit (LD) of 9 x 10-15 g mL-1. It had been used to determine AFP-V in human serum with the results agreeing with enzyme-link immunoassay (ELISA), showing promise for the prediction of PHC due to the intimate association between AFP-V and primary hepatocellular carcinoma (PHC). The mechanism of the promethod was also discussed.

  14. Light-driven molecular current switch

    Nešpůrek, Stanislav; Toman, Petr; Sworakowski, J.; Lipinski, J.

    2002-01-01

    Roč. 2, č. 4 (2002), s. 299-304. ISSN 1567-1739. [Multilateral Symposium between the Korean Academy of Science and Technology and the Foreign Academies. Seoul, 08.05.2002-10.05.2002] R&D Projects: GA AV ČR IAA1050901 Grant ostatní: GA-(PL) 4T09A 13222 Institutional research plan: CEZ:AV0Z4050913 Keywords : molecular switch * molecular electronics * charge transport Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.117, year: 2002

  15. Active Molecular Plasmonics: Controlling Plasmon Resonances with Molecular Switches

    Zheng, Yue Bing

    2009-02-11

    A gold nanodisk array, coated with bistable, redox-controllable [2]rotaxane molecules, when exposed to chemical oxidants and reductants, undergoes switching of its plasmonic properties reversibly. By contrast, (i) bare gold nanodisks and (ii) disks coated with a redox-active, but mechanically inert, control compound do not display surface-plasmon-based switching. Along with calculations based on time-dependent density functional theory, these experimental observations suggest that the nanoscale movements within surface-bound “molecular machines” can be used as the active components in plasmonic devices.

  16. Molecular machines: stimulation of cation motion in molecular switches

    The theoretical aspects of the mechanism of the motion of cations and ligands in molecular machines referred to as redox switches are presented. The interrelated properties of cations - the energetic, electrochemical, spectral, and magnetic properties; their propensity to form either covalent or ionic bonds; and the relative softness and hardness of cations and ligands - stimulate molecular motion. These properties determine the thermal stability and stability to destruction caused by electrochemical processes and, eventually, the maximal number of transformation cycles. The maximal efficiency of redox switches is attained when the redox reaction involves a cation with a half-filled (d5, f7) or complete (d10, f14) electronic shell. The role of the Jahn-Teller effect is considered: it is responsible for geometry distortion, which stimulates cation motion. The properties of nd- and 4f-block cations are compared from the standpoint of their use for designing redox switches. In switches constructed on the basis of supramolecular compounds containing hard and soft moieties, softer cations (Fe2+, Co2+, Cu+, etc.) prefer to coordinate to soft ligands and harder cations (Fe3+, Co3+, Cu2+, etc.) prefer to coordinate to hard ligands. A cation moves due to the soft-hard change of its coordination sphere in the course of the redox reaction. Design of redox switches based on solid compounds with a cation in mixed oxidation state is shown to be promising. Cations can change their oxidation state with a change in temperature or pressure. The possibility of designing magnetic switches is considered

  17. An acidic loop and cognate phosphorylation sites define a molecular switch that modulates ubiquitin charging activity in Cdc34-like enzymes

    Papaleo, Elena; Ranzani, Valeria; Tripodi, Farida; Vitriolo, Alessandro; Cirulli, Claudia; Fantucci, Piercarlo; Alberghina, Lilia; Vanoni, Marco; De Gioia, Luca; Coccetti, Paola

    2011-01-01

    mechanism for cellular regulation, which modulates protein conformation. In this contribution, we provide the first rationale, at the molecular level, of the regulatory mechanism mediated by casein kinase 2 (CK2) phosphorylation of E2 Cdc34-like enzymes. In particular, we identify two co-evolving signature...... elements in one of the larger families of E2 enzymes: an acidic insertion in β4α2 loop in the proximity of the catalytic cysteine and two conserved key serine residues within the catalytic domain, which are phosphorylated by CK2. Our investigations, using yeast Cdc34 as a model, through 2.5 µs molecular...

  18. Determination of trace alkaline phosphatase by affinity adsorption solid substrate room temperature phosphorimetry based on wheat germ agglutinin labeled with 8-quinolineboronic acid phosphorescent molecular switch and prediction of diseases

    Liu, Jia-Ming; Gao, Hui; Li, Fei-Ming; Shi, Xiu-Mei; Lin, Chang-Qing; Lin, Li-Ping; Wang, Xin-Xing; Li, Zhi-Ming

    2010-09-01

    The 8-quinolineboronic acid phosphorescent molecular switch (abbreviated as PMS-8-QBA. Thereinto, 8-QBA is 8-quinolineboronic acid, and PMS is phosphorescent molecular switch) was found for the first time. PMS-8-QBA, which was in the "off" state, could only emit weak room temperature phosphorescence (RTP) on the acetyl cellulose membrane (ACM). However, PMS-8-QBA turned "on" automatically for its changed structure, causing that the RTP of 8-QBA in the system increased, after PMS-8-QBA-WGA (WGA is wheat germ agglutinin) was formed by reaction between -OH of PMS-8-QBA and -COOH of WGA. More interesting is that the -NH 2 of PMS-8-QBA-WGA could react with the -COOH of alkaline phosphatase (AP) to form the affinity adsorption (AA) product WGA-AP-WGA-8-QBA-PMS (containing -NH-CO- bond), which caused RTP of the system to greatly increase. Thus, affinity adsorption solid substrate room temperature phosphorimetry using PMS-8-QBA as labelling reagent (PMS-8-QBA-AA-SSRTP) for the determination of trace AP was established. The method had many advantages, such as high sensitivity (the detection limit (LD) was 2.5 zg spot -1. For sample volume of 0.40 μl spot -1, corresponding concentration was 6.2 × 10 -18 g ml -1), good selectivity (the allowed concentration of coexisting material was higher, when the relative error was ±5%), high accuracy (applied to detection of AP content in serum samples, the result was coincided with those obtained by enzyme-linked immunoassay), which was suitable for the detection of trace AP content in serum samples and the forecast of human diseases. Meanwhile, the mechanism of PMS-8-QBA-AASSRTP was discussed. The new field of analytical application and clinic diagnosis technique of molecule switch are exploited, based on the phosphorescence characteristic of PMS-8-QBA, the AA reaction between WGA and AP, as well as the relation between AP content and human diseases. The research results promote the development and interpenetrate among molecule

  19. Tunneling Nanoelectromechanical Switches Based on Compressible Molecular Thin Films.

    Niroui, Farnaz; Wang, Annie I; Sletten, Ellen M; Song, Yi; Kong, Jing; Yablonovitch, Eli; Swager, Timothy M; Lang, Jeffrey H; Bulović, Vladimir

    2015-08-25

    Abrupt switching behavior and near-zero leakage current of nanoelectromechanical (NEM) switches are advantageous properties through which NEMs can outperform conventional semiconductor electrical switches. To date, however, typical NEMs structures require high actuation voltages and can prematurely fail through permanent adhesion (defined as stiction) of device components. To overcome these challenges, in the present work we propose a NEM switch, termed a "squitch," which is designed to electromechanically modulate the tunneling current through a nanometer-scale gap defined by an organic molecular film sandwiched between two electrodes. When voltage is applied across the electrodes, the generated electrostatic force compresses the sandwiched molecular layer, thereby reducing the tunneling gap and causing an exponential increase in the current through the device. The presence of the molecular layer avoids direct contact of the electrodes during the switching process. Furthermore, as the layer is compressed, the increasing surface adhesion forces are balanced by the elastic restoring force of the deformed molecules which can promote zero net stiction and recoverable switching. Through numerical analysis, we demonstrate the potential of optimizing squitch design to enable large on-off ratios beyond 6 orders of magnitude with operation in the sub-1 V regime and with nanoseconds switching times. Our preliminary experimental results based on metal-molecule-graphene devices suggest the feasibility of the proposed tunneling switching mechanism. With optimization of device design and material engineering, squitches can give rise to a broad range of low-power electronic applications. PMID:26244821

  20. Arylazopyrazoles as Light-Responsive Molecular Switches in Cyclodextrin-Based Supramolecular Systems.

    Stricker, Lucas; Fritz, Eva-Corinna; Peterlechner, Martin; Doltsinis, Nikos L; Ravoo, Bart Jan

    2016-04-01

    A simple and high yield synthesis of water-soluble arylazopyrazoles (AAPs) featuring superior photophysical properties is reported. The introduction of a carboxylic acid allows the diverse functionalization of AAPs. Based on structural modifications of the switching unit the photophysical properties of the AAPs could be tuned to obtain molecular switches with favorable photostationary states. Furthermore, AAPs form stable and light-responsive host-guest complexes with β-cyclodextrin (β-CD). Our most efficient AAP shows binding affinities comparable to azobenzenes, but more effective switching and higher thermal stability of the Z-isomer. As a proof-of-principle, we investigated two CD-based supramolecular systems, containing either cyclodextrin vesicles (CDVs) or cyclodextrin-functionalized gold nanoparticles (CDAuNPs), which revealed excellent reversible, light-responsive aggregation and dispersion behavior. To conclude, AAPs have great potential to be incorporated as molecular switches in highly demanding and multivalent photoresponsive systems. PMID:26972671

  1. Switching Molecular Orientation of Individual Fullerene at Room Temperature

    Liu, Lacheng; Liu, Shuyi; Chen, Xiu; Li, Chao; Ling, Jie; Liu, Xiaoqing; Cai, Yingxiang; Wang, Li

    2013-01-01

    Reversible molecular switches with molecular orientation as the information carrier have been achieved on individual fullerene molecules adsorbed on Si (111) surface at room temperature. Scanning tunneling microscopy imaging directly demonstrates that the orientation of individual fullerene with an adsorption geometry of 5-6 bond is rotated by integral times as 30 degree after a pulse bias is applied between the STM tip and the molecule. Dependences of the molecular rotation probability on th...

  2. An Acidic Loop and Cognate Phosphorylation Sites Define a Molecular Switch That Modulates Ubiquitin Charging Activity in Cdc34-Like Enzymes

    Papaleo, Elena; Ranzani, Valeria; Tripodi, Farida; Vitriolo, Alessandro; Cirulli, Claudia; Fantucci, Piercarlo; Alberghina, Lilia; Vanoni, Marco; De Gioia, Luca; Coccetti, Paola

    2011-01-01

    E2 ubiquitin-conjugating enzymes are crucial mediators of protein ubiquitination, which strongly influence the ultimate fate of the target substrates. Recently, it has been shown that the activity of several enzymes of the ubiquitination pathway is finely tuned by phosphorylation, an ubiquitous mechanism for cellular regulation, which modulates protein conformation. In this contribution, we provide the first rationale, at the molecular level, of the regulatory mechanism mediated by casein kin...

  3. Single-walled carbon nanotube based molecular switch tunnel junctions.

    Diehl, Michael R; Steuerman, David W; Tseng, Hsian-Rong; Vignon, Scott A; Star, Alexander; Celestre, Paul C; Stoddart, J Fraser; Heath, James R

    2003-12-15

    This article describes two-terminal molecular switch tunnel junctions (MSTJs) which incorporate a semiconducting, single-walled carbon nanotube (SWNT) as the bottom electrode. The nanotube interacts noncovalently with a monolayer of bistable, nondegenerate [2]catenane tetracations, self-organized by their supporting amphiphilic dimyristoylphosphatidyl anions which shield the mechanically switchable tetracations from a two-micrometer wide metallic top electrode. The resulting 0.002 micron 2 area tunnel junction addresses a nanometer wide row of approximately 2000 molecules. Active and remnant current-voltage measurements demonstrated that these devices can be reconfigurably switched and repeatedly cycled between high and low current states under ambient conditions. Control compounds, including a degenerate [2]catenane, were explored in support of the mechanical origin of the switching signature. These SWNT-based MSTJs operate like previously reported silicon-based MSTJs, but differently from similar devices incorporating bottom metal electrodes. The relevance of these results with respect to the choice of electrode materials for molecular electronics devices is discussed. PMID:14714382

  4. Simple technique for sequential Q-switching of molecular lasers.

    Lucht, R. A.; Allario, F.; Jarrett, O., Jr.

    1972-01-01

    A simple technique for sequentially Q-switching molecular lasers is discussed in which an optical scanner is used as an optical folding element in a laser cavity consisting of a stationary diffraction grating and partially reflecting mirror. Sequential Q-switching of a conventional CO2 laser is demonstrated in which over sixty-two transitions between 9.2 and 10.8 microns are observed. Rapid repetition rates (200 Hz) and narrow laser pulses (less than 5 microsec) allow conventional signal processing techniques to be used with this multiwavelength laser source which is a versatile tool for laser propagation studies, absorption spectroscopy, and gain measurements. Results of a preliminary experiment demonstrating the utility of measuring selective absorption of CO2 laser wavelengths by C2H4 are shown.

  5. Light-Triggered Control of Plasmonic Refraction and Group Delay by Photochromic Molecular Switches

    Großmann, Malte; Klick, Alwin; Lemke, Christoph; Falke, Julian; Black, Maximilian; Fiutowski, Jacek; Goszczak, Arkadiusz Jaroslaw; Sobolewska, Elzbieta; Zillohu, Ahnaf Usman; Hedayati, Mehdi Keshavarz; Rubahn, Horst-Günter; Faupel, Franz; Elbahri, Mady; Bauer, Michael

    2015-01-01

    An interface supporting plasmonic switching is prepared from a gold substrate coated with a polymerfilm doped with photochromic molecular switches. A reversible light-induced change in the surface plasmon polariton dispersion curve of the interface is experimentally demonstrated, evidencing...

  6. Charge mobilities in molecular materials reversibly modified by light: towards a molecular switch

    Nešpůrek, Stanislav; Sworakowski, J.; Wang, Geng; Toman, Petr; Bartkowiak, W.; Combellas, C.

    Arcachon : University of Bordeaux, 2004. s. P111. [International Symposium on Photochromism /4./. 12.09.2004-15.09.2004, Arcachon] R&D Projects: GA MŠk OC D14.30 Keywords : molecular switch * charge mobility * photochromism Subject RIV: BM - Solid Matter Physics ; Magnetism

  7. Nonmechanical Conductance Switching in a Molecular Tunnel Junction.

    Baratz, Adva; Baer, Roi

    2012-02-16

    We present a molecular junction composed of a donor (polyacetylene strands) and an acceptor (malononitrile) connected together via a benzene ring and coupled weakly to source and drain electrodes on each side, for which a gate electrode induces intramolecular charge transfer, switching reversibly the character of conductance. Using a new brand of density functional theory, for which orbital energies are similar to the quasiparticle energies, we show that the junction displays a single, gate-tunable differential conductance channel in a wide energy range. The gate field must align parallel to the displacement vector between donors and acceptor to affect their potential difference; for strong enough fields, spontaneous intramolecular electron transfer occurs. This event radically affects conductance, reversing the charge of carriers, enabling a spin-polarized current channel. We discuss the physical principles controlling the operation of the junction and find interplay of quantum interference, charging, Coulomb blockade, and electron-hole binding energy effects. We expect that this switching behavior is a generic property for similar donor-acceptor systems of sufficient stability. PMID:26286054

  8. Symmetry as a new element to control molecular switches.

    Schweighauser, Luca; Häussinger, Daniel; Neuburger, Markus; Wegner, Hermann A

    2014-06-01

    The isomerization properties of an azocarbazole macrocycle in solution were investigated utilizing NMR spectroscopy with in situ irradiation in combination with DFT calculations. It was demonstrated that the position of azo units in a rigid macrocyclic system influences the photoisomerization pathway even if the initial all-E isomer is highly symmetric. Furthermore, the effect of ring strain on lowering the rates of thermal isomerization was demonstrated and a mechanism via an inversion-rotation proposed. The herein presented results and methods give new insights into the general nature of the azobenzene unit. In particular we illustrate the effect of symmetry changes due to macrocyclic arrangement on the photochemical and thermal isomerization properties, which will stimulate future development towards multinary molecular switches. PMID:24691779

  9. Electronic Transport Properties of a Naphthopyran-Based Optical Molecular Switch:an ab initio Study

    XIA Cai-Juan; LIU De-Sheng; ZHANG Ying-Tang

    2011-01-01

    The electronic transport properties of a. Naphthopyran-based molecular optical switch are investigated by using the nonequilibrium Green's Function formalism combined with first-principles density functional theory. The molecule that comprises the switch can convert between its open and closed forms upon photoexcitation. Theoretical results show that the current through the open form is significantly larger than that through the closed form, which is different from other optical switches based on ring-opening reactions of the molecular bridge. The maximum on-off ratio (about 90) can be obtained at 1.4 V. The physical origin of the switching behavior is interpreted based on the spatial distributions of molecular orbitals and the HOMO-LUMO gap. Our result shows that the naphthopyran-based molecule is a good candidate for optical molecular switches and will be useful in the near future.%@@ ronic transport properties of a naphthopyran-based molecular optical switch are investigated by using the nonequilibrium Green's function formalism combined with first-principles density functional theory.The molecule that comprises the switch can convert between its open and closed forms upon photoexcitation.Theoretical results show that the current through the open form is significantly larger than that through the closed form,which is different from other optical switches based on ring-opening reactions of the molecular bridge.The maximum on-off ratio(about 90)can be obtained at 1.4 V.The physical origin of the switching behavior is interpreted based on the spatial distributions of molecular orbitals and the HOMO-LUMO gap.Our result shows that the naphthopyran-based molecule is a good candidate for optical molecular switches and will be useful in the near future.

  10. Molecular Interaction of Pinic Acid with Sulfuric Acid

    Elm, Jonas; Kurten, Theo; Bilde, Merete;

    2014-01-01

    We investigate the molecular interactions between the semivolatile α-pinene oxidation product pinic acid and sulfuric acid using computational methods. The stepwise Gibbs free energies of formation have been calculated utilizing the M06-2X functional, and the stability of the clusters is evaluated...... from the corresponding ΔG values. The first two additions of sulfuric acid to pinic acid are found to be favorable with ΔG values of -9.06 and -10.41 kcal/mol. Addition of a third sulfuric acid molecule is less favorable and leads to a structural rearrangement forming a bridged sulfuric acid-pinic acid...... without the further possibility for attachment of either sulfuric acid or pinic acid. This suggests that pinic acid cannot be a key species in the first steps in nucleation, but the favorable interactions between sulfuric acid and pinic acid imply that pinic acid can contribute to the subsequent growth of...

  11. Switching dynamics in reaction networks induced by molecular discreteness

    To study the fluctuations and dynamics in chemical reaction processes, stochastic differential equations based on the rate equation involving chemical concentrations are often adopted. When the number of molecules is very small, however, the discreteness in the number of molecules cannot be neglected since the number of molecules must be an integer. This discreteness can be important in biochemical reactions, where the total number of molecules is not significantly larger than the number of chemical species. To elucidate the effects of such discreteness, we study autocatalytic reaction systems comprising several chemical species through stochastic particle simulations. The generation of novel states is observed; it is caused by the extinction of some molecular species due to the discreteness in their number. We demonstrate that the reaction dynamics are switched by a single molecule, which leads to the reconstruction of the acting network structure. We also show the strong dependence of the chemical concentrations on the system size, which is caused by transitions to discreteness-induced novel states

  12. A biomimetic molecular switch at work: coupling photoisomerization dynamics to peptide structural rearrangement.

    García-Iriepa, Cristina; Gueye, Moussa; Léonard, Jérémie; Martínez-López, David; Campos, Pedro J; Frutos, Luis Manuel; Sampedro, Diego; Marazzi, Marco

    2016-03-01

    In spite of considerable interest in the design of molecular switches towards photo-controllable (bio)materials, few studies focused on the major influence of the surrounding environment on the switch photoreactivities. We present a combined experimental and computational study of a retinal-like molecular switch linked to a peptide, elucidating the effects on the photoreactivity and on the α-helix secondary structure. Temperature-dependent, femtosecond UV-vis transient absorption spectroscopy and high-level hybrid quantum mechanics/molecular mechanics methods were applied to describe the photoisomerization process and the subsequent peptide rearrangement. It was found that the conformational heterogeneity of the ground state peptide controls the excited state potential energy surface and the thermally activated population decay. Still, a reversible α-helix to α-hairpin conformational change is predicted, paving the way for a fine photocontrol of different secondary structure elements, hence (bio)molecular functions, using retinal-inspired molecular switches. PMID:26876376

  13. STM investigation of imine-based molecular switches on Au(111)

    Mielke, Johannes; Grill, Leonhard [Institut fuer Experimentalphysik, Freie Universitaet Berlin (Germany); Luo, Ying; Haag, Rainer [Institut fuer Chemie und Biochemie - Organische Chemie, Freie Universitaet Berlin (Germany)

    2009-07-01

    In the field of molecular electronics, molecular switches are highly relevant because they can control the conductance. Switches based on azobenzene molecules have attracted large interest in the last years. A very similar molecular switch can be created by replacing the functional azo group by an imine group, which does not considerably alter the electronic structure of the molecule and conserves the capability of undergoing a reversible trans-cis isomerisation. Such processes have already been studied in solution and the gas phase but not on surfaces. In this work, imine molecules with four tert-butyl groups were adsorbed on Au(111) and their adsorption and switching behaviour were studied using a low temperature STM. The molecules were found to form two types of ordered islands and an interesting irreversible switching behaviour was observed when looking at their temperature dependence, because the number of trans isomers was reduced upon heating of the sample.

  14. Magnesium coordination controls the molecular switch function of DNA mismatch repair protein MutS

    J.H.G. Lebbink (Joyce); A. Fish (Alexander); A. Reumer (Annet); G. Natrajan; H.H.K. Winterwerp (Herrie); T.K. Sixma (Titia)

    2010-01-01

    textabstractThe DNA mismatch repair protein MutS acts as a molecular switch. It toggles between ADP and ATP states and is regulated by mismatched DNA. This is analogous to G-protein switches and the regulation of their "on" and "off" states by guanine exchange factors. Although GDP release in monome

  15. A pH-Sensitive Peptide-Containing Lasso Molecular Switch

    Karine Fournel-Marotte; Caroline Clavel; Frédéric Coutrot

    2013-01-01

    The synthesis of a peptide-containing lasso molecular switch by a self-entanglement strategy is described. The interlocked [1] rotaxane molecular machine consists of a benzometaphenylene[25]crown-8 (BMP25C8) macrocycle surrounding a molecular axle. This molecular axle contains a tripeptidic sequence and two molecular stations: a N-benzyltriazolium and a pH-sensitive anilinium station. The tripeptide is located between the macrocycle and the triazolium station, so that its conformation can be ...

  16. Electronic transport properties of a molecular switch with carbon nanotube electrodes: A first-principles study

    Zhao, P., E-mail: ss_zhaop@ujn.edu.c [School of Science, University of Jinan, Jinan 250022 (China); School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100 (China); Wang, P.J.; Zhang, Z. [School of Science, University of Jinan, Jinan 250022 (China); Liu, D.S. [School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100 (China); Department of Physics, Jining University, Qufu 273155 (China)

    2010-01-01

    We have studied the electronic transport properties of a new kind of optical molecular switch with two single-walled carbon nanotube (SWCNT) electrodes using first-principles transport calculations. It is shown that the enol form shows an overall higher conductance than the keto form at low-bias voltage, which is independent of the SWCNTs' chirality. Meantime, it is possible to tune the conductance of the molecular switch by changing the chirality of the SWCNTs.

  17. Laser Field Alignment of Organic Molecules on Semiconductor Surfaces: Toward Ultrafast Molecular Switches

    An ultrafast, nanoscale molecular switch is proposed, based on extension of the concept of nonadiabatic alignment to surface-adsorbed molecules. The switch consists of a conjugated organic molecule adsorbed onto a semiconducting surface and placed near a scanning tunneling microscope tip. A low-frequency, polarized laser field is used to switch the system by orienting the molecule with the field polarization axis, enabling conductance through the junction. Enhancement and spatial localization of the incident field by the metallic tip allow operation at low intensities. The principles of nonadiabatic alignment lead to switch on and off time scales far below rotational time scales

  18. Asymmetric Stochastic Switching Driven by Intrinsic Molecular Noise

    David Frigola; Laura Casanellas; Sancho, José M.; Marta Ibañes

    2012-01-01

    Low-copy-number molecules are involved in many functions in cells. The intrinsic fluctuations of these numbers can enable stochastic switching between multiple steady states, inducing phenotypic variability. Herein we present a theoretical and computational study based on Master Equations and Fokker-Planck and Langevin descriptions of stochastic switching for a genetic circuit of autoactivation. We show that in this circuit the intrinsic fluctuations arising from low-copy numbers, which are i...

  19. Oxidized Fatty Acid Analysis by Charge Switch Derivatization, Selected Reaction Monitoring and Accurate Mass Quantification

    Liu, Xinping; Moon, Sung Ho; Mancuso, David J.; Jenkins, Christopher M.; Guan, Shaoping; Sims, Harold F.; Gross, Richard W.

    2013-01-01

    A highly sensitive, specific and robust method for the analysis of oxidized metabolites of linoleic, acid (LA), arachidonic acid (AA) and docosahexaenoic acid (DHA) was developed using charge-switch derivatization, LC-ESI MS/MS with selected reaction monitoring (SRM) and quantitation by high mass accuracy analysis of product ions thereby minimizing interferences from contaminating ions. Charge-switch derivatization of LA, AA and DHA metabolites with N-(4-aminomethylphenyl)-pyridinium resulted...

  20. Molecular modeling and molecular dynamics simulation of the polarization switching phenomena in the ferroelectric polymers PVDF at the nanoscale

    The molecular modeling and molecular dynamics of polarization switching for the ferroelectric films model of polyvinylidene fluoride (PVDF) are investigated at the nanoscale. We consider a molecular model of PVDF film, consisting of two and four a chains [–CH2–CF2–]n limited by n=6 elementary units. The first-principle approach is applied to the switching and kinetics of these models. Two types of behavior were established for PVDF chains: simultaneous and sequential rotation in high and low electric fields. Kinetics of sequential polarization switching shows a homogeneous critical behavior in the low electric field with a critical point at Landau–Ginzburg–Devonshire (LGD) coercive field E=EC. This type of kinetics demonstrates a kink-like behavior for polarization solitary wave propagation. The simultaneous type of kinetics demonstrates the total domain-like polarization switching, corresponding to exponential behavior of switching time in high electric field as for bulk samples. Corresponding LGD intrinsic coercive field for a two-chain and four-chains model is EC∼2.0 GV/m with revealing size effect. Obtained results show common quantum nature of PVDF chains switching phenomena—the quantum interaction of the PVDF molecular orbitals under applied electric field at the nanoscale level. The results obtained are compared with experimental data

  1. Molecular modeling of nucleic acid structure

    Galindo-Murillo, Rodrigo; Bergonzo, Christina; Cheatham, Thomas E

    2001-01-01

    This unit is the first in a series of four units covering the analysis of nucleic acid structure by molecular modeling. This unit provides an overview of computer simulation of nucleic acids. Topics include the static structure model, computational graphics and energy models, generation of an initial model, and characterization of the overall three-dimensional structure.

  2. Amino acid properties conserved in molecular evolution.

    Witold R Rudnicki

    Full Text Available That amino acid properties are responsible for the way protein molecules evolve is natural and is also reasonably well supported both by the structure of the genetic code and, to a large extent, by the experimental measures of the amino acid similarity. Nevertheless, there remains a significant gap between observed similarity matrices and their reconstructions from amino acid properties. Therefore, we introduce a simple theoretical model of amino acid similarity matrices, which allows splitting the matrix into two parts - one that depends only on mutabilities of amino acids and another that depends on pairwise similarities between them. Then the new synthetic amino acid properties are derived from the pairwise similarities and used to reconstruct similarity matrices covering a wide range of information entropies. Our model allows us to explain up to 94% of the variability in the BLOSUM family of the amino acids similarity matrices in terms of amino acid properties. The new properties derived from amino acid similarity matrices correlate highly with properties known to be important for molecular evolution such as hydrophobicity, size, shape and charge of amino acids. This result closes the gap in our understanding of the influence of amino acids on evolution at the molecular level. The methods were applied to the single family of similarity matrices used often in general sequence homology searches, but it is general and can be used also for more specific matrices. The new synthetic properties can be used in analyzes of protein sequences in various biological applications.

  3. Insight into the molecular switch mechanism of human Rab5a from molecular dynamics simulations

    Rab5a is currently a most interesting target because it is responsible for regulating the early endosome fusion in endocytosis and possibly the budding process. We utilized longtime-scale molecular dynamics simulations to investigate the internal motion of the wild-type Rab5a and its A30P mutant. It was observed that, after binding with GTP, the global flexibility of the two proteins is increasing, while the local flexibility in their sensitive sites (P-loop, switch I and II regions) is decreasing. Also, the mutation of Ala30 to Pro30 can cause notable flexibility variations in the sensitive sites. However, this kind of variations is dramatically reduced after binding with GTP. Such a remarkable feature is mainly caused by the water network rearrangements in the sensitive sites. These findings might be of use for revealing the profound mechanism of the displacements of Rab5a switch regions, as well as the mechanism of the GDP dissociation and GTP association.

  4. X-ray Analyses of the Ribosomal A-Site Molecular Switches

    Kondo, Jiro

    The aminoacyl-tRNA decoding site (A-site) on the small ribosomal subunit is an RNA molecular switch guaranteeing high translation fidelity. Due to the similarity of the secondary structure of the A-site, it has long been believed that the functional characteristics and tertiary structure of the A-site molecular switch are basically conserved in three main cell types, bacteria, mitochondria and eukaryotic cytoplasm. However, these three cell types are noticeably different in their biological properties such as life cycle, genome size, structural component of ribosome and number of tRNA species. In our structural studies, we have shown how a small difference of nucleotide sequences affects the dynamics of the A-site molecular switches underlying the decoding mechanism adapted to their biological properties and environments. The observed structural insights into the decoding process allowed us to understand molecular mechanisms of non-syndromic hearing loss and toxicity mechanism of aminoglycoside antibiotics.

  5. The stochastic behavior of a molecular switching circuit with feedback

    Smith Eric

    2007-05-01

    Full Text Available Abstract Background Using a statistical physics approach, we study the stochastic switching behavior of a model circuit of multisite phosphorylation and dephosphorylation with feedback. The circuit consists of a kinase and phosphatase acting on multiple sites of a substrate that, contingent on its modification state, catalyzes its own phosphorylation and, in a symmetric scenario, dephosphorylation. The symmetric case is viewed as a cartoon of conflicting feedback that could result from antagonistic pathways impinging on the state of a shared component. Results Multisite phosphorylation is sufficient for bistable behavior under feedback even when catalysis is linear in substrate concentration, which is the case we consider. We compute the phase diagram, fluctuation spectrum and large-deviation properties related to switch memory within a statistical mechanics framework. Bistability occurs as either a first-order or second-order non-equilibrium phase transition, depending on the network symmetries and the ratio of phosphatase to kinase numbers. In the second-order case, the circuit never leaves the bistable regime upon increasing the number of substrate molecules at constant kinase to phosphatase ratio. Conclusion The number of substrate molecules is a key parameter controlling both the onset of the bistable regime, fluctuation intensity, and the residence time in a switched state. The relevance of the concept of memory depends on the degree of switch symmetry, as memory presupposes information to be remembered, which is highest for equal residence times in the switched states. Reviewers This article was reviewed by Artem Novozhilov (nominated by Eugene Koonin, Sergei Maslov, and Ned Wingreen.

  6. Proteomic analysis of mitochondria reveals a metabolic switch from fatty acid oxidation to glycolysis in the failing heart

    2009-01-01

    This work characterizes the mitochondrial proteomic profile in the failing heart and elucidates the molecular basis of mitochondria in heart failure. Heart failure was induced in rats by myocardial infarction, and mitochondria were isolated from hearts by differential centrifugation. Using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry, a system biology approach was employed to investigate differences in mitochondrial proteins between normal and failing hearts. Mass spectrometry identified 27 proteins differentially expressed that involved in energy metabolism. Among those, the up-regulated proteins included tricarboxylic acid cycle enzymes and pyruvate dehydrogenase complex subunits while the down-regulated proteins were involved in fatty acid oxidation and the OXPHOS complex. These results suggest a substantial metabolic switch from free fatty acid oxidation to glycolysis in heart failure and provide molecular evidence for alterations in the structural and functional parameters of mitochondria that may contribute to cardiac dysfunction during ischemic injury.

  7. Nanoscale switch based on interacting molecular dipoles: Cooperativity can improve the device characteristics

    Mafé, , Salvador; Manzanares, , José A.; Reiss, Howard

    2011-02-01

    We propose a nanoscale switch, giving a nonlinear function with two conductive states separated by a sharp transition region, on the basis of an array of molecular dipoles. We show theoretically that the local interactions between dipoles result in cooperative phenomena that can significantly improve the switching characteristics. We demonstrate the general validity of the concept in the cases of (i) an electrical switch robust to the finite size and variability effects inherent to the nanoscale and (ii) a sensing layer based on the voltage and ligand concentration dependence of the dipole array conductance.

  8. Synthetic molecular machines and polymer/monomer size switches that operate through dynamic and non-dynamic covalent changes.

    Stadler, Adrian-Mihail; Ramírez, Juan

    2012-01-01

    The present chapter is focused on how synthetic molecular machines (e.g. shuttles, switches and molecular motors) and size switches (conversions between polymers and their units, i.e., conversions between relatively large and small molecules) can function through covalent changes. Amongst the interesting examples of devices herein presented are molecular motors and size switches based on dynamic covalent chemistry which is an area of constitutional dynamic chemistry. PMID:22169959

  9. Molecular Epigenetic Switches in Neurodevelopment in Health and Disease

    Dietmar Spengler

    2015-05-01

    Full Text Available Epigenetic mechanisms encode information above and beyond DNA sequence and play a critical role in brain development and the long-lived effects of environmental cues on the pre- and postnatal brain. Switch-like, rather than graded changes, illustrate par excellence how epigenetic events perpetuate altered activity states in the absence of the initial cue. They occur from early neural development to maturation and can give rise to distinct diseases upon deregulation. Many neurodevelopmental genes harbor bivalently marked chromatin domains, states of balanced inhibition, which guide dynamic ‘ON or OFF’ decisions once the balance is tilted in response to developmental or environmental cues. Examples discussed in this review include neuronal differentiation of embryonic stem cells into progenitors and beyond, activation of Kiss1 at puberty onset, and early experience-dependent programming of Avp, a major stress gene. At the genome-scale, genomic imprinting can be epigenetically switched on or off at select genes in a tightly controlled temporospatial manner and provides a versatile mechanism for dosage regulation of genes with important roles in stem cell quiescence or differentiation. Moreover, retrotransposition in neural progenitors provides an intriguing example of an epigenetic-like switch, which is stimulated by bivalently marked neurodevelopmental genes and possibly results in increased genomic flexibility regarding unprecedented challenge. Overall, we propose that epigenetic switches illuminate the catalyzing function of epigenetic mechanisms in guiding dynamic changes in gene expression underpinning robust transitions in cellular and organismal phenotypes as well as in the mediation between dynamically changing environments and the static genetic blueprint.

  10. Light controlled charge carrier mobilities on polymer chains. Towards a molecular switch

    Sworakowski, J.; Nešpůrek, Stanislav; Wang, Geng; Weiter, M.

    Saclay: Atomic Energy Research Centre, Saclay, 2003. s. 131. [European Conference on Molecular Electronics /7./. 10.09.2003-14.09.2003, Avignon] R&D Projects: GA MŠk OC D14.30 Grant ostatní: Polish State Committee for Sci. Res.(PL) T09A 132 22 Institutional research plan: CEZ:AV0Z4050913 Keywords : molecular switch * molecular wire * poly[methyl-(phenyl)silylene] Subject RIV: BM - Solid Matter Physics ; Magnetism

  11. Biodegradation of high molecular weight polylactic acid

    Stloukal, Petr; Koutný, Marek; Sedlařík, Vladimír; Kucharczyk, Pavel

    2012-01-01

    Polylactid acid seems to be an appropriate replacement of conventional non-biodegradable synthetic polymer primarily due to comparable mechanical, thermal and processing properties in its high molecular weight form. Biodegradation of high molecular PLA was studied in compost for various forms differing in their specific surface area. The material proved its good biodegradability under composting conditions and all investigated forms showed to be acceptable for industrial composting. Despite e...

  12. Do nucleic acids moonlight as molecular chaperones?

    Docter, Brianne E.; Horowitz, Scott; Gray, Michael J.; Jakob, Ursula; Bardwell, James C.A.

    2016-01-01

    Organisms use molecular chaperones to combat the unfolding and aggregation of proteins. While protein chaperones have been widely studied, here we demonstrate that DNA and RNA exhibit potent chaperone activity in vitro. Nucleic acids suppress the aggregation of classic chaperone substrates up to 300-fold more effectively than the protein chaperone GroEL. Additionally, RNA cooperates with the DnaK chaperone system to refold purified luciferase. Our findings reveal a possible new role for nucleic acids within the cell: that nucleic acids directly participate in maintaining proteostasis by preventing protein aggregation. PMID:27105849

  13. Molecular circuits, biological switches, and nonlinear dose-response relationships.

    Andersen, Melvin E.; Yang, Raymond S.H.; French, C. Tenley; Chubb, Laura S; Dennison, James E

    2002-01-01

    Signaling motifs (nuclear transcriptional receptors, kinase/phosphatase cascades, G-coupled protein receptors, etc.) have composite dose-response behaviors in relation to concentrations of protein receptors and endogenous signaling molecules. "Molecular circuits" include the biological components and their interactions that comprise the workings of these signaling motifs. Many of these molecular circuits have nonlinear dose-response behaviors for endogenous ligands and for exogenous toxicants...

  14. Molecular transformations in connective tissue hyaluronic acid

    Free radicals, either induced by the action of ionizing radiations or produced by metal ion induced electron transfer reactions in situ, can initiate a marked reduction in the viscoelasticity of the connective tissue matrix. This paper examines the dominant role of hyaluronic acid in controlling this behavior at molecular level. The results indicate that after a dose of 5Gy (500 rads), the average molecular weight of hyaluronic acid in skin would be reduced by a factor of 4, which would lead to a 60-fold reduction in viscosity of the glycosaminoglycan. Shorter chains so produced would further inhibit hyperentanglement and chain-chain interactions which are responsible for the viscoelasticity of the hyaluronic acid-polymer network. The results are relevant to preservation of skin grafts and to the effects of low-dose radiation in vivo

  15. Two-terminal nanoelectromechanical bistable switches based on molybdenum-sulfur-iodine molecular wire bundles

    Andzane, J.; Prikulis, J.; Dvorsek, D.; Mihailovic, D.; Erts, D.

    2010-03-01

    We demonstrate the application of Mo6S3I6 molecular wire bundles for electrically controllable two-terminal on-off switches. We investigate how changes in the contact electrode material and geometry influence the device characteristics, hysteretic switching behavior and device stability. We also determine the device operating parameters, particularly the Young's moduli (40-270 GPa), operating current densities (3.2 × 105-7 × 106 A m - 2) and force constants. Although qualitatively, the properties of Mo6S3I6 nanowires in nanoelectromechanical (NEM) switches are similar to those of carbon nanotubes (CNTs), their lower friction coefficient, higher mechanical stability and higher operation voltages give specific advantages in terms of smaller differences in on-off operating potentials, higher switching speeds and lower energy consumption than CNTs, which are critical for applications in NEM devices.

  16. Two-terminal nanoelectromechanical bistable switches based on molybdenum-sulfur-iodine molecular wire bundles

    We demonstrate the application of Mo6S3I6 molecular wire bundles for electrically controllable two-terminal on-off switches. We investigate how changes in the contact electrode material and geometry influence the device characteristics, hysteretic switching behavior and device stability. We also determine the device operating parameters, particularly the Young's moduli (40-270 GPa), operating current densities (3.2 x 105-7 x 106 A m-2) and force constants. Although qualitatively, the properties of Mo6S3I6 nanowires in nanoelectromechanical (NEM) switches are similar to those of carbon nanotubes (CNTs), their lower friction coefficient, higher mechanical stability and higher operation voltages give specific advantages in terms of smaller differences in on-off operating potentials, higher switching speeds and lower energy consumption than CNTs, which are critical for applications in NEM devices.

  17. Hydrochromic molecular switches for water-jet rewritable paper

    Sheng, Lan; Li, Minjie; Zhu, Shaoyin; Li, Hao; Xi, Guan; Li, Yong-Gang; Wang, Yi; Li, Quanshun; Liang, Shaojun; Zhong, Ke; Zhang, Sean Xiao-An

    2014-01-01

    The days of rewritable paper are coming, printers of the future will use water-jet paper. Although several kinds of rewritable paper have been reported, practical usage of them is rare. Herein, a new rewritable paper for ink-free printing is proposed and demonstrated successfully by using water as the sole trigger to switch hydrochromic dyes on solid media. Water-jet prints with various colours are achieved with a commercial desktop printer based on these hydrochromic rewritable papers. The prints can be erased and rewritten dozens of times with no significant loss in colour quality. This rewritable paper is promising in that it can serve an eco-friendly information display to meet the increasing global needs for environmental protection.

  18. Infrared spectroscopic characterization of [2]rotaxane molecular switch tunnel junction devices.

    DeIonno, Erica; Tseng, Hsian-Rong; Harvey, Desmond D; Stoddart, J Fraser; Heath, James R

    2006-04-20

    Langmuir-Blodgett monolayers of a bistable [2]rotaxane were prepared at packing densities of 118, 73, and 54 A(2)/molecule. The monolayers were both characterized via infrared spectroscopy before and after evaporation of a 2 nm film of titanium and incorporated into molecular switch tunnel junction devices. The study suggests that the evaporation process primarily affects portions of the molecule exposed to the metal atom source. Thus, in tightly packed monolayers (73 and 54 A(2)/molecule), only the portions of the [2]rotaxane that are present at the molecule/air interface are clearly affected, leaving key functionality necessary for switching intact. Monolayers transferred at a lower pressure (118 A(2)/molecule) exhibit nonspecific damage and poor switching behavior following Ti deposition. These results indicate that tightly packed monolayers and sacrificial functionality displayed at the molecule/air interface are important design principles for molecular electronic devices. PMID:16610848

  19. Deciphering mechanism of the 'myristoyl switch' with classical and accelerated molecular dynamics

    Magarkar, Aniket; Kohagen, Miriam; Jungwirth, Pavel

    2015-01-01

    Roč. 44, Suppl 1 (2015), S169. ISSN 0175-7571. [EBSA European Biophysics Congress /10./. 18.07.2015-22.07.2015, Dresden] Institutional support: RVO:61388963 Keywords : molecular dynamics * myristoyl switch * calcium ion binding Subject RIV: CF - Physical ; Theoretical Chemistry

  20. Chemical Talking with Living Systems: Molecular Switches Steer Quorum Sensing in Bacteria.

    Schweighauser, Luca; Wegner, Hermann A

    2015-08-17

    New avenues in bacterial engineering: An azobenzene molecular switch has been incorporated into an autoinducer for quorum sensing (QS) in bacteria. The authors demonstrated that irradiation with different wavelengths of light influences the QS system thereby controlling gene expression as well as the phenotype, as exemplified by pyocyanin production. PMID:26078043

  1. Electrospun Nanofibers from a Tricyanofuran-Based Molecular Switch for Colorimetric Recognition of Ammonia Gas.

    Khattab, Tawfik A; Abdelmoez, Sherif; Klapötke, Thomas M

    2016-03-14

    A chromophore based on tricyanofuran (TCF) with a hydrazone (H) recognition moiety was developed. Its molecular-switching performance is reversible and has differential sensitivity towards aqueous ammonia at comparable concentrations. Nanofibers were fabricated from the TCF-H chromophore by electrospinning. The film fabricated from these nanofibers functions as a solid-state optical chemosensor for probing ammonia vapor. Recognition of ammonia vapor occurs by proton transfer from the hydrazone fragment of the chromophore to the ammonia nitrogen atom and is facilitated by the strongly electron withdrawing TCF fragment. The TCF-H chromophore was added to a solution of poly(acrylic acid), which was electrospun to obtain a nanofibrous sensor device. The morphology of the nanofibrous sensor was determined by SEM, which showed that nanofibers with a diameter range of 200-450 nm formed a nonwoven mat. The resultant nanofibrous sensor showed very good sensitivity in ammonia-vapor detection. Furthermore, very good reversibility and short response time were also observed. PMID:26864701

  2. Thermodynamic principles for the engineering of pH-driven conformational switches and acid insensitive proteins

    Bell-Upp, Peregrine; Robinson, Aaron C.; Whitten, Steven; Wheeler, Erika L.; Lin, Janine; Stites, Wesley E.; García-Moreno E., Bertrand

    2011-01-01

    The general thermodynamic principles behind pH driven conformational transitions of biological macromolecules are well understood. What is less obvious is how they can be used to engineer pH switches in proteins. The acid unfolding of staphylococcal nuclease (SNase) was used to illustrate different factors that can affect pH-driven conformational transitions. Acid unfolding is a structural transition driven by preferential H+ binding to the acid unfolded state (U) over the native (N) state of...

  3. Understanding and Controlling Regime Switching in Molecular Diffusion

    Hallerberg, S.; de Wijn, A. S.

    2013-01-01

    Diffusion can be strongly affected by ballistic flights (long jumps) as well as long-lived sticking trajectories (long sticks). Using statistical inference techniques in the spirit of Granger causality, we investigate the appearance of long jumps and sticks in molecular-dynamics simulations of diffusion in a prototype system, a benzene molecule on a graphite substrate. We find that specific fluctuations in certain, but not all, internal degrees of freedom of the molecule can be linked to eith...

  4. Models of charge transport and transfer in molecular switch tunnel junctions of bistable catenanes and rotaxanes

    The processes by which charge transfer can occur play a foundational role in molecular electronics. Here we consider simplified models of the transfer processes that could be present in bistable molecular switch tunnel junction (MSTJ) devices during one complete cycle of the device from its low- to high- and back to low-conductance state. The bistable molecular switches, which are composed of a monolayer of either switchable catenanes or rotaxanes, exist in either a ground-state co-conformation or a metastable one in which the conduction properties of the two co-conformations, when measured at small biases (+0.1 V), are significantly different irrespective of whether transport is dominated by tunneling or hopping. The voltage-driven generation (±2 V) of molecule-based redox states, which are sufficiently long-lived to allow the relative mechanical movements necessary to switch between the two co-conformations, rely upon unequal charge transfer rates on to and/or off of the molecules. Surface-enhanced Raman spectroscopy has been used to image the ground state of the bistable rotaxane in MSTJ-like devices. Consideration of these models provide new ways of looking at molecular electronic devices that rely, not only on nanoscale charge-transport, but also upon the bustling world of molecular motion in mechanically interlocked bistable molecules

  5. Adsorption and switching properties of a N-benzylideneaniline based molecular switch on a Au(111) surface

    High resolution electron energy loss spectroscopy has been employed to analyze the adsorption geometry and the photoisomerization ability of the molecular switch carboxy-benzylideneaniline (CBA) adsorbed on Au(111). CBA on Au(111) adopts a planar (trans) configuration in the first monolayer (ML) as well as for higher coverages (up to 6 ML), in contrast to the strongly nonplanar geometry of the molecule in solution. Illumination with UV light of CBA in direct contact with the Au(111) surface (≤1 ML) caused no changes in the vibrational structure, whereas at higher coverages (>1 ML) pronounced modifications of vibrational features were observed, which we assign to a trans→cis isomerization. Thermal activation induced the back reaction to trans-CBA. We propose that the photoisomerization is driven by a direct (intramolecular) electronic excitation of the adsorbed CBA molecules in the second ML (and above) analogous to CBA in the liquid phase.

  6. Investigation of a metal-organic interface. Realization and understanding of a molecular switch

    Neucheva, Olga [Forschungszentrum Juelich (DE). Institute of Bio- and Nanosystems (IBN), Functional Nanostructures at Surfaces (IBN-3)

    2010-07-01

    The field of molecular organic electronics is an emerging and very dynamic area. The continued trend to miniaturisation, combined with increasing complexity and cost of production in conventional semiconductor electronics, forces companies to turn their attention to alternatives that promise the next levels of scale at significantly lower cost. After consumer electronic devices based on organic transistors, such as TVs and book readers, have already been presented, molecular electronics is expected to offer the next breakthrough in feature size. Unfortunately, most of the organic/metal interfaces contain intrinsic defects that break the homogeneity of the interface properties. In this thesis, the electronic and structural properties of such defects were examined in order to understand the influence of the inhomogeneities on the quality of the interface layer. However, the main focus of this work was the investigation of the local properties of a single molecule. Taking advantage of the Scanning Tunnelling Microscope's (STM's) ability to act as a local probe, a single molecular switch was realized and studied. Moreover, in close collaboration with theory groups, the underlying mechanism driving the switching process was identified and described. Besides the investigation of the switching process, the ability of the STM to build nanostructures of different shapes from large organic molecules was shown. Knowing the parameters for realization and control of the switching process and for building the molecular corrals, the results of this investigation enable the reconstruction of the studied molecular ensemble and its deployment in electric molecular circuits, constituting a next step towards further miniaturization of electronic devices. (orig.)

  7. Single Molecule Switches and Molecular Self-Assembly: Low Temperature STM Investigations and Manipulations

    This dissertation is devoted to single molecule investigations and manipulations of two porphyrin-based molecules, chlorophyll-a and Co-popphyrin. The molecules are absorbed on metallic substrates and studied at low temperatures using a scanning tunneling microscope. The electronic, structural and mechanical properties of the molecules are investigated in detail with atomic level precision. Chlorophyll-a is the key ingredient in photosynthesis processes while Co-porphyrin is a magnetic molecule that represents the recent emerging field of molecular spintronics. Using the scanning tunneling microscope tip and the substrate as electrodes, and the molecules as active ingredients, single molecule switches made of these two molecules are demonstrated. The first switch, a multiple and reversible mechanical switch, is realized by using chlorophyll-a where the energy transfer of a single tunneling electron is used to rotate a C-C bond of the molecule's tail on a Au(111) surface. Here, the det

  8. Ab initio theory for current-induced molecular switching: Melamine on Cu(001)

    Ohto, Tatsuhiko

    2013-05-28

    Melamine on Cu(001) is mechanically unstable under the current of a scanning tunneling microscope tip and can switch among configurations. However, these are not equally accessible, and the switching critical current depends on the bias polarity. In order to explain such rich phenomenology, we have developed a scheme to evaluate the evolution of the reaction paths and activation barriers as a function of bias, which is rooted in the nonequilibrium Green\\'s function method implemented within density functional theory. This, combined with the calculation of the inelastic electron tunneling spectroscopy signal, allows us to identify the vibrational modes promoting the observed molecular conformational changes. Finally, once our ab initio results are used within a resonance model, we are able to explain the details of the switching behavior, such as its dependence on the bias polarity, and the noninteger power relation between the reaction rate constants and both the bias voltage and the electric current. © 2013 American Physical Society.

  9. Quantum current of a molecular photo-switch between two graphene sheets

    Brivio, G. P.; Motta, C.; Trioni, M. I.; Sebastian, K. L.

    2011-03-01

    Light responsive materials that reversibly change shape under alternate UV and visible irradiation have attracted much interest because they can be used as optical switches, since the isomers show different features in the dimension, HOMO-LUMO gap and transmission spectrum. In view to integrate the photo-switch in the carbon based electronics devices, the conductance of a system constituted by a photochromic molecule between two graphene electrodes is investigated. In this work the conductance of the junction formed by diarylperfluorocyclopentene between two semi-infinite graphene sheets was computed using the non-equilibrium Green's function method combined with density functional theory via the TranSiesta code. The results emphasize the role of the graphene and the molecular electronic states in the switching behaviour of this hybrid system.

  10. The importance of the rotor in hydrazone-based molecular switches

    Xin Su

    2012-06-01

    Full Text Available The pH-activated E/Z isomerization of a series of hydrazone-based systems having different functional groups as part of the rotor (R = COMe, CN, Me, H, was studied. The switching efficiency of these systems was compared to that of a hydrazone-based molecular switch (R = COOEt whose E/Z isomerization is fully reversible. It was found that the nature of the R group is critical for efficient switching to occur; the R group should be a moderate H-bond acceptor in order to (i provide enough driving force for the rotor to move upon protonation, and (ii stabilize the obtained Z configuration, to achieve full conversion.

  11. Understanding and controlling regime switching in molecular diffusion

    Hallerberg, S.; de Wijn, A. S.

    2014-12-01

    Diffusion can be strongly affected by ballistic flights (long jumps) as well as long-lived sticking trajectories (long sticks). Using statistical inference techniques in the spirit of Granger causality, we investigate the appearance of long jumps and sticks in molecular-dynamics simulations of diffusion in a prototype system, a benzene molecule on a graphite substrate. We find that specific fluctuations in certain, but not all, internal degrees of freedom of the molecule can be linked to either long jumps or sticks. Furthermore, by changing the prevalence of these predictors with an outside influence, the diffusion of the molecule can be controlled. The approach presented in this proof of concept study is very generic and can be applied to larger and more complex molecules. Additionally, the predictor variables can be chosen in a general way so as to be accessible in experiments, making the method feasible for control of diffusion in applications. Our results also demonstrate that data-mining techniques can be used to investigate the phase-space structure of high-dimensional nonlinear dynamical systems.

  12. Single molecular switch based on thiol tethered iron(II)clathrochelate on gold

    Molecular electronics has been associated with high density nano-electronic devices. Developments of molecular electronic devices were based on reversible switching of molecules between the two conductive states. In this paper, self-assembled monolayers of dodecanethiol (DDT) and thiol tethered iron(II)clathrochelate (IC) have been prepared on gold film. The electrochemical and electronic properties of IC molecules inserted into the dodecanethiol monolayer (IC-DDT SAM) were investigated using voltammetric, electrochemical impedance spectroscopy (EIS), scanning tunneling microscopy (STM) and cross-wire tunneling measurements. The voltage triggered switching behaviour of IC molecules on mixed SAM was demonstrated. Deposition of polyaniline on the redox sites of IC-DDT SAM using electrochemical polymerization of aniline was performed in order to confirm that this monolayer acts as nano-patterned semiconducting electrode surface.

  13. The Limiting Dynamics of a Bistable Molecular Switch With and Without Noise

    Mackey, Michael C.; Tyran-Kaminska, Marta

    2015-01-01

    We consider the dynamics of a population of organisms containing two mutually inhibitory gene regulatory networks, that can result in a bistable switch-like behaviour. We completely characterize their local and global dynamics in the absence of any noise, and then go on to consider the effects of either noise coming from bursting (transcription or translation), or Gaussian noise in molecular degradation rates when there is a dominant slow variable in the system. We show analytically how the s...

  14. Multitarget Molecular Hybrids of Cinnamic Acids

    Aikaterini Peperidou

    2014-12-01

    Full Text Available In an attempt to synthesize potential new multitarget agents, 11 novel hybrids incorporating cinnamic acids and paracetamol, 4-/7-hydroxycoumarin, benzocaine, p-aminophenol and m-aminophenol were synthesized. Three hybrids—2e, 2a, 2g—and 3b were found to be multifunctional agents. The hybrid 2e derived from the phenoxyphenyl cinnamic acid and m-acetamidophenol showed the highest lipoxygenase (LOX inhibition and analgesic activity (IC50 = 0.34 μΜ and 98.1%, whereas the hybrid 3b of bromobenzyloxycinnamic acid and hymechromone exhibited simultaneously good LOX inhibitory activity (IC50 = 50 μΜ and the highest anti-proteolytic activity (IC50= 5 μΜ. The hybrid 2a of phenyloxyphenyl acid with paracetamol showed a high analgesic activity (91% and appears to be a promising agent for treating peripheral nerve injuries. Hybrid 2g which has an ester and an amide bond presents an interesting combination of anti-LOX and anti-proteolytic activity. The esters were found very potent and especially those derived from paracetamol and m-acetamidophenol. The amides follow. Based on 2D-structure–activity relationships it was observed that both steric and electronic parameters play major roles in the activity of these compounds. Molecular docking studies point to the fact that allosteric interactions might govern the LOX-inhibitor binding.

  15. Research Update: Molecular electronics: The single-molecule switch and transistor

    Kai Sotthewes

    2014-01-01

    Full Text Available In order to design and realize single-molecule devices it is essential to have a good understanding of the properties of an individual molecule. For electronic applications, the most important property of a molecule is its conductance. Here we show how a single octanethiol molecule can be connected to macroscopic leads and how the transport properties of the molecule can be measured. Based on this knowledge we have realized two single-molecule devices: a molecular switch and a molecular transistor. The switch can be opened and closed at will by carefully adjusting the separation between the electrical contacts and the voltage drop across the contacts. This single-molecular switch operates in a broad temperature range from cryogenic temperatures all the way up to room temperature. Via mechanical gating, i.e., compressing or stretching of the octanethiol molecule, by varying the contact's interspace, we are able to systematically adjust the conductance of the electrode-octanethiol-electrode junction. This two-terminal single-molecule transistor is very robust, but the amplification factor is rather limited.

  16. The limiting dynamics of a bistable molecular switch with and without noise.

    Mackey, Michael C; Tyran-Kamińska, Marta

    2016-08-01

    We consider the dynamics of a population of organisms containing two mutually inhibitory gene regulatory networks, that can result in a bistable switch-like behaviour. We completely characterize their local and global dynamics in the absence of any noise, and then go on to consider the effects of either noise coming from bursting (transcription or translation), or Gaussian noise in molecular degradation rates when there is a dominant slow variable in the system. We show analytically how the steady state distribution in the population can range from a single unimodal distribution through a bimodal distribution and give the explicit analytic form for the invariant stationary density which is globally asymptotically stable. Rather remarkably, the behaviour of the stationary density with respect to the parameters characterizing the molecular behaviour of the bistable switch is qualitatively identical in the presence of noise coming from bursting as well as in the presence of Gaussian noise in the degradation rate. This implies that one cannot distinguish between either the dominant source or nature of noise based on the stationary molecular distribution in a population of cells. We finally show that the switch model with bursting but two dominant slow genes has an asymptotically stable stationary density. PMID:26692266

  17. Lactobacillus plantarum possesses the capability for wall teichoic acid backbone alditol switching

    Bron Peter A

    2012-09-01

    Full Text Available Abstract Background Specific strains of Lactobacillus plantarum are marketed as health-promoting probiotics. The role and interplay of cell-wall compounds like wall- and lipo-teichoic acids (WTA and LTA in bacterial physiology and probiotic-host interactions remain obscure. L. plantarum WCFS1 harbors the genetic potential to switch WTA backbone alditol, providing an opportunity to study the impact of WTA backbone modifications in an isogenic background. Results Through genome mining and mutagenesis we constructed derivatives that synthesize alternative WTA variants. The mutants were shown to completely lack WTA, or produce WTA and LTA that lack D-Ala substitution, or ribitol-backbone WTA instead of the wild-type glycerol-containing backbone. DNA micro-array experiments established that the tarIJKL gene cluster is required for the biosynthesis of this alternative WTA backbone, and suggest ribose and arabinose are precursors thereof. Increased tarIJKL expression was not observed in any of our previously performed DNA microarray experiments, nor in qRT-PCR analyses of L. plantarum grown on various carbon sources, leaving the natural conditions leading to WTA backbone alditol switching, if any, to be identified. Human embryonic kidney NF-κB reporter cells expressing Toll like receptor (TLR-2/6 were exposed to purified WTAs and/or the TA mutants, indicating that WTA is not directly involved in TLR-2/6 signaling, but attenuates this signaling in a backbone independent manner, likely by affecting the release and exposure of immunomodulatory compounds such as LTA. Moreover, human dendritic cells did not secrete any cytokines when purified WTAs were applied, whereas they secreted drastically decreased levels of the pro-inflammatory cytokines IL-12p70 and TNF-α after stimulation with the WTA mutants as compared to the wild-type. Conclusions The study presented here correlates structural differences in WTA to their functional characteristics, thereby

  18. Age-associated Cognitive Decline: Insights into Molecular Switches and Recovery Avenues

    Konar, Arpita; Singh, Padmanabh; Thakur, Mahendra K.

    2016-01-01

    Age-associated cognitive decline is an inevitable phenomenon that predisposes individuals for neurological and psychiatric disorders eventually affecting the quality of life. Scientists have endeavored to identify the key molecular switches that drive cognitive decline with advancing age. These newly identified molecules are then targeted as recovery of cognitive aging and related disorders. Cognitive decline during aging is multi-factorial and amongst several factors influencing this trajectory, gene expression changes are pivotal. Identifying these genes would elucidate the neurobiological underpinnings as well as offer clues that make certain individuals resilient to withstand the inevitable age-related deteriorations. Our laboratory has focused on this aspect and investigated a wide spectrum of genes involved in crucial brain functions that attribute to senescence induced cognitive deficits. We have recently identified master switches in the epigenome regulating gene expression alteration during brain aging. Interestingly, these factors when manipulated by chemical or genetic strategies successfully reverse the age-related cognitive impairments. In the present article, we review findings from our laboratory and others combined with supporting literary evidences on molecular switches of brain aging and their potential as recovery targets.

  19. Proteomic analysis of mitochondria reveals a metabolic switch from fatty acid oxidation to glycolysis in the failing heart

    WANG Jun; WANG TingZhong; LIU Ping; FAN FenLing; GUAN YouFei; MA AiQun; BAI Ling; LI Jing; SUN ChaoFeng; ZHAO Jin; CUI ChangCong; HAN Ke; LIU Yu; ZHUO XiaoZhen

    2009-01-01

    This work characterizes the mitochondrial proteomic profile in the failing heart and elucidates the molecular basis of mitochondria in heart failure.Heart failure was induced in rats by myocardial infarction,and mitochondria were isolated from hearts by differential centrifugation.Using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry,a system biology approach was employed to investigate differences in mitochondrial proteins between normal and failing hearts.Mass spectrometry identified 27 proteins differentially expressed that involved in energy metabolism.Among those,the up-regulated proteins included tricarboxylic acid cycle enzymes and pyruvate dehydrogenase complex subunita while the down-regulated proteins were involved in fatty acid oxidation and the OXPHOS complex.These results suggest a substantial metabolic switch from free fatty acid oxidation to glycolysis in heart failure and provide molecular evidence for alterations in the structural and functional parameters of mitochondria that may contribute to cardiac dysfunction during ischemic injury.

  20. Photocontrolled Reversible Luminescent Lanthanide Molecular Switch Based on a Diarylethene-Europium Dyad.

    Cheng, Hong-Bo; Hu, Guo-Fei; Zhang, Zhan-Hui; Gao, Liang; Gao, Xingfa; Wu, Hai-Chen

    2016-08-15

    A new europium complex coordinated between a Eu(III) ion and an unsymmetrical diarylperfluorocyclopentene yields a light-controlled diarylethene-europium dyad, DAE@TpyEu(tta)3, whose photophysical properties can be reversibly switched by optical stimuli. When DAE@TpyEu(tta)3 is exposed to 365 nm UV light, an efficient intramolecular photochromic fluorescence resonance energy transfer (pc-FRET) occurs between the emission of the Eu(3+) donor (D) and the absorption of the diarylethene acceptor (A) in closed-form DAE@TpyEu(tta)3 accompanied by luminescence quenching. However, the pc-FRET process could be effectively inhibited by visible light (λ > 600 nm) irradiation, and the lanthanide emission of DAE@TpyEu(tta)3 is rapidly recovered. Furthermore, this luminescent lanthanide molecular switch could serve as a highly reliable and sensitive "turn on" fluorescent marker in living cells irradiated by red light without any optical interference. PMID:27447742

  1. 'Molecular switch' vectors for hypoxia- and radiation-mediated gene therapy of cancer

    Intratumoral areas of low oxygen concentration are known to be refractive to radiotherapy treatment. However, this physiological condition can be exploited for selective cancer gene therapy. We have developed a series of synthetic promoters selectively responsive to both hypoxia and ionizing radiation (IR). These promoters contain hypoxia regulatory elements (HREs) from the erythropoietin (Epo), the phosphoglycerate kinase1(PGK1) and vascular endothelial growth factor (VEGF) genes, and/or IR-responsive CArG elements from the Early Growth Response 1 (Egr1) gene. The HRE and CArG promoters were able to regulate expression of reporter and suicide genes in human tumor cells, following corresponding stimulation with hypoxia (0.1% O2) or X-irradiation (5Gy) [Greco et al, 2002, Gene Therapy 9:1403]. Furthermore, the chimeric HRE + CArG promoters could be activated by these stimuli independently or even more significantly when given in combination, with the Epo HRE/CArG promoter proving to be the most responsive and robust. In order to amplify and maintain transgene expression even following withdrawal of the triggering stimuli, we have developed a 'molecular switch' system [Scott et al, 2000, Gene Therapy 7:1121]. This 'switch' system has now been engineered as a single vector molecule, containing HRE and CArG promoters. This new series of HRE/CArG switch vectors have been tested in a herpes simplex thymidine kinase (HSVtk)/ganciclovir (GCV) suicide gene assay. Results indicate that a) higher and more selective tumor cell kill is achieved with the switch when compared with the HRE and CArG promoters directly driving HSVtk expression and b) the Epo HRE/CArG switch vectors appear to function as efficiently as the strong constitutive cytomegalovirus (CMV) promoter construct

  2. Transient photocurrent in molecular junctions: singlet switching on and triplet blocking.

    Petrov, E G; Leonov, V O; Snitsarev, V

    2013-05-14

    The kinetic approach adapted to describe charge transmission in molecular junctions, is used for the analysis of the photocurrent under conditions of moderate light intensity of the photochromic molecule. In the framework of the HOMO-LUMO model for the single electron molecular states, the analytic expressions describing the temporary behavior of the transient and steady state sequential (hopping) as well as direct (tunnel) current components have been derived. The conditions at which the current components achieve their maximal values are indicated. It is shown that if the rates of charge transmission in the unbiased molecular diode are much lower than the intramolecular singlet-singlet excitation/de-excitation rate, and the threefold degenerated triplet excited state of the molecule behaves like a trap blocking the charge transmission, a possibility of a large peak-like transient switch-on photocurrent arises. PMID:23676066

  3. Mucosal transmissibility, disease induction and coreceptor switching of R5 SHIVSF162P3N molecular clones in rhesus macaques

    Ren Wuze

    2013-01-01

    Full Text Available Abstract Background Mucosally transmissible and pathogenic CCR5 (R5-tropic simian-human immunodeficiency virus (SHIV molecular clones are useful reagents to identity neutralization escape in HIV-1 vaccine experiments and to study the envelope evolutionary process and mechanistic basis for coreceptor switch during the course of natural infection. Results We observed progression to AIDS in rhesus macaques infected intrarectally with molecular clones of the pathogenic R5 SHIVSF162P3N isolate. Expansion to CXCR4 usage was documented in one diseased macaque that mounted a neutralizing antibody response and in another that failed to do so, with the latter displaying a rapid progressor phenotype. V3 loop envelop glycoprotein gp120 sequence changes that are predictive of a CXCR4 (X4-using phenotype in HIV-1 subtype B primary isolates, specifically basic amino acid substations at positions 11 (S11R, 24 (G24R and 25 (D25K of the loop were detected in the two infected macaques. Functional assays showed that envelopes with V3 S11R or D25K mutation were dual-tropic, infecting CD4+ target cells that expressed either the CCR5 or CXCR4 coreceptor. And, consistent with findings of coreceptor switching in macaques infected with the pathogenic isolate, CXCR4-using variant was first detected in the lymph node of the chronically infected rhesus monkey several weeks prior to its presence in peripheral blood. Moreover, X4 emergence in this macaque coincided with persistent peripheral CD4+ T cell loss and a decline in neutralizing antibody titer that are suggestive of immune deterioration, with macrophages as the major virus-producing cells at the end-stage of disease. Conclusions The data showed that molecular clones derived from the R5 SHIVSF162P3N isolate are mucosally transmissible and induced disease in a manner similar to that observed in HIV-1 infected individuals, providing a relevant and useful animal infection model for in-depth analyses of host selection

  4. Novel tailor-made externally triggerable single-molecular switches for molecular electronics

    Harzmann, Gero

    2015-01-01

    Molecular electronics marks a highly interdisciplinary scientific field, in which physicists, chemists, and biologist jointly investigate electronic phenomena on a molecular level. Herein, the foremost task of the chemist is the design and synthesis of novel, tailor-made model compounds bearing externally addressable or controllable functions, which are predominantly of electronic nature. This present PhD thesis mainly focusses on the synthetic aspects towards innovative metalorga...

  5. A molecular beacon-based DNA switch for reversible pH sensing in vesicles and live cells.

    Narayanaswamy, Nagarjun; Nair, Raji R; Suseela, Y V; Saini, Deepak Kumar; Govindaraju, T

    2016-07-01

    In this Communication, a molecular beacon-based DNA switch (LMB) is developed as an efficient and reversible pH sensing probe. Remarkably, LMB exhibited reversible structural transition between the closed (molecular beacon) and open (A-motif) states very efficiently in synthetic vesicles and live cells without the need for any transfection agents. PMID:27338808

  6. Electron induced conformational changes of imine-based molecular switches on a Au(111) surface

    Lotze, Christian; Pascual, Jose Ignacio [Inst. f. Experimentalphysik, Freie Universitaet Berlin (Germany); Luo, Ying; Haag, Rainer [Inst. f. Organische Chemie, Freie Universitaet Berlin (Germany)

    2010-07-01

    Organic molecules exhibiting controllable reversible transitions between isomeric states on surfaces promise an enormous potential in the field of molecular electronics. The reversible cis-trans isomerization of azobenzene-like molecules is often hindered by a strong interaction of the nitrogen lone-pair electrons of the di-azo bridge (-N=N-) with the substrate. In order to improve the isomerization capabilities, the di-azo bridge is substituted by an imine-group (-N=CH-). Here, we use low-temperature scanning tunneling microscopy to investigate a sub-monolayer of the newly designed imine-based molecular switch NPCI on a Au(111) surface. Its carboxylic termination mediates the formation of hydrogen-bonded dimers, which align in rows along the herringbone reconstruction. We were able to induce reversible conformational changes with the tunneling electrons from the STM tip and determine its efficiency as a function of electron energy.

  7. Ferroelectric molecular field-switch based on double proton transfer process: Static and dynamical simulations

    Rode, Michał F.; Jankowska, Joanna; Sobolewski, Andrzej L.

    2016-04-01

    In this work, we present a reversible ferroelectric molecular switch controlled by an external electric field. The studied (2Z)-1-(6-((Z)-2-hydroxy-2-phenylvinyl)pyridin-3-yl)-2-(pyridin-2(1H)-ylidene)ethanone (DSA) molecule is polarized by two uniaxial intramolecular hydrogen bonds. Two protons can be transferred along hydrogen bonds upon an electric field applied along the main molecular axis. The process results in reversion of the dipole moment of the system. Static ab initio and on-the-fly dynamical simulations of the DSA molecule placed in an external electric field give insight into the mechanism of the double proton transfer (DPT) in the system and allow for estimation of the time scale of this process. The results indicate that with increasing strength of the electric field, the step-wise mechanism of DPT changes into the downhill barrierless process in which the synchronous and asynchronous DPTs compete with each other.

  8. Simultaneous and coordinated rotational switching of all molecular rotors in a network.

    Zhang, Y; Kersell, H; Stefak, R; Echeverria, J; Iancu, V; Perera, U G E; Li, Y; Deshpande, A; Braun, K-F; Joachim, C; Rapenne, G; Hla, S-W

    2016-08-01

    A range of artificial molecular systems has been created that can exhibit controlled linear and rotational motion. In the further development of such systems, a key step is the addition of communication between molecules in a network. Here, we show that a two-dimensional array of dipolar molecular rotors can undergo simultaneous rotational switching when applying an electric field from the tip of a scanning tunnelling microscope. Several hundred rotors made from porphyrin-based double-decker complexes can be simultaneously rotated when in a hexagonal rotor network on a Cu(111) surface by applying biases above 1 V at 80 K. The phenomenon is observed only in a hexagonal rotor network due to the degeneracy of the ground-state dipole rotational energy barrier of the system. Defects are essential to increase electric torque on the rotor network and to stabilize the switched rotor domains. At low biases and low initial rotator angles, slight reorientations of individual rotors can occur, resulting in the rotator arms pointing in different directions. Analysis reveals that the rotator arm directions are not random, but are coordinated to minimize energy via crosstalk among the rotors through dipolar interactions. PMID:27159740

  9. Molecular and Supramolecular Information Processing From Molecular Switches to Unconventional Computing

    Katz, Evgeny

    2012-01-01

    Edited by a renowned and much cited chemist, this book covers the whole span of molecular computers that are based on non-biological systems. The contributions by all the major scientists in the field provide an excellent overview of the latest developments in this rapidly expanding area. A must-have for all researchers working on this very hot topic. Perfectly complements Biomolecular Information Processing, also by Prof. Katz, and available as a two-volume set.

  10. Molecular Simulation of Naphthenic Acid Removal on Acidic Catalyst Ⅱ. Experimental results of catalytic decarboxylation over acidic catalysts

    Fu Xiaoqin; Tian Songbai; Hou Shuandi; Longjun; Wang Xieqing

    2008-01-01

    The energy barriers of thermal decarboxylation reactions of petroleum acids and catalytic decarboxylation reactions of Br(o)nsted acid and Lewis acid were analyzed using molecular simulation technology.Compared with thermal decarboxylation reactions of petroleum acids, the decarboxylation reactions by acid catalysts were easier to occur. The decarboxylaton effect by Lewis acid was better than Br(o)nsted acid. The mechanisms of catalytic decarboxylation over acid catalyst were also verified by experiments on a fixed bed and a fluidized bed, the experimental results showed that the rate of acid removal could reach up to 97% over the acidic catalyst at a temperature above 400℃.

  11. Photoisomerization dynamics of a rhodopsin-based molecule (potential molecular switch) with high quantum yields

    Allen, Roland; Jiang, Chen-Wei; Zhang, Xiu-Xing; Fang, Ai-Ping; Li, Hong-Rong; Xie, Rui-Hua; Li, Fu-Li

    2015-03-01

    It is worthwhile to explore the detailed reaction dynamics of various candidates for molecular switches, in order to understand, e.g., the differences in quantum yields and switching times. Here we report density-functional-based simulations for the rhodopsin-based molecule 4-[4-Methylbenzylidene]-5-p-tolyl-3,4-dihydro-2H-pyrrole (MDP), synthesized by Sampedro et al. We find that the photoisomerization quantum yields are remarkably high: 82% for cis-to-trans, and 68% for trans-to-cis. The lifetimes of the S1 excited state in cis-MDP in our calculations are in the range of 900-1800 fs, with a mean value of 1270 fs, while the range of times required for full cis-to-trans isomerization are 1100-2000 fs, with a mean value of 1530 fs. In trans-MDP, the calculated S1 excited state lifetimes are 860-2140 fs, with a mean value of 1330 fs, and with the full trans-to-cis isomerization completed about 200 fs later. In both cases, the dominant reaction mechanism is rotation around the central C =C bond (connected to the pyrroline ring), and de-excitation occurs at an avoided crossing between the ground state and the lowest singlet state, near the midpoint of the rotational pathway. Research Fund for the Doctoral Program of Higher Education of China; Fundamental Research Funds for the Central Universities; Robert A. Welch Foundation; National Natural Science Foundation of China.

  12. Selective detection of fenaminosulf via a molecularly imprinted fluorescence switch and silver nano-film amplification.

    Li, Shuhuai; Yin, Guihao; Zhang, Qun; Li, Chunli; Luo, Jinhui; Xu, Zhi; Qin, Anli

    2015-09-15

    A novel fluorescence switch sensor was constructed for detecting the fungicide fenaminosulf (FM), based on a dye-doped molecularly imprinted polymer (MIP) and silver nanofilm amplification. The MIP was prepared by electropolymerization of hydroquinone doped with neutral red on the silver nanofilm modified electrode. A fluorescence signal was produced by the neutral red and the fluorescence intensity was diminished by the ion pair that formed via electrostatic forces between FM and the dye. Therefore, elution and adsorption of FM by the MIP acted as a switch to control the fluorescence intensity, which was effectively amplified by the silver nanofilm. The decrease in fluorescence intensity was linear with the FM concentration, establishing a new method for FM detection. Under optimal conditions, good linear correlation was obtained for FM concentrations over the range from 2.0 × 10(-10) to 4.0 × 10(-8)mol/L, with a detection limit of 1.6 × 10(-11)mol/L. This method was utilized to determine residual FM in vegetable samples, and recoveries ranging from 92.0% to 110% were obtained. PMID:25930004

  13. Photoinduced reversible switching of porosity in molecular crystals based on star-shaped azobenzene tetramers

    Baroncini, Massimo; D'Agostino, Simone; Bergamini, Giacomo; Ceroni, Paola; Comotti, Angiolina; Sozzani, Piero; Bassanetti, Irene; Grepioni, Fabrizia; Hernandez, Taylor M.; Silvi, Serena; Venturi, Margherita; Credi, Alberto

    2015-08-01

    The development of solid materials that can be reversibly interconverted by light between forms with different physico-chemical properties is of great interest for separation, catalysis, optoelectronics, holography, mechanical actuation and solar energy conversion. Here, we describe a series of shape-persistent azobenzene tetramers that form porous molecular crystals in their E-configuration, the porosity of which can be tuned by changing the peripheral substituents on the molecule. Efficient E→Z photoisomerization of the azobenzene units takes place in the solid state and converts the crystals into a non-porous amorphous melt phase. Crystallinity and porosity are restored upon Z→E isomerization promoted by visible light irradiation or heating. We demonstrate that the photoisomerization enables reversible on/off switching of optical properties such as birefringence as well as the capture of CO2 from the gas phase. The linear design, structural versatility and synthetic accessibility make this new family of materials potentially interesting for technological applications.

  14. Photodynamic activation as a molecular switch to promote osteoblast cell differentiation via AP-1 activation.

    Kushibiki, Toshihiro; Tu, Yupeng; Abu-Yousif, Adnan O; Hasan, Tayyaba

    2015-01-01

    In photodynamic therapy (PDT), cells are impregnated with a photosensitizing agent that is activated by light irradiation, thereby photochemically generating reactive oxygen species (ROS). The amounts of ROS produced depends on the PDT dose and the nature of the photosensitizer. Although high levels of ROS are cytotoxic, at physiological levels they play a key role as second messengers in cellular signaling pathways, pluripotency, and differentiation of stem cells. To investigate further the use of photochemically triggered manipulation of such pathways, we exposed mouse osteoblast precursor cells and rat primary mesenchymal stromal cells to low-dose PDT. Our results demonstrate that low-dose PDT can promote osteoblast differentiation via the activation of activator protein-1 (AP-1). Although PDT has been used primarily as an anti-cancer therapy, the use of light as a photochemical "molecular switch" to promote differentiation should expand the utility of this method in basic research and clinical applications. PMID:26279470

  15. Synthesis and Characterization of Molecularly Imprinted Polymers for Phenoxyacetic Acids

    Canping Pan

    2008-01-01

    Full Text Available 2-methylphenoxyacetic acid (2-MPA, 2-methyl-4-chlorophenxyacetic acid (MCPA and 4-chlorophenoxyacetic acid (4-CPA were imprinted to investigate the cross-selectivities of molecularly imprinted polymers (MIPs. The result indicates that 2-MPA, which is similar in shape, size and functionality with phenoxyacetic herbicides, are suitable to be used as a suitable template to prepare the MIPs for retaining phenoxyacetic herbicides. To study the ion-pair interactions between template molecules and functional monomer 4-vinylpiridine (4-VP, computational molecular modeling was employed. The data indicate that the cross-selectivities of MIPs for phenoxyacetic acid herbicides depend on the binding energies of complexes.

  16. The molecular physiology of uric acid homeostasis.

    Mandal, Asim K; Mount, David B

    2015-01-01

    Uric acid, generated from the metabolism of purines, has proven and emerging roles in human disease. Serum uric acid is determined by production and the net balance of reabsorption or secretion by the kidney and intestine. A detailed understanding of epithelial absorption and secretion of uric acid has recently emerged, aided in particular by the results of genome-wide association studies of hyperuricemia. Novel genetic and regulatory networks with effects on uric acid homeostasis have also emerged. These developments promise to lead to a new understanding of the various diseases associated with hyperuricemia and to novel, targeted therapies for hyperuricemia. PMID:25422986

  17. Molecular Modeling of Nucleic Acid Structure: Energy and Sampling

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E.

    2001-01-01

    An overview of computer simulation techniques as applied to nucleic acid systems is presented. This unit discusses methods used to treat the energy and to sample representative configurations. Emphasis is placed on molecular mechanics and empirical force fields.

  18. Contribution of the metal/SiO2 interface potential to photoinduced switching in molecular single-electron tunneling junctions

    Photoinduced switching of the Coulomb staircase in molecular single-electron tunneling junctions was previously observed. These junctions consisted of evaporated SiO2 insulator (∼5 nm), with tetrakis-3,5-di-t-butylphenyl-porphyrin (H2-TBPP) molecules as Coulomb islands, sandwiched between top and bottom electrodes. The reversible response and the relaxation time of the photoinduced switching suggest that this phenomenon depends on the properties of the metal/SiO2 interface rather than those of the H2-TBPP molecule or SiO2 tunneling layer. We analyzed the photoinduced switching according to the theory of single-electron tunneling taking into account the discrete molecular energy states and the metal/SiO2 interfacial electrostatic phenomena. We conclude that the main contributor to the photoinduced shift was the electrostatic potential formed through the space-charge exchange at the metal/SiO2 interface

  19. Tip-induced domain structures and polarization switching in ferroelectric amino acid glycine

    Bioorganic ferroelectrics and piezoelectrics are becoming increasingly important in view of their intrinsic compatibility with biological environment and biofunctionality combined with strong piezoelectric effect and a switchable polarization at room temperature. Here, we study tip-induced domain structures and polarization switching in the smallest amino acid β-glycine, representing a broad class of non-centrosymmetric amino acids. We show that β-glycine is indeed a room-temperature ferroelectric and polarization can be switched by applying a bias to non-polar cuts via a conducting tip of atomic force microscope (AFM). Dynamics of these in-plane domains is studied as a function of an applied voltage and pulse duration. The domain shape is dictated by polarization screening at the domain boundaries and mediated by growth defects. Thermodynamic theory is applied to explain the domain propagation induced by the AFM tip. Our findings suggest that the properties of β-glycine are controlled by the charged domain walls which in turn can be manipulated by an external bias

  20. Tip-induced domain structures and polarization switching in ferroelectric amino acid glycine

    Seyedhosseini, E., E-mail: Seyedhosseini@ua.pt; Ivanov, M. [CICECO-Aveiro Institute of Materials and Department of Physics, University of Aveiro, 3810-193 Aveiro (Portugal); Bdikin, I. [TEMA and Department of Mechanical Engineering, University of Aveiro, 3810-193 Aveiro (Portugal); Vasileva, D. [Institute of Natural Sciences, Ural Federal University, 620000 Ekaterinburg (Russian Federation); Kudryavtsev, A. [Moscow State Institute of Radioengineering, Electronics and Automation, 119454 Moscow (Russian Federation); Rodriguez, B. J. [Conway Institute of Biomolecular and Biomedical Research and School of Physics, University College Dublin, Dublin (Ireland); Kholkin, A. L. [CICECO-Aveiro Institute of Materials and Department of Physics, University of Aveiro, 3810-193 Aveiro (Portugal); Institute of Natural Sciences, Ural Federal University, 620000 Ekaterinburg (Russian Federation)

    2015-08-21

    Bioorganic ferroelectrics and piezoelectrics are becoming increasingly important in view of their intrinsic compatibility with biological environment and biofunctionality combined with strong piezoelectric effect and a switchable polarization at room temperature. Here, we study tip-induced domain structures and polarization switching in the smallest amino acid β-glycine, representing a broad class of non-centrosymmetric amino acids. We show that β-glycine is indeed a room-temperature ferroelectric and polarization can be switched by applying a bias to non-polar cuts via a conducting tip of atomic force microscope (AFM). Dynamics of these in-plane domains is studied as a function of an applied voltage and pulse duration. The domain shape is dictated by polarization screening at the domain boundaries and mediated by growth defects. Thermodynamic theory is applied to explain the domain propagation induced by the AFM tip. Our findings suggest that the properties of β-glycine are controlled by the charged domain walls which in turn can be manipulated by an external bias.

  1. Mucosal transmissibility, disease induction and coreceptor switching of R5 SHIVSF162P3N molecular clones in rhesus macaques

    Ren Wuze; Mumbauer Alexandra; Zhuang Ke; Harbison Carole; Knight Heather; Westmoreland Susan; Gettie Agegnehu; Blanchard James; Cheng-Mayer Cecilia

    2013-01-01

    Abstract Background Mucosally transmissible and pathogenic CCR5 (R5)-tropic simian-human immunodeficiency virus (SHIV) molecular clones are useful reagents to identity neutralization escape in HIV-1 vaccine experiments and to study the envelope evolutionary process and mechanistic basis for coreceptor switch during the course of natural infection. Results We observed progression to AIDS in rhesus macaques infected intrarectally with molecular clones of the pathogenic R5 SHIVSF162P3N isolate. ...

  2. Controlling the color of cholesteric liquid-crystalline films by photoirradiation of a chiroptical molecular switch used as dopant

    van Delden, RA; Huck, NPM; Feringa, BL; Delden, Richard A. van; Gelder, Marc B. van; Huck, Nina P.M.

    2003-01-01

    Using thin films of a cholesteric mixture of acrylates 2 and 3 doped with the chiroptical molecular switch (M)-trans-1, photo-control of the reflection color between red and green is possible. This doped liquid-crystal (LC) film can be used for photoinduced writing, color reading, and photoinduced l

  3. Accurate Molecular Dimensions from Stearic Acid Monolayers.

    Lane, Charles A.; And Others

    1984-01-01

    Discusses modifications in the fatty acid monolayer experiment to reduce the inaccurate moleculary data students usually obtain. Copies of the experimental procedure used and a Pascal computer program to work up the data are available from the authors. (JN)

  4. Molecular Modeling of Trifluoromethanesulfonic Acid for Solvation Theory

    Paddison, S J; Zawodzinski, T; Reagor, D W; Paddison, Stephen J.; Pratt, Lawrence R.; Zawodzinski, Thomas; Reagor, David W.

    1997-01-01

    Reported here are theoretical calculations on the triflic acid and water, establishing molecular scale information necessary to modeling of the structure, thermodynamics, and ionic transport of Nafion membranes. To characterize side chain flexibility and accessibility of the acid proton, free energies for rotation of both carbon-sulfur and sulfur-oxygen (hydroxyl) bonds are presented. The energetic barrier to rotation of the acid proton away from the sulfonic acid oxygen plane is substantially flattened, with barrier less than one kcal/mol, by electrostatic solvation. The activation free energy for acid-water proton interchange is about 4.7 kcal/mol.

  5. Synthesis and Characterization of Molecularly Imprinted Polymers for Phenoxyacetic Acids

    Canping Pan; Tiechun Chen; Fulin Zong; Tao Song; Huiting Zhang

    2008-01-01

    2-methylphenoxyacetic acid (2-MPA), 2-methyl-4-chlorophenxyacetic acid (MCPA) and 4-chlorophenoxyacetic acid (4-CPA) were imprinted to investigate the cross-selectivities of molecularly imprinted polymers (MIPs). The result indicates that 2-MPA, which is similar in shape, size and functionality with phenoxyacetic herbicides, are suitable to be used as a suitable template to prepare the MIPs for retaining phenoxyacetic herbicides. To study the ion-pair interactions between template molecules a...

  6. The Molecular Switching Mechanism at the Conserved D(E)RY Motif in Class-A GPCRs.

    Sandoval, Angelica; Eichler, Stefanie; Madathil, Sineej; Reeves, Philip J; Fahmy, Karim; Böckmann, Rainer A

    2016-07-12

    The disruption of ionic and H-bond interactions between the cytosolic ends of transmembrane helices TM3 and TM6 of class-A (rhodopsin-like) G protein-coupled receptors (GPCRs) is a hallmark for their activation by chemical or physical stimuli. In the bovine photoreceptor rhodopsin, this is accompanied by proton uptake at Glu(134) in the class-conserved D(E)RY motif. Studies on TM3 model peptides proposed a crucial role of the lipid bilayer in linking protonation to stabilization of an active state-like conformation. However, the molecular details of this linkage could not be resolved and have been addressed in this study by molecular dynamics (MD) simulations on TM3 model peptides in a bilayer of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). We show that protonation of the conserved glutamic acid alters the peptide insertion depth in the membrane, its side-chain rotamer preferences, and stabilizes the C-terminal helical structure. These factors contribute to the rise of the side-chain pKa (> 6) and to reduced polarity around the TM3 C terminus as confirmed by fluorescence spectroscopy. Helix stabilization requires the protonated carboxyl group; unexpectedly, this stabilization could not be evoked with an amide in MD simulations. Additionally, time-resolved Fourier transform infrared (FTIR) spectroscopy of TM3 model peptides revealed a different kinetics for lipid ester carbonyl hydration, suggesting that the carboxyl is linked to more extended H-bond clusters than an amide. Remarkably, this was seen as well in DOPC-reconstituted Glu(134)- and Gln(134)-containing bovine opsin mutants and demonstrates that the D(E)RY motif is a hydrated microdomain. The function of the D(E)RY motif as a proton switch is suggested to be based on the reorganization of the H-bond network at the membrane interface. PMID:27410736

  7. A dynamic view of molecular switch behavior at serotonin receptors: implications for functional selectivity.

    Martí-Solano, Maria; Sanz, Ferran; Pastor, Manuel; Selent, Jana

    2014-01-01

    Functional selectivity is a property of G protein-coupled receptors that allows them to preferentially couple to particular signaling partners upon binding of biased agonists. Publication of the X-ray crystal structure of serotonergic 5-HT1B and 5-HT2B receptors in complex with ergotamine, a drug capable of activating G protein coupling and β-arrestin signaling at the 5-HT1B receptor but clearly favoring β-arrestin over G protein coupling at the 5-HT2B subtype, has recently provided structural insight into this phenomenon. In particular, these structures highlight the importance of specific residues, also called micro-switches, for differential receptor activation. In our work, we apply classical molecular dynamics simulations and enhanced sampling approaches to analyze the behavior of these micro-switches and their impact on the stabilization of particular receptor conformational states. Our analysis shows that differences in the conformational freedom of helix 6 between both receptors could explain their different G protein-coupling capacity. In particular, as compared to the 5-HT1B receptor, helix 6 movement in the 5-HT2B receptor can be constrained by two different mechanisms. On the one hand, an anchoring effect of ergotamine, which shows an increased capacity to interact with the extracellular part of helices 5 and 6 and stabilize them, hinders activation of a hydrophobic connector region at the center of the receptor. On the other hand, this connector region in an inactive conformation is further stabilized by unconserved contacts extending to the intracellular part of the 5-HT2B receptor, which hamper opening of the G protein binding site. This work highlights the importance of considering receptor capacity to adopt different conformational states from a dynamic perspective in order to underpin the structural basis of functional selectivity. PMID:25313636

  8. A dynamic view of molecular switch behavior at serotonin receptors: implications for functional selectivity.

    Maria Martí-Solano

    Full Text Available Functional selectivity is a property of G protein-coupled receptors that allows them to preferentially couple to particular signaling partners upon binding of biased agonists. Publication of the X-ray crystal structure of serotonergic 5-HT1B and 5-HT2B receptors in complex with ergotamine, a drug capable of activating G protein coupling and β-arrestin signaling at the 5-HT1B receptor but clearly favoring β-arrestin over G protein coupling at the 5-HT2B subtype, has recently provided structural insight into this phenomenon. In particular, these structures highlight the importance of specific residues, also called micro-switches, for differential receptor activation. In our work, we apply classical molecular dynamics simulations and enhanced sampling approaches to analyze the behavior of these micro-switches and their impact on the stabilization of particular receptor conformational states. Our analysis shows that differences in the conformational freedom of helix 6 between both receptors could explain their different G protein-coupling capacity. In particular, as compared to the 5-HT1B receptor, helix 6 movement in the 5-HT2B receptor can be constrained by two different mechanisms. On the one hand, an anchoring effect of ergotamine, which shows an increased capacity to interact with the extracellular part of helices 5 and 6 and stabilize them, hinders activation of a hydrophobic connector region at the center of the receptor. On the other hand, this connector region in an inactive conformation is further stabilized by unconserved contacts extending to the intracellular part of the 5-HT2B receptor, which hamper opening of the G protein binding site. This work highlights the importance of considering receptor capacity to adopt different conformational states from a dynamic perspective in order to underpin the structural basis of functional selectivity.

  9. An electrostatic/hydrogen bond switch as the basis for the specific interaction of phosphatidic acid with proteins.

    Kooijman, Edgar E; Tieleman, D Peter; Testerink, Christa; Munnik, Teun; Rijkers, Dirk T S; Burger, Koert N J; de Kruijff, Ben

    2007-04-13

    Phosphatidic acid (PA) is a minor but important phospholipid that, through specific interactions with proteins, plays a central role in several key cellular processes. The simple yet unique structure of PA, carrying just a phosphomonoester head group, suggests an important role for interactions with the positively charged essential residues in these proteins. We analyzed by solid-state magic angle spinning 31P NMR and molecular dynamics simulations the interaction of low concentrations of PA in model membranes with positively charged side chains of membrane-interacting peptides. Surprisingly, lysine and arginine residues increase the charge of PA, predominantly by forming hydrogen bonds with the phosphate of PA, thereby stabilizing the protein-lipid interaction. Our results demonstrate that this electrostatic/hydrogen bond switch turns the phosphate of PA into an effective and preferred docking site for lysine and arginine residues. In combination with the special packing properties of PA, PA may well be nature's preferred membrane lipid for interfacial insertion of positively charged membrane protein domains. PMID:17277311

  10. Electropolymerized Molecularly Imprinted Polypyrrole Film for Sensing of Clofibric Acid

    Bianca Schweiger

    2015-02-01

    Full Text Available Piezoelectric quartz crystals and analogous gold substrates were electrochemically coated with molecularly imprinted polypyrrole films for pulsed amperometric detection (PAD of clofibric acid, a metabolite of clofibrate. Cyclic voltammetry data obtained during polymerization and deposited weight estimations revealed a decrease of the polymerization rate with increasing clofibric acid concentration. XPS measurements indicated that clofibric acid could be removed after imprinting with an aqueous ethanol solution, which was further optimized by using PAD. Zeta potential and contact angle measurements revealed differences between molecularly imprinted (MIP and non-imprinted polymer (NIP layers. Binding experiments with clofibric acid and other substances showed a pronounced selectivity of the MIP for clofibric acid vs. carbamazepine, but the response of MIP and NIP to 2,4-dichlorophenoxyacetic acid was higher than that for clofibric acid. A smooth surface, revealed by AFM measurements, with roughness of 6–8 nm for imprinted and non-imprinted layers, might be a reason for an excessively low density of specific binding sites for clofibric acid. Furthermore, the decreased polymerization rate in the presence of clofibric acid might not result in well-defined polymer structures, which could be the reason for the lower sensitivity.

  11. A novel colorimetric triple-helix molecular switch aptasensor for ultrasensitive detection of tetracycline.

    Ramezani, Mohammad; Mohammad Danesh, Noor; Lavaee, Parirokh; Abnous, Khalil; Mohammad Taghdisi, Seyed

    2015-08-15

    Detection methods of antibiotic residues in blood serum and animal derived foods are of great interest. In this study a colorimetric aptasensor was designed for sensitive, selective and fast detection of tetracycline based on triple-helix molecular switch (THMS) and gold nanoparticles (AuNPs). As a biosensor, THMS shows distinct advantages including high stability, sensitivity and preserving the selectivity and affinity of the original aptamer. In the absence of tetracycline, THMS is stable, leading to the aggregation of AuNPs by salt and an obvious color change from red to blue. In the presence of tetracycline, aptamer binds to its target, signal transduction probe (STP) leaves the THMS and adsorbs on the surface of AuNPs. So the well-dispersed AuNPs remain stable against salt-induced aggregation with a red color. The presented aptasensor showed high selectivity toward tetracyclines with a limit of detection as low as 266 pM for tetracycline. The designed aptasensor was successfully applied to detect tetracycline in serum and milk. PMID:25814407

  12. Molecular switch for tuning ions across nanopores by an external electric field

    Active control of ion transport in nanoscale channels is attracting increasing attention. Recently, experimental and theoretical results have verified that depending on the charged surface of nanopores, the solution inside nanopores can contain either negative or positive ions, which does not happen in macroscale channels. However, the control of the surface chemistry of synthetic nanopores is difficult and the design of nanotubes with novel recognition mechanisms that regulate the ionic selectivity of negative and positive charges remains a challenge. We present here a design for an ion-selective nanopore that is controllable by external charges. Our molecular dynamics simulations show that this remarkable selectivity can be switched from predominantly negative to positive ions and that the magnitude of the ionic flux can be varied by changing the distance of the external charges. The results suggest that the hydration structures around ions play a prominent role in the selectivity process, which is tuned by the external charge. These studies may be useful for developing ways to control the behavior, properties and chemical composition of liquids and provide possible technical applications for nanofluidic field effect transistors. (paper)

  13. Temperature control of molecular circuit switch responsible for virulent phenotype expression in uropathogenic Escherichia coli

    Samoilov, Michael

    2010-03-01

    The behavior and fate of biological organisms are to a large extent dictated by their environment, which can be often viewed as a collection of features and constraints governed by physics laws. Since biological systems comprise networks of molecular interactions, one such key physical property is temperature, whose variations directly affect the rates of biochemical reactions involved. For instance, temperature is known to control many gene regulatory circuits responsible for pathogenicity in bacteria. One such example is type 1 fimbriae (T1F) -- the foremost virulence factor in uropathogenic E. coli (UPEC), which accounts for 80-90% of all community-acquired urinary tract infections (UTIs). The expression of T1F is randomly `phase variable', i.e. individual cells switch between virulent/fimbriate and avirulent/afimbriate phenotypes, with rates regulated by temperature. Our computational investigation of this process, which is based on FimB/FimE recombinase-mediated inversion of fimS DNA element, offers new insights into its discrete-stochastic kinetics. In particular, it elucidates the logic of T1F control optimization to the host temperature and contributes further understanding toward the development of novel therapeutic approaches to UPEC-caused UTIs.

  14. Simultaneous determination of amino acids and carbohydrates in culture media of Clostridium thermocellum by valve-switching ion chromatography.

    Fa, Yun; Yang, Haiyan; Ji, Chengshuai; Cui, He; Zhu, Xinshu; Du, Juan; Gao, Jun

    2013-10-10

    An improved method for the simultaneous determination of 20 amino acids and 7 carbohydrates using one-valve switching after injection, ion chromatography, and integrated pulsed amperometric detection is proposed. The resolution of the amino acids and carbohydrates in the cation trap column was investigated. In addition, parameters including flow liquid type, flow rate, concentration, and valve-switch timing were optimized. The method is time-saving, effective, and accurate for the simultaneous separation of amino acids and carbohydrates, with a mean correlation coefficient of >0.99 and repeatability of 0.5-4.6% for eight replicates. The method was successfully applied in the analysis of amino acids and carbohydrates in aseptic media and in extracellular culture media of three phenotypes of Clostridium thermocellum. PMID:24070489

  15. Ultrafast quantum spin-state switching in the Co-octaethylporphyrin molecular magnet with a terahertz pulsed magnetic field

    Farberovich, Oleg V.; Mazalova, Victoria L.

    2016-05-01

    Molecular spin crossover switches are the objects of intense theoretical and experimental studies in recent years. This interest is due to the fact that these systems allow one to control their spin state by applying an external photo-, thermo-, piezo-, or magnetic stimuli. The greatest amount of research is currently devoted to the study of the effect of the photoexcitation on the bi-stable states of spin crossover single molecular magnets (SMMs). The main limitation of photo-induced bi-stable states is their short lifetime. In this paper we present the results of a study of the spin dynamics of the Co-octaethylporphyrin (CoOEP) molecule in the Low Spin (LS) state and the High Spin (HS) state induced by applying the magnetic pulse of 36.8 T. We show that the spin switching in case of the HS state of the CoOEP molecule is characterized by a long lifetime and is dependent on the magnitude and duration of the applied field. Thus, after applying an external stimuli the system in the LS state after the spin switching reverts to its ground state, whereas the system in the HS state remains in the excited state for a long time. We found that the temperature dependency of magnetic susceptibility shows an abrupt thermal spin transition between two spin states at 40 K. Here the proposed theoretical approach opens the way to create modern devices for spintronics with the controllable spin switching process.

  16. Isomerization of Orthogonal Molecular Switches Encapsulated within Micelles Solubilizing Carbon Nanotubes

    Kreft, Stefanie K.; Petersen, Michael Åxman; Nielsen, Mogens Brøndsted;

    2015-01-01

    We study the effects of the proximity of the orthogonal dipole-switching moiety dihydroazulene/vinylheptafulvene (DHA/VHF) to carbon nanotubes (CNTs). The switches are introduced into a micelle surrounding the CNTs, thereby achieving very close proximity between the molecules and the CNTs for the...... first time. The change of the molecules' configuration is not hindered by its encapsulation: We report the reversible switching of molecules inside CNT surrounding micelles. The orthogonality of the switch also allows us for the first time to observe the effect of the molecule on the emission spectra of...

  17. Identification of the molecular switch that regulates access of 5α-DHT to the androgen receptor.

    Penning, Trevor M.; Bauman, David R.; Jin, Yi; Rizner, Tea Lanisik

    2007-01-01

    Pairs of hydroxysteroid dehydrogenases (HSDs) govern ligand access to steroid receptors in target tissues and act as molecular switches. By acting as reductases or oxidases, HSDs convert potent ligands into their cognate inactive metabolites or vice-versa. This pre-receptor regulation of steroid hormone action may have profound effects on hormonal response. We have identified the HSDs responsible for regulating ligand access to the androgen receptor (AR) in human prostate. Type 3 3α-hydroxyst...

  18. Study on Triplex DNA by Use of Molecular "Light Switch" Complex of Ru(phen)2(dppx)2+

    2003-01-01

    A new method for the study of triplex DNA is established according the fluorescence enhancement of molecular "Light Switch" complex of Ru(phen)2(dppx)2+ when it intercalate into triplex DNA. Because the fluorescence intensity of Ru(phen)2(dppx)2+ bonded to triplex DNA is in the case higher than that bonded to duplex DNA in certain range of DNA concentration, the method is much more sensitive than other methods reported previously.

  19. A Redox-Controllable Molecular Switch Based on Weak Recognition of BPX26C6 at a Diphenylurea Station

    Jia-Cheng Chang

    2015-01-01

    Full Text Available The Na+ ion–assisted recognition of urea derivatives by BPX26C6 has allowed the construction of a redox-controllable [2]rotaxane-type molecular switch based on two originally very weakly interacting host/guest systems. Using NOBF4 to oxidize the triarylamine terminus into a corresponding radical cation attracted the macrocyclic component toward its adjacent carbamate station; subsequent addition of Zn powder moved the macrocyclic component back to its urea station.

  20. Preparing and regulating a bi-stable molecular switch by atomic manipulation

    We present a scanning tunneling microscopy (STM) investigation into the influence of the STM tip on the adsorption site switching of polychlorinatedbiphenyl (PCB) molecules on the Si(111)-7 × 7 surface at room temperature. From an initially stable adsorption configuration, atomic manipulation by charge injection from the STM tip prepared a new bi-stable configuration that switched between two bonding arrangements. No switching rate bias dependence was found for + 1.0 to + 2.2 V. Assuming a thermally driven switching process we find that the measured energy barriers to switching are influenced by the exact location of the STM tip by more than 10%. We propose that this energy difference is due the dispersion interaction between the tip and the molecule.

  1. Aptamer contained triple-helix molecular switch for rapid fluorescent sensing of acetamiprid.

    Liu, Xin; Li, Ying; Liang, Jing; Zhu, Wenyue; Xu, Jingyue; Su, Ruifang; Yuan, Lei; Sun, Chunyan

    2016-11-01

    In this study, an aptamer-based fluorescent sensing platform using triple-helix molecular switch (THMS) was developed for the pesticide screening represented by acetamiprid. The THMS was composed of two tailored DNA probes: a label-free central target specific aptamer sequence flanked by two arm segments acting as a recognition probe; a hairpin-shaped structure oligonucleotide serving as a signal transduction probe (STP), labeled with a fluorophore and a quencher at the 3' and 5'-end, respectively. In the absence of acetamiprid, complementary bindings of two arm segments of the aptamers with the loop sequence of STP enforce the formation of THMS with the "open" configuration of STP, and the fluorescence of THMS is on. In the presence of target acetamiprid, the aptamer-target binding results in the formation of a structured aptamer/target complex, which disassembles the THMS and releases the STP. The free STP is folded to a stem loop structure, and the fluorescence is quenched. The quenched fluorescence intensity was proportional to the concentration of acetamiprid in the range from 100 to 1200nM, with the limit of detection (LOD) as low as 9.12nM. In addition, this THMS-based method has been successfully used to test and quantify acetamiprid in Chinese cabbage with satisfactory recoveries, and the results were in full agreement with those from LC-MS. The aptamer-based THMS presents distinct advantages, including high stability, remarkable sensitivity, and preservation of the affinity and specificity of the original aptamer. Most importantly, this strategy is convenient and generalizable by virtue of altering the aptamer sequence without changing the triple-helix structure. So, it is expected that this aptamer-based fluorescent assay could be extensively applied in the field of food safety inspection. PMID:27591592

  2. Molecular phylogeny of beetle associated diplogastrid nematodes suggests host switching rather than nematode-beetle coevolution

    Sommer Ralf J

    2009-08-01

    diplogastrid nematodes and their beetle hosts. Instead, frequent host switching is observed. The molecular phylogeny of the Diplogastridae provides a framework for further examinations of the evolution of these associations, for the study of interactions within the ecosystems, and for investigations of diplogastrid genome evolution.

  3. Incorporation of oxygen into abscisic acid and phaseic acid for molecular oxygen

    Abscisic acid accumulates in detached, wilted leaves of Xanthium strumariu. When these leaves are subsequently rehydrated, phaseic acid, a catabolite of abscisic acid, accumulates. Analysis by gas chromatography-mass spectrometry of phaseic acid isolated from stressed and subsequently rehydrated leaves placed in an atmosphere containing 20% 18O2 and 80% N2 indicates that one atom of 18O is incorporated in the 6'-hydroxymethyl group of phaseic acid. This suggests that the enzyme that converts abscisic acid to phaseic acid is an oxygenase. Analysis by gas chromatography-mass spectrometry of abscisic acid isolated from stressed leaves kept in an atmosphere containing 18O2 indicates that one atom of 18O is presented in the carboxyl group of abscisic acid. Thus, when abscisic acid accumulates in water-streesed leaves, only one of the four oxygens present in the abscisic acid molecule is derived from molecular oxygen. This suggest that either (a) the oxygen present in the 1'-, 4'-, and one of the two oxygens at the 1-position of abscisic acid arise from water, or (b) there exists a stored precursor with oxygen atoms already present in the 1'- and 4'-positions of abscisic acid which is converted to abscisic acid under conditions of water stress. 17 references, 2 figures, 1 tables

  4. Kinetics of molecular transformations in connective tissue hyaluronic acid

    When exposed to ionizing radiations or inflammatory disease, the glycosaminolycan component of connective tissue is preferentially degraded, probably by a free-radical mediate pathway. The resulting changes in molecular structure adversely change the properties of the matrix. Rooster comb hyaluronic acid of high molecular weight was used to investigate the mechanisms of these structural changes at macro and molecular level. Intrinsic viscosity and gel permeation chromatography measurements are suitable for demonstrating that random chain session occurs. Fast kinetic techniques are necessary to identify the mechanisms of single strand breaks. Pulse conductivity and low-angle laser light scattering pulse radiolysis can quantify the rate and yield of strand breaks. Competitive radical scavenging methods have also allowed the quantification of the rate of spontaneous and alkali-catalyzed hydrolysis of a-hydroxy radicals on polysaccharide chains, which control molecular structure changes

  5. Cyclic Zinc(II) Bisporphyrin-Based Molecular Switches: Supramolecular Control of Complexation-Mediated Conformational Switching and Photoinduced Electron Transfer.

    Mondal, Pritam; Rath, Sankar Prasad

    2016-04-11

    A cyclic zinc(II) bisporphyrin with flexible linker was employed as a dynamic molecular switch under the regulation of π-acceptors (tetracyanoquinodimethane, trinitrofluorenone, 9-dicyanomethylenefluorene) and bidentate N-donor ligands (1,4-diazabicyclo[2.2.2]octane, pyrazine, 4,4'-bipyridine). The cyclic bisporphyrin host can efficiently encapsulate the π-acceptor guests through the strong π-π interaction, which can be replaced again by using a bidentate N-donor ligand, which coordinates strongly with the metal centers. The open conformation of the bisporphyrin can be efficiently recovered by removing the bidentate ligands using Cu(+) ion. During the process, two porphyrin rings also reversibly change their relative orientation between perpendicular and parallel. The behavior of the cyclic bisporphyrin was followed by using UV/Vis, (1) H NMR, fluorescence, and electrochemical analyses along with X-ray structure determination of the complexes. Moreover, control of photoinduced electron transfer (PET "ON-OFF") is also achieved by the use of guest exchange. Association constants for the host-guest binding were very high, which further explains the robust nature of such assemblies in solution. The experimental evidence is supported by DFT calculations. Such controllable dynamic features can constitute a new step towards "smart" adaptive molecular devices and the emergence of such systems is of significant interest in supramolecular chemistry. PMID:27062017

  6. Molecular Dynamic Studies on Langmuir Monolayers of Stearic Acid

    KONG Chui-peng; ZHANG Hong-xing; ZHAO Zeng-xia; ZHENG Qing-chuan

    2013-01-01

    Compression isotherm for stearic acid was obtained by means of molecular dynamic simulation and compared to experimentally measured values for the Langmuir monolayers.Compared to the previous simulation,the present simulation has provided a method to reproduce the compression of the monolayer.The result is consistent with other experimental results.By analyzing the alkyl tails,the configuration of stearic acid molecules during the compression process was studied and a uniform monolayer was obtained after compression.Stearic acid molecules were observed to form fine organized monolayer from completely random structure.Hexatic order of the arrangement has been identified for the distribution of stearic acid molecules in the monolayer.At the end of the compression,the stearic acid molecules were tightly packed in the gap of two other molecules.At last,the hydrogen bonds in the system were analyzed.The main hydrogen bonds were from stearic acid-water interaction and their intensities constantly decreased with the decreased of surface area per molecule.The weak hydrogen bond interaction between stearic acid molecules may be the reason of easy collapse.

  7. Solvent extraction of molybdophosphoric acid with high-molecular alkylamines

    Extraction of dodecamolibdophosphoric acid H3PMo12O40 by nitrates of some high molecular amines (di-(2-ethylene-hexyl)-amine, diponylamine, diisoamyloctylamine) dichlorthane solution has been studied. The composition of associates in the organic phase may be presented as (BH3)PMo12O40, where BH+ is the protonized form of the amine. The overall conventional equilibrium constant of complex formation and extraction equals (1.51+-0.35)x1011

  8. A theoretical study of magnetoelectronic and switching properties of molecular magnetic tunnel junctions

    Soti, V.; Ravan, B. Abedi

    2016-01-01

    Electronic transport and switching properties of molecule-based magnetic tunnel junctions are investigated using the first-principles density functional theory and non-equilibrium Green function methods. As a result of being sandwiched between the ferromagnetic electrodes, a spin-polarization is induced in the nonmagnetic organic atoms. Magnitudes of the spin-polarizations in the trans-polyacetylene, cis-polyacetylene, terphenyl and pentacene chains are calculated and it is suggested that among these the pentacene molecules, because of showing a relatively higher magnetization can theoretically be more appropriate for utilization in spintronic devices. Furthermore, electrical switching capabilities of the junctions are studied and the results reveal that the pentacene junction due to having a larger ON/OFF ratio shows a better switching behavior. Finally, magnetoresistive properties are studied and it is shown that applying torsion can be an effective method to enhance and also adjust magnitudes of the magnetoresistances of the junctions.

  9. Single electron bipolar conductance switch driven by the molecular Aharonov-Bohm effect.

    Lee, Joonhee; Tallarida, Nicholas; Rios, Laura; Perdue, Shawn M; Apkarian, Vartkess Ara

    2014-06-24

    We demonstrate a conductance switch controlled by the spin-vibronic density of an odd electron on a single molecule. The junction current is modulated by the spin-flip bistability of the electron. Functional images are provided as wiring diagrams for control of the switch's frequency, amplitude, polarity, and duty-cycle. The principle of operation relies on the quantum mechanical phase associated with the adiabatic circulation of a spin-aligned electron around a conical intersection. The functional images quantify the governing vibronic Hamiltonian. PMID:24824563

  10. Voltage Regulated Uptake and Release of L-Glutamate from a Molecularly Selective Switch for Physiological Applications

    Fuchs, Kathrin; Hauff, Elizabeth von; Parisi, Jürgen; Weiler, Reto

    2009-12-01

    In this paper results are presented on the development of a device demonstrating the uptake and release of L-glutamate in solutions with neutral pH. A device which selectively regulates the concentration of biomolecules, such as the primary neural transmitter L-glutamate, could be useful for many biological and medical applications. In the literature it has been demonstrated that polypyrrole (PPy) is a promising material for the recognition basis of molecularly selective devices [1, 2]. In this study we investigated the feasibility of the PPy based "glutamate switch" for the voltage dependent uptake and release of L-glutamate for physiological applications

  11. First Acetic Acid Survey with CARMA in Hot Molecular Cores

    Shiao, Y -S Jerry; Remijan, Anthony J; Snyder, Lewis E; Friedel, Douglas N

    2010-01-01

    Acetic acid (CH$_3$COOH) has been detected mainly in hot molecular cores where the distribution between oxygen (O) and nitrogen (N) containing molecular species is co-spatial within the telescope beam. Previous work has presumed that similar cores with co-spatial O and N species may be an indicator for detecting acetic acid. However, does this presumption hold as higher spatial resolution observations become available of large O and N-containing molecules? As the number of detected acetic acid sources is still low, more observations are needed to support this postulate. In this paper, we report the first acetic acid survey conducted with the Combined Array for Research in Millimeter-wave Astronomy (CARMA) at 3 mm wavelengths towards G19.61-0.23, G29.96-0.02 and IRAS 16293-2422. We have successfully detected CH$_3$COOH via two transitions toward G19.61-0.23 and tentatively confirmed the detection toward IRAS 16293-2422 A. The determined column density of CH$_3$COOH is 2.0(1.0)$\\times 10^{16}$ cm$^{-2}$ and the...

  12. Memory effect of photoinduced conductivity switching controlled by pulsed voltages in a molecular conductor

    Iimori, Toshifumi; Ohta, Nobuhiro [Research Institute for Electronic Science, Hokkaido University, Sapporo 001-0020 (Japan); Naito, Toshio, E-mail: nohta@es.hokudai.ac.j [Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810 (Japan)

    2009-02-01

    Transient photoresponses of the electrical conductivity in single crystals of an organic conductor alpha-(BEDT-TTF){sub 2}I{sub 3} are studied in the charge-ordered insulating phase. Electrical conductivity switching is observed in the presence of pulsed voltages and synchronous irradiation of nanosecond laser pulse. Current in the photoirradiated crystal as a function of applied voltages shows a bistability in a certain range of voltage. For the initial triggering of the conductivity switching, not only pulsed voltages but also photoirradiation is necessary. A high conductivity state produced by the switching can be repeatedly recovered by applying the pulsed voltages without further photoirradiation even after the current has been reduced to zero. This observation indicates a memory effect of the photoinduced conductivity switching. The appearance of the memory effect depends on the temporal width of the pulsed voltages, which are applied at a rate of approximately 8 Hz. In the measurement using short pulse widths, the memory effect is not observed. This controllability of the memory effect with the pulse width is related to the bistability of the current with respect to the photoirradiation intensity. The shape of the hysteresis loop appearing in the current versus photoirradiation intensity curve can be varied by changing the pulse width.

  13. Molecular Simulation of Naphthenic Acid Removal on Acidic Catalyst (Ⅰ) Mechanism of Catalytic Decarboxylation

    Fu Xiaoqin; Dai Zhenyu; Tian Songbai; Hou Suandi; Wang Xieqing

    2008-01-01

    In this paper, the charge distribution, the chemical bond order and the reactive performance of carboxylic acid model compounds on acidic catalyst were investigated by using molecular simulation technology. The simulation results showed that the bond order of C-O was higher than that of C-C,and C-C bond connected to the carbon atom in the carboxyl radical had the lowest bond order. The charge distributions of model naphthenic acids were similar in characteristics that the negative charges were concentrated on carboxyls. According to the simulation results, the mechanisms of catalytic decarboxylation over acidic solid catalyst were proposed, and a new route was put forward regarding removal of the naphthenic acid from crude oil through catalytic decarboxylation.

  14. Electrochemical control of quantum interference in anthraquinone-based molecular switches

    Markussen, Troels; Schiøtz, Jakob; Thygesen, Kristian Sommer

    2010-01-01

    absent in the hydroquinone molecular bridge. A simple explanation of the interference effect is achieved by transforming the frontier molecular orbitals into localized molecular orbitals thereby obtaining a minimal tight-binding model describing the transport in the relevant energy range in terms of...

  15. Determination of Acid Herbicides Using Modified QuEChERS with Fast Switching ESI(+)/ESI(-) LC-MS/MS.

    Sack, Chris; Vonderbrink, John; Smoker, Michael; Smith, Robert E

    2015-11-01

    A method for the determination of 35 acid herbicides in food matrices was developed, validated, and implemented. It utilizes a modified QuEChERS extraction procedure coupled with quantitation by liquid chromatography tandem mass spectrometry (LC-MS/MS). The acid herbicides analyzed are all organic carboxylic acids, including the older chlorophenoxy acid herbicides such as 2,4-dichlorophenoxyacetic acid (2,4-D), dicamba, 4-chlorophenoxyacetic acid (4-CPA), quinclorac, and many of the newer imidazolinone herbicides such as imazethapyr and imazaquin. In the procedure, 10 mL of water is added to 5 g of sample and then extracted with 1% formic acid in acetonitrile for 1 min. The acetonitrile phase is salted out of the extract by adding sodium chloride and magnesium sulfate, followed by centrifugation. The acetonitrile is diluted 1:1 with water to enable quantitation by LC-MS/MS using fast switching between positive and negative electrospray ionization modes. The average recoveries for all the compounds except aminocyclopyrachlor were 95% with a precision of 8%. The method detection limits for all residues were less than 10 ng/g, and the correlation coefficients for the calibration curves was greater than 0.99 for all but two compounds tested. The method was used successfully for the quantitation of acid herbicides in the FDA's total diet study. The procedure proved to be accurate, precise, linear, sensitive, and rugged. PMID:26473587

  16. Multilayered proteomics reveals molecular switches dictating ligand-dependent EGFR trafficking

    Francavilla, Chiara; Papetti, Moreno; Rigbolt, Kristoffer T G;

    2016-01-01

    , we devised an integrated multilayered proteomics approach (IMPA). We analyzed dynamic changes in the receptor interactome, ubiquitinome, phosphoproteome, and late proteome in response to both ligands in human cells by quantitative MS and identified 67 proteins regulated at multiple levels. We...... identified RAB7 phosphorylation and RCP recruitment to EGFR as switches for EGF and TGF-α outputs, controlling receptor trafficking, signaling duration, proliferation, and migration. By manipulating RCP levels or phosphorylation of RAB7 in EGFR-positive cancer cells, we were able to switch a TGF......-α-mediated response to an EGF-like response or vice versa as EGFR trafficking was rerouted. We propose IMPA as an approach to uncover fine-tuned regulatory mechanisms in cell signaling....

  17. Extrapolative Analysis of Fast-Switching Free Energy Estimates in a Molecular System

    Zuckerman, Daniel M.; Woolf, Thomas B.

    2001-01-01

    We perform an extrapolative analysis of "fast-growth" free-energy-difference (DF) estimates of a computer-modeled, fully-solvated ethanemethanol transformation. The results suggest that extrapolation can greatly reduce the systematic error in DF estimated from a small number of very fast switches. Our extrapolation procedure uses block-averages of finite-data estimates, and appears to be particularly useful for broad, non-Gaussian distributions of data which produce substantial systematic err...

  18. First principle calculations of molecular polarization switching in P(VDF-TrFE) ferroelectric thin Langmuir-Blodgett films

    This paper reports first principle calculations and analysis of the molecular mechanism of the polarization switching in polyvinylidene fluoride and its copolymer with trifluoroethylene (P(VDF-TrFE)) using semi-empirical and ab initio quantum chemical methods based on the HyperChem 7.5 and Gaussian98 programs. The simulations were performed for different copolymer contents in P(VDF-TrFE)-(70:30), (60:40) and pure PVDF. The calculated values of the dipole moment and average polarization of the molecular chains show a clear hysteresis under varying electric field with polarization saturated at ∼0.1-0.14 C m-2. The calculated coercive fields (corresponding to the rotation of molecular chains to opposite orientation) are consistent (within an order of magnitude) with experimental data obtained for thin films (Ec = 5-18 MV cm-1). In the absence of external electric fields, the interactions between several molecular chains lead to the orientation of all dipole moments along one direction parallel to the chain plane. This model corresponds to the PVDF layer on the dielectric surface. For the electric field in the perpendicular direction, all chains are rotated along this direction corresponding to the model of conductive substrate

  19. Molecular phylogeny of the bivalve superfamily Galeommatoidea (Heterodonta, Veneroida reveals dynamic evolution of symbiotic lifestyle and interphylum host switching

    Goto Ryutaro

    2012-09-01

    Full Text Available Abstract Background Galeommatoidea is a superfamily of bivalves that exhibits remarkably diverse lifestyles. Many members of this group live attached to the body surface or inside the burrows of other marine invertebrates, including crustaceans, holothurians, echinoids, cnidarians, sipunculans and echiurans. These symbiotic species exhibit high host specificity, commensal interactions with hosts, and extreme morphological and behavioral adaptations to symbiotic life. Host specialization to various animal groups has likely played an important role in the evolution and diversification of this bivalve group. However, the evolutionary pathway that led to their ecological diversity is not well understood, in part because of their reduced and/or highly modified morphologies that have confounded traditional taxonomy. This study elucidates the taxonomy of the Galeommatoidea and their evolutionary history of symbiotic lifestyle based on a molecular phylogenic analysis of 33 galeommatoidean and five putative galeommatoidean species belonging to 27 genera and three families using two nuclear ribosomal genes (18S and 28S ribosomal DNA and a nuclear (histone H3 and mitochondrial (cytochrome oxidase subunit I protein-coding genes. Results Molecular phylogeny recovered six well-supported major clades within Galeommatoidea. Symbiotic species were found in all major clades, whereas free-living species were grouped into two major clades. Species symbiotic with crustaceans, holothurians, sipunculans, and echiurans were each found in multiple major clades, suggesting that host specialization to these animal groups occurred repeatedly in Galeommatoidea. Conclusions Our results suggest that the evolutionary history of host association in Galeommatoidea has been remarkably dynamic, involving frequent host switches between different animal phyla. Such an unusual pattern of dynamic host switching is considered to have resulted from their commensalistic lifestyle, in

  20. How Ligands Throw the Molecular Switch in an Ion Channel: What >Patch-Clamping can Reveal.

    Tibbs, Gareth R.

    1998-03-01

    Ion channels are integral membrane proteins with two distinctive characteristics: they are gated (opened and closed) by specific signals such as membrane voltage or the direct binding of chemical ligands and, once open, they conduct ions across the cell membrane at very high rates (>10^7 s-1). Although analysis of the atomic structure of membrane proteins presents a daunting challenge, the relatively large currents carried by ion channels enable their active (open) state(s) to be readily distinguished from their inactive (closed) state(s). Coupled with the use of molecular biological techniques, this permits us to 1. Obtain details of kinetically distinguishable states of the channel, 2. Identify and characterize the functional roles of specific domains of the protein, and 3. Explore the thermodynamic contribution of domains or individual bonds to activation. I shall present data that explores such structure-function relationships within the cyclic nucleotide-gated (CNG) channel branch of the voltage-gated (VG) channel superfamily. Like the closely related VG K+ channels, the CNG channels are tetramers with each subunit having six putative transmembrane helices and cytoplasmic N and C termini. By measuring the amplitude of the current flowing through single chimeric channels we have demonstrated that the loop between the fifth and sixth helices is the major determinant of the ion-conducting pore. Guided by homology to cyclic nucleotide-binding (CNB) proteins whose crystal structure is known, it has been established that an 120 amino acid sequence within the C-terminus of each subunit forms a CNB site. By making selective mutations within this pocket and measuring the affinity and ability of bound agonist to activate the channel, it has been possible to establish whether the free energy of specific channel-agonist bonds contributes to activation of the protein or stabilization of ligand in the binding pocket. Finally, we have measured the ability of the channel to

  1. A theoretical investigation on anomalous switching of single-stranded deoxyribonucleic acid (ssDNA) monolayers by water vapor

    Zhao, Xin-Jun; Gao, Zhi-Fu; Jiang, Zhong-Ying

    2015-04-01

    In this paper, we use a molecular theory to study the anomalous switching of ssDNA monolayers. Here, both ssDNA-water and water-water hydrogen bonds and their explicit coupling to the ssDNA conformations are considered. We find that hydrogen bonding becomes a key element in inducing the anomalous switching of ssDNA monolayers. This finding accords well with the experimental observations. Based on our theoretical model, we predict that the anomalous switching induced by water vapor will be applicable to a wide range of hydrogen bonds polymers, and ssDNA-water hydrogen bonds and water-water hydrogen bonds hybridization will lead to the hydrogen-bond network formation of 3D ssDNA monolayers. Project supported by the National Natural Science Foundation of China (Grant Nos. 21264016, 11464047, and 21364016), the National Basic Research Program of China (Grant No. 2012CB821500), and the Natural Science Foundation of Xinjiang Uygur Autonomous Region, China (Grant No. 2013211A053).

  2. Design and Synthesis of Chiral Molecular Tweezers Based on Deoxycholic Acid

    2001-01-01

    A series of new chiral molecular tweezers have been designed and synthesized by using deoxycholic acid as spacer and aromatic amines as arms.Instead of using toxic phosgene,the triphosgene was employed in synthesis of the molecular tweezers receptors.These chiral molecular tweezers showed good enantioselectivity for D-amino acid methyl esters.

  3. PRODUCTION OF LOW MOLECULAR WEIGHT CHITOSAN BY HOT DILUTE SULFURIC ACID

    Akram Zamani; Mohammad Taherzadeh

    2010-01-01

    new method was developed for production of low molecular weight chitosan, in which high molecular weight chitosan was treated with dilute sulfuric acid at 120°C. Chitosan was dissolved in the acid solution in a few minutes, and as depolymerized to low molecular weight chitosan by longer times. Low molecular weight chitosan was recovered from the acid by cooling down the solution and increasing the pH to 8-10. A low molecular weight chitosan with Mv (viscosity average molecular weight) of 174×...

  4. Molecular current switch: principles and photoelectronic characterization of the model system

    Vala, M.; Weiter, M.; Nešpůrek, Stanislav

    2005-01-01

    Roč. 15, č. 3 (2005), s. 28. ISSN 1210-7409 Institutional research plan: CEZ:AV0Z40500505 Keywords : molecular electronics * photochromism * charge transport Subject RIV: CD - Macromolecular Chemistry

  5. Voltage-Induced Switching Dynamics of a Coupled Spin Pair in a Molecular Junction.

    Saygun, T; Bylin, J; Hammar, H; Fransson, J

    2016-04-13

    Molecular spintronics is made possible by the coupling between electronic configuration and magnetic polarization of the molecules. For control and application of the individual molecular states, it is necessary to both read and write their spin states. Conventionally, this is achieved by means of external magnetic fields or ferromagnetic contacts, which may change the intentional spin state and may present additional challenges when downsizing devices. Here, we predict that coupling magnetic molecules together opens up possibilities for all electrical control of both the molecular spin states as well as the current flow through the system. By tuning between the regimes of ferromagnetic and antiferromagnetic exchange interaction, the current can be at least an order of magnitude enhanced or reduced. The effect is susceptible to the tunnel coupling and molecular level alignment that can be used to achieve current rectification. PMID:27010805

  6. Deep molecular responses achieved in patients with CML-CP who are switched to nilotinib after long-term imatinib.

    Hughes, Timothy P; Lipton, Jeffrey H; Spector, Nelson; Cervantes, Francisco; Pasquini, Ricardo; Clementino, Nelma Cristina D; Dorlhiac Llacer, Pedro Enrique; Schwarer, Anthony P; Mahon, Francois-Xavier; Rea, Delphine; Branford, Susan; Purkayastha, Das; Collins, LaTonya; Szczudlo, Tomasz; Leber, Brian

    2014-07-31

    Patients in complete cytogenetic response (CCyR) with detectable BCR-ABL1 after ≥2 years on imatinib were randomized to nilotinib (400 mg twice daily, n = 104) or continued imatinib (n = 103) in the Evaluating Nilotinib Efficacy and Safety in clinical Trials-Complete Molecular Response (ENESTcmr) trial. By 1 and 2 years, confirmed undetectable BCR-ABL1 was achieved by 12.5% vs 5.8% (P = .108) and 22.1% vs 8.7% of patients in the nilotinib and imatinib arms, respectively (P = .0087). Among patients without molecular response 4.5 (BCR-ABL1(IS) ≤0.0032%; MR(4.5)) and those without major molecular response at study start, MR(4.5) by 2 years was achieved by 42.9% vs 20.8% and 29.2% vs 3.6% of patients in the nilotinib and imatinib arms, respectively. No patient in the nilotinib arm lost CCyR, vs 3 in the imatinib arm. Adverse events were more common in the nilotinib arm, as expected with the introduction of a new drug vs remaining on a well-tolerated drug. The safety profile of nilotinib was consistent with other reported studies. In summary, switching to nilotinib enabled more patients with chronic myeloid leukemia in chronic phase (CML-CP) to sustain lower levels of disease burden vs remaining on imatinib. This trial was registered at www.clinicaltrials.gov as #NCT00760877. PMID:24948656

  7. Voltage induced switching dynamics of a coupled spin pair in a molecular junction

    Saygun, T.; Bylin, J.; Hammar, H.; J. Fransson

    2016-01-01

    Molecular spintronics is made possible by the coupling between electronic configuration and magnetic po- larization of the molecules. For control and application of the individual molecular states it is necessary to both read and write their spin states. Conventionally, this is achieved by means of external magnetic fields or ferromagnetic contacts, which may change the intentional spin state and may present additional challenges when downsizing devices. Here, we predict that coupling magneti...

  8. A solid-state electrochemiluminescence biosensing switch for detection of DNA hybridization based on ferrocene-labeled molecular beacon

    A solid-state electrochemiluminescence (ECL) biosensing switch incorporating quenching of ECL of ruthenium(II) tris-(bipyridine) (Ru(bpy)32+) by ferrocene (Fc) has been successfully developed for DNA hybridization detection. The important issue for this biosensing system is based on the ferrocene-labeled molecular beacon (Fc-MB), i.e. using the special Fc-MB to react with the target DNA and then change its structure, resulting in an ECL intensity change. Under the optimal conditions, the difference of ECL intensity before and after the hybridization reaction (ΔIECL) was linearly related to the concentration of the complementary sequence in the range of 10 fM-10 pM and the detection limit was down to 1.0 fM.

  9. Current-induced forces: a new mechanism to induce negative differential resistance and current-switching effect in molecular junctions

    Gu, Lei; Fu, Hua-Hua

    2015-12-01

    Current-induced forces can excite molecules, polymers and other low-dimensional materials, which in turn leads to an effective gate voltage through Holstein interaction. Here, by taking a short asymmetric DNA junction as an example, and using the Langevin approach, we find that when suppression of charge transport by the effective gate voltage surpasses the current increase from an elevated voltage bias, the current-voltage (I-V) curves display strong negative differential resistance (NDR) and perfect current-switching characteristics. The asymmetric DNA chain differs in mechanical stability under inverse voltages and the I-V curve is asymmetric about inverse biases, which can be used to understand recent transport experiments on DNA chains, and meanwhile provides a new strategy to realize NDR in molecular junctions and other low-dimensional quantum systems.

  10. Sensitive and selective detection of uracil-DNA glycosylase activity with a new pyridinium luminescent switch-on molecular probe.

    Lu, Yu-Jing; Hu, Dong-Ping; Deng, Qiang; Wang, Zheng-Ya; Huang, Bao-Hua; Fang, Yan-Xiong; Zhang, Kun; Wong, Wing-Leung

    2015-09-01

    Uracil-deoxyribonucleic acid glycosylase (UDG) is known to function as an important base-excision repair enzyme and eliminate uracil from DNA molecules to maintain genomic integrity. A new small organic molecule (DID-VP) with interesting structural properties was synthesized as a G-quadruplex selective ligand and was demonstrated to be a sensitive luminescent switch-on probe in a convenient luminescent assay specifically for UDG detection in fetal bovine serum samples under rapid and simple conditions. This newly developed analytical method is based on the UDG enzymatic activity to unwind a duplex DNA substrate, and comprises a G-quadruplex-forming sequence (ON1) and uracil-containing DNA strand (ON2) to generate a remarkable fluorescence signal through the specific interaction of DID-VP with ON1. This luminescent switch-on assay is able to achieve high sensitivity and specificity for UDG over other enzymes. The application range of the present analytical system is found to be 0.05 to 1.00 U mL(-1) UDG with a very low detection limit of 0.005 U mL(-1). The recovery study of UDG in real samples gave a very good performance with 75.05%-102.7% recovery. In addition, an extended application of the assay in screening of UDG inhibitors is demonstrated. A good dose-dependence of the luminescence response with respect to the concentration of UDG inhibitors in samples was observed. PMID:26185800

  11. Lewis acid enhanced switching of the 1,1-dicyanodihydroazulene/vinylheptafulvene photo/thermoswitch

    Parker, Christian Richard; Tortzen, Christian Gregers; Broman, Søren Lindbæk;

    2011-01-01

    Mild Lewis acids enhance the rate of the thermal conversion of vinylheptafulvene (VHF) to dihydroazulene (DHA). In the absence of light, stronger Lewis acids promote the otherwise photoinduced DHA to VHF conversion....

  12. A novel purification process for dodecanedioic acid by molecular distillation

    Jiang Yu; Xigang Yuan; Aiwu Zeng

    2015-01-01

    A novel purification process is involved to obtain the high purity [N 99%(by mass)] dodecanedioic acid (DC12). It involves a re-crystal ization followed by molecular distil ation from the crude product. The objective of this study is to investigate general conditions, feed rate, distil ing temperature and vacuum, necessary for centrifugal distil-lation of DC12. Under the optimum conditions, distilling temperature 180 °C, pressure 30 Pa and feed flow rate 700 ml·h−1, the purity of DC12 in the residence reached 97.55%with a yield of 53.18%by the analysis of gas chromatography. Multiple-pass distillation made a considerable contribution by improving the purity to 99.22%. Additionally, the effect of pretreatment (re-crystallization) on distillation process was revealed through a series of comparative experiments.

  13. Fast transient current response to switching events in short chains of molecular islands

    Kalvová, Anděla; Špička, Václav; Velický, B.

    2013-01-01

    Roč. 26, č. 4 (2013), s. 773-777. ISSN 1557-1939 R&D Projects: GA ČR GAP204/12/0897 Institutional support: RVO:68378271 Keywords : nonequilibrium * molecular islands * initial correlations * transient currents Subject RIV: BE - Theoretical Physics Impact factor: 0.930, year: 2013

  14. The measurement of the molecular weight of humic acid by ultracentrifugation

    This report is concerned with the application of ultracentrifuge methods to the determination of humic acid molecular weights. The work has been undertaken as part of the Co-Co club intercomparison exercise on humic acid characterisation. Knowledge of the molecular weight distribution of humic acid will be an important parameter in assessing the likely physical and chemical behaviour under the near-field environment. Molecular weights of a sample of purified Aldrich humic acid have been obtained by sedimentation velocity and sedimentation equilibrium studies using an analytical ultracentrifuge. The results have shown the material to be polydisperse with a weight average molecular weight in the region 2700 to 4000. (author)

  15. Amino acid detection using fluoroquinolone–Cu2+ complex as a switch-on fluorescent probe by competitive complexation without derivatization

    In this work, we describe the use of fluoroquinolone–Cu2+ complex as a competitive switch-on fluorescence probe for amino acid determination without derivatization. The fluorescence intensity of this probe, which has been reduced due to effective quenching by Cu2+ ion, increases drastically by an addition of amino acid (glycine, phenylalanine, sarcosine, aspargine, alanine, proline, arginine, aspartic acid, glutamic acid, lysine, leucine and isoleucine). The overall stability constants of Cu2+ ion complexes with amino acids were determined by fluorometric titration of fluoroquinolone-Cu2+ complex with the amino acid solution. Furthermore, the probe shows high calibration sensitivity toward aspartic acid. The fluorescence signal depends linearly on the amino acid concentration within the range of concentration from 1.2×10−7 to 1.1×10−5 mol L−1 for aspartic acid. The detection limit was found 2.7×10−8 mol L−1 with the relative standard deviation (RSD%) about 2.1% (five replicate). -- Highlights: • Amino acids are detected by using fluoroquinolone–Cu2+ complex as fluorescent probe. • Amino acids were detected based on a competitive complexation reaction. • Probe has been able to recognize amino acids through switch-on fluorescence behavior. • Ultra-trace level of aspartic and glutamic acid is determined without derivatization

  16. Amino acid detection using fluoroquinolone–Cu{sup 2+} complex as a switch-on fluorescent probe by competitive complexation without derivatization

    Farokhcheh, Alireza; Alizadeh, Naader, E-mail: alizaden@modares.ac.ir

    2014-01-15

    In this work, we describe the use of fluoroquinolone–Cu{sup 2+} complex as a competitive switch-on fluorescence probe for amino acid determination without derivatization. The fluorescence intensity of this probe, which has been reduced due to effective quenching by Cu{sup 2+} ion, increases drastically by an addition of amino acid (glycine, phenylalanine, sarcosine, aspargine, alanine, proline, arginine, aspartic acid, glutamic acid, lysine, leucine and isoleucine). The overall stability constants of Cu{sup 2+} ion complexes with amino acids were determined by fluorometric titration of fluoroquinolone-Cu{sup 2+} complex with the amino acid solution. Furthermore, the probe shows high calibration sensitivity toward aspartic acid. The fluorescence signal depends linearly on the amino acid concentration within the range of concentration from 1.2×10{sup −7} to 1.1×10{sup −5} mol L{sup −1} for aspartic acid. The detection limit was found 2.7×10{sup −8} mol L{sup −1} with the relative standard deviation (RSD%) about 2.1% (five replicate). -- Highlights: • Amino acids are detected by using fluoroquinolone–Cu{sup 2+} complex as fluorescent probe. • Amino acids were detected based on a competitive complexation reaction. • Probe has been able to recognize amino acids through switch-on fluorescence behavior. • Ultra-trace level of aspartic and glutamic acid is determined without derivatization.

  17. Molecular weight distribution broadening of polypropylene by periodic switching of hydrogen and catalyst additions

    Ali, M. Al-Haj; Stroomer, J.; Betlem, B.; Weickert, G.; Roffel, B.

    2008-01-01

    This study presents a feasibility study of the broadening of the polypropylene molecular weight distribution produced using a multisite Ziegler-Natta catalyst in a continuous liquid-pool polymerization reactor. The broadening is achieved by operating the reactor under periodic forcing of both hydrogen and catalyst feed flows. Model-based dynamic optimization is used to determine the cycle period and peak width for these inputs. Through simulation it is shown that limited widening (similar to ...

  18. Electron induced conformational changes of an imine-based molecular switch on a Au(111) surface

    Lotze, Christian; Henningsen, Nils; Franke, Katharina; Schulze, Gunnar; Pascual, Jose Ignacio [Inst. f. Experimentalphysik, Freie Universitaet Berlin (Germany); Luo, Ying; Haag, Rainer [Inst. f. Organische Chemie, Freie Universitaet Berlin (Germany)

    2009-07-01

    Azobenzene-based molecules exhibit a cis-trans configurational photoisomerisation in solution. Recently, the adsorption properties of azobenzene derivatives have been investigated on different metal surfaces in order to explore the possible changes in the film properties induced by external stimuli. In azobenzene, the diazo-bridge is a key group for the isomerization process. Its interaction with a metal surface is dominated through the N lone-pair electrons, which reduces the efficiency of the conformational change. In order to reduce the molecule-surface interaction, we explore an alternative molecular architecture by substituting the diazo-bridge (-N=N-) of azobenzene by an imine-group (-N=CH-). We have investigated the imine-based compound para-carboxyl-di-benzene-imine (PCI) adsorbed on a Au(111) surface. The carboxylic terminations mediates the formation of strongly bonded molecular dimers, which align in ordered rows preferentially following the fcc regions of the Au(111) herringbone reconstruction. Low temperature scanning tunneling microscopy was used to induce conformational changes between trans and cis state of individual molecules in a molecular monolayer.

  19. Solvent extraction studies on uranium (VI) with high molecular weight carboxylic acids from acetate medium

    Carboxylic acids are cation exchanger type of extractant which extract metal ions from weak acidic solutions by ion exchange mechanism. They are present as dimer (H2A2) in the non polar organic diluents. High molecular weight carboxylic acids such as versatic 10 acid and naphthenic acid are used for the separation of high purity of yttrium from heavy fraction of rare earths. Extraction behavior of rare earths with different types of carboxylic acids is also reported. Literature survey revealed that the extraction behavior of uranium from aqueous solutions with carboxylic acids is scanty. An attempt has been made in the present work to examine the extraction behavior of U(VI) with three different types of high molecular weight carboxylic acids namely cekanoic acid, neoheptanoic acid and versatic 10 acid dissolved in xylene. Extraction of metal ions is very much dependent on pH of the solution

  20. Investigation of molecular interactions in the complex formation of tartaric acid derivatives with di(2-ethylhexyl) phosphoric acid

    2008-01-01

    The molecular interactions in the complex formation of two tartaric acid derivatives with di(2-ethylhexyl) phosphoric acid are investigated. The complex formation with a 1:1 stoichiometry between tartaric acid derivatives and D2EHPA can be obtained through UV-Vis titration, NMR chemical shifts and molecular dynamic simulations. Furthermore, the differences of the two complexes on the binding constants and strength of hydrogen bonds can also be determined. Such research will ideally provide insight into ways of regulating the complex forming properties of tartaric acid derivatives for composing or syn- thesizing new chiral resolving agents.

  1. Investigation of molecular interactions in the complex formation of tartaric acid derivatives with di(2-ethylhexyl) phosphoric acid

    TAN Bin; ZHAI Zheng; LUO GuangSheng; WANG JiaDing

    2008-01-01

    The molecular interactions in the complex formation of two tartaric acid derivatives with di(2-ethylhexyl) phosphoric acid are investigated. The complex formation with a 1:1 stoichiometry between tartaric acid derivatives and D2EHPA can be obtained through UV-Vis titration, NMR chemical shifts and molecular dynamic simulations. Furthermore, the differences of the two complexes on the binding constants and strength of hydrogen bonds can also be determined. Such research will ideally provide insight into ways of regulating the complex forming properties of tartaric acid derivatives for composing or syn-thesizing new chiral resolving agents.

  2. Interplay of Oct4 with Sox2 and Sox17: a molecular switch from stem cell pluripotency to specifying a cardiac fate.

    Stefanovic, Sonia; Abboud, Nesrine; Désilets, Stéphanie; Nu, David; Cowan, Chad; Pucéat, Michel

    2009-01-01

    Oct4 exerts a dose-dependent dual action, as both a gatekeeper for stem cell pluripotency and in driving cells toward specific lineages. Here, we identify the molecular mechanism underlying this dual function. BMP2- or transgene-induced Oct4 up-regulation drives human embryonic and induced pluripotent stem cells to become cardiac progenitors. When embryonic stem cell pluripotency is achieved, Oct4 switches from the Sox2 to the Sox17 promoter. This switch allows the cells to turn off the pluri...

  3. Bistability in a Metabolic Network Underpins the De Novo Evolution of Colony Switching in Pseudomonas fluorescens

    Gallie, Jenna; Libby, Eric; Bertels, Frederic;

    2015-01-01

    central metabolism (carB) generates such a striking phenotype. We show that colony switching is underpinned by ON/OFF expression of capsules consisting of a colanic acid-like polymer. We use molecular genetics, biochemical analyses, and experimental evolution to establish that capsule switching results...

  4. Amino Acid Molecular Units: Building Primary and Secondary Protein Structures

    Aparecido R. Silva

    2008-05-01

    Full Text Available In order to guarantee the learning quality and suitable knowledge  use  about structural biology, it is fundamental to  exist, since the beginning of  students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring  schematic  drawings; even more elaborated figures and graphic computation  do not permit the necessary interaction.  The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to  visualize such structures and correlate them to the real molecules.  The design and applicability of the representative units were discussed with researchers and teachers before mould implementation.  In this stage  it  will be presented the  developed  kit  containing the  representative  plastic parts of the main amino acids.  The kit can demonstrate the interaction among the amino acids  functional groups  (represented by colors, shapes,  sizes and  the peptidic bonds between them  facilitating the assembly and visuali zation of the primary and secondary protein structure.  The models were designed for  Ca,  amino,  carboxyl groups  and  hydrogen. The  lateral chains have  well defined models that represent their geometrical shape.  The completed kit set  will be presented in this meeting (patent requested.  In the last phase of the project will be realized  an effective evaluation  of the kit  as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.

  5. Retinoic acid receptors: from molecular mechanisms to cancer therapy.

    di Masi, Alessandra; Leboffe, Loris; De Marinis, Elisabetta; Pagano, Francesca; Cicconi, Laura; Rochette-Egly, Cécile; Lo-Coco, Francesco; Ascenzi, Paolo; Nervi, Clara

    2015-02-01

    Retinoic acid (RA), the major bioactive metabolite of retinol or vitamin A, induces a spectrum of pleiotropic effects in cell growth and differentiation that are relevant for embryonic development and adult physiology. The RA activity is mediated primarily by members of the retinoic acid receptor (RAR) subfamily, namely RARα, RARβ and RARγ, which belong to the nuclear receptor (NR) superfamily of transcription factors. RARs form heterodimers with members of the retinoid X receptor (RXR) subfamily and act as ligand-regulated transcription factors through binding specific RA response elements (RAREs) located in target genes promoters. RARs also have non-genomic effects and activate kinase signaling pathways, which fine-tune the transcription of the RA target genes. The disruption of RA signaling pathways is thought to underlie the etiology of a number of hematological and non-hematological malignancies, including leukemias, skin cancer, head/neck cancer, lung cancer, breast cancer, ovarian cancer, prostate cancer, renal cell carcinoma, pancreatic cancer, liver cancer, glioblastoma and neuroblastoma. Of note, RA and its derivatives (retinoids) are employed as potential chemotherapeutic or chemopreventive agents because of their differentiation, anti-proliferative, pro-apoptotic, and anti-oxidant effects. In humans, retinoids reverse premalignant epithelial lesions, induce the differentiation of myeloid normal and leukemic cells, and prevent lung, liver, and breast cancer. Here, we provide an overview of the biochemical and molecular mechanisms that regulate the RA and retinoid signaling pathways. Moreover, mechanisms through which deregulation of RA signaling pathways ultimately impact on cancer are examined. Finally, the therapeutic effects of retinoids are reported. PMID:25543955

  6. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    Marcia, Marco, E-mail: marco.marcia@yale.edu; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas [Yale University, New Haven, CT 06511 (United States); Rajashankar, Kanagalaghatta [Argonne National Laboratory, Argonne, IL 60439 (United States); Pyle, Anna Marie, E-mail: marco.marcia@yale.edu [Yale University, New Haven, CT 06511 (United States); Yale University, New Haven, CT 06511 (United States); Howard Hughes Medical Institute, Chevy Chase, MD 20815 (United States)

    2013-11-01

    Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts.

  7. Study on fluorescence spectra of molecular association of acetic acid-water

    Caiqin Han; Ying Liu; Yang Yang; Xiaowu Ni; Jian Lu; Xiaosen Luo

    2009-01-01

    Fluorescence spectra of acetic acid-water solution excited by ultraviolet (UV) light are studied, and the relationship between fluorescence spectra and molecular association of acetic acid is discussed. The results indicate that when the exciting light wavelength is longer than 246 nm, there are two fluorescence peaks located at 305 and 334 nm, respectively. By measuring the excitation spectra, the optimal wavelengths of the two fluorescence peaks are obtained, which are 258 and 284 nm, respectively. Fluorescence spectra of acetic acid-water solution change with concentrations, which is primarily attributed to changes of molecular association of acetic acid in aqueous solution. Through theoretical analysis, three variations of molecular association have been obtained in acetic acid-water solution, which are the hydrated monomers, the linear dimers, and the water separated dimers. This research can provide references to studies of molecular association of acetic acid-water, especially studies of hydrogen bonds.

  8. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts

  9. A Molecular Switch Abrogates Glycoprotein 100 (gp100) T-cell Receptor (TCR) Targeting of a Human Melanoma Antigen*

    Bianchi, Valentina; Bulek, Anna; Fuller, Anna; Lloyd, Angharad; Attaf, Meriem; Rizkallah, Pierre J.; Dolton, Garry; Sewell, Andrew K.; Cole, David K.

    2016-01-01

    Human CD8+ cytotoxic T lymphocytes can mediate tumor regression in melanoma through the specific recognition of HLA-restricted peptides. Because of the relatively weak affinity of most anti-cancer T-cell receptors (TCRs), there is growing emphasis on immunizing melanoma patients with altered peptide ligands in order to induce strong anti-tumor immunity capable of breaking tolerance toward these self-antigens. However, previous studies have shown that these immunogenic designer peptides are not always effective. The melanocyte differentiation protein, glycoprotein 100 (gp100), encodes a naturally processed epitope that is an attractive target for melanoma immunotherapies, in particular peptide-based vaccines. Previous studies have shown that substitutions at peptide residue Glu3 have a broad negative impact on polyclonal T-cell responses. Here, we describe the first atomic structure of a natural cognate TCR in complex with this gp100 epitope and highlight the relatively high affinity of the interaction. Alanine scan mutagenesis performed across the gp100280–288 peptide showed that Glu3 was critically important for TCR binding. Unexpectedly, structural analysis demonstrated that the Glu3 → Ala substitution resulted in a molecular switch that was transmitted to adjacent residues, abrogating TCR binding and T-cell recognition. These findings help to clarify the mechanism of T-cell recognition of gp100 during melanoma responses and could direct the development of altered peptides for vaccination. PMID:26917722

  10. Postprandial fate of amino acids: adaptation to molecular forms

    Nolles, J.A.

    2006-01-01

    During the postprandial phase dietary proteins are digested to peptides and amino acids and absorbed. Once absorbed the peptides are further hydrolyzed to amino acids and transported to the tissues. These amino acids are largely incorporated into body proteins. Not all amino acids are, however, inco

  11. Characterization of Hydroxyphthioceranoic and Phthioceranoic Acids by Charge-Switch Derivatization and CID Tandem Mass Spectrometry

    Hsu, Fong-Fu

    2016-04-01

    Hydroxyphthioceranoic (HPA) and phthioceranoic (PA) acids are polymethylated long chain fatty acids with and without a hydroxyl group attached to the carbon next to the terminal methyl-branched carbon distal to the carboxylic end of the long-chain fatty acid, respectively. They are the major components of the sulfolipids found in the cell wall of Mycobacterium tuberculosis (M. tuberculosis) strain H37Rv. In this report, I describe CID linear ion-trap MSn mass spectrometric approaches combined with charge-reverse derivatization strategy toward characterization of these complex lipids, which were released from sulfolipids by alkaline hydrolysis and sequentially derivatized to the N-(4-aminomethylphenyl) pyridinium (AMPP) derivatives. This method affords complete characterization of HPA and PA, including the location of the hydroxyl group and the multiple methyl side chains. The study also led to the notion that the hydroxyphthioceranoic acid in sulfolipid consists of two (for hC24) to 12 (for hC52) methyl branches, and among them 2,4,6,8,10,12,14,16-octamethyl-17-hydroxydotriacontanoic acid (hC40) is the most prominent, while phthioceranoic acids are the minor constituents. These results confirm our previous findings that sulfolipid II, a family of homologous 2-stearoyl(palmitoyl)-3,6,6'-tris(hydroxyphthioceranoy1)-trehalose 2'-sulfates is the predominant species, and sulfolipid I, a family of homologous 2-stearoyl(palmitoyl)-3-phthioceranoyl-6,6'-bis(hydroxyphthioceranoy1)-trehalose 2'-sulfates is the minor species in the cell wall of M. tuberculosis.

  12. A molecular switch driving inactivation in the cardiac K+ channel HERG.

    David A Köpfer

    Full Text Available K(+ channels control transmembrane action potentials by gating open or closed in response to external stimuli. Inactivation gating, involving a conformational change at the K(+ selectivity filter, has recently been recognized as a major K(+ channel regulatory mechanism. In the K(+ channel hERG, inactivation controls the length of the human cardiac action potential. Mutations impairing hERG inactivation cause life-threatening cardiac arrhythmia, which also occur as undesired side effects of drugs. In this paper, we report atomistic molecular dynamics simulations, complemented by mutational and electrophysiological studies, which suggest that the selectivity filter adopts a collapsed conformation in the inactivated state of hERG. The selectivity filter is gated by an intricate hydrogen bond network around residues S620 and N629. Mutations of this hydrogen bond network are shown to cause inactivation deficiency in electrophysiological measurements. In addition, drug-related conformational changes around the central cavity and pore helix provide a functional mechanism for newly discovered hERG activators.

  13. A metal-ion-responsive adhesive material via switching of molecular recognition properties

    Nakamura, Takashi; Takashima, Yoshinori; Hashidzume, Akihito; Yamaguchi, Hiroyasu; Harada, Akira

    2014-08-01

    Common adhesives stick to a wide range of materials immediately after they are applied to the surfaces. To prevent indiscriminate sticking, smart adhesive materials that adhere to a specific target surface only under particular conditions are desired. Here we report a polymer hydrogel modified with both β-cyclodextrin (βCD) and 2,2‧-bipyridyl (bpy) moieties (βCD-bpy gel) as a functional adhesive material responding to metal ions as chemical stimuli. The adhesive property of βCD-bpy gel based on interfacial molecular recognition is expressed by complexation of metal ions to bpy that controlled dissociation of supramolecular cross-linking of βCD-bpy. Moreover, adhesion of βCD-bpy gel exhibits selectivity on the kinds of metal ions, depending on the efficiency of metal-bpy complexes in cross-linking. Transduction of two independent chemical signals (metal ions and host-guest interactions) is achieved in this adhesion system, which leads to the development of highly orthogonal macroscopic joining of multiple objects.

  14. Postprandial fate of amino acids: adaptation to molecular forms

    Nolles, J.A.

    2006-01-01

    During the postprandial phase dietary proteins are digested to peptides and amino acids and absorbed. Once absorbed the peptides are further hydrolyzed to amino acids and transported to the tissues. These amino acids are largely incorporated into body proteins. Not all amino acids are, however, incorporated into body proteins part of these amino acids are oxidized, and can, thus, no longer be utilized to support protein metabolism in the body. The objective of this thesis was to increase the ...

  15. Towards single molecule switches.

    Zhang, Jia Lin; Zhong, Jian Qiang; Lin, Jia Dan; Hu, Wen Ping; Wu, Kai; Xu, Guo Qin; Wee, Andrew T S; Chen, Wei

    2015-05-21

    The concept of using single molecules as key building blocks for logic gates, diodes and transistors to perform basic functions of digital electronic devices at the molecular scale has been explored over the past decades. However, in addition to mimicking the basic functions of current silicon devices, molecules often possess unique properties that have no parallel in conventional materials and promise new hybrid devices with novel functions that cannot be achieved with equivalent solid-state devices. The most appealing example is the molecular switch. Over the past decade, molecular switches on surfaces have been intensely investigated. A variety of external stimuli such as light, electric field, temperature, tunneling electrons and even chemical stimulus have been used to activate these molecular switches between bistable or even multiple states by manipulating molecular conformations, dipole orientations, spin states, charge states and even chemical bond formation. The switching event can occur either on surfaces or in break junctions. The aim of this review is to highlight recent advances in molecular switches triggered by various external stimuli, as investigated by low-temperature scanning tunneling microscopy (LT-STM) and the break junction technique. We begin by presenting the molecular switches triggered by various external stimuli that do not provide single molecule selectivity, referred to as non-selective switching. Special focus is then given to selective single molecule switching realized using the LT-STM tip on surfaces. Single molecule switches operated by different mechanisms are reviewed and discussed. Finally, molecular switches embedded in self-assembled monolayers (SAMs) and single molecule junctions are addressed. PMID:25757483

  16. Activation of coherent lattice phonon following ultrafast molecular spin-state photo-switching: A molecule-to-lattice energy transfer

    A. Marino

    2016-03-01

    Full Text Available We combine ultrafast optical spectroscopy with femtosecond X-ray absorption to study the photo-switching dynamics of the [Fe(PM-AzA2(NCS2] spin-crossover molecular solid. The light-induced excited spin-state trapping process switches the molecules from low spin to high spin (HS states on the sub-picosecond timescale. The change of the electronic state (<50 fs induces a structural reorganization of the molecule within 160 fs. This transformation is accompanied by coherent molecular vibrations in the HS potential and especially a rapidly damped Fe-ligand breathing mode. The time-resolved studies evidence a delayed activation of coherent optical phonons of the lattice surrounding the photoexcited molecules.

  17. Effect of Molecular Structure on the Performance of Polyacrylic Acid Superplasticizer

    ZHANG Rongguo; GUO Huiling; LEI Jiaheng; ZHANG Anfu; GU Huajun

    2007-01-01

    The effects of structure parameters, such as molecular structure, segment kinds, molecular weight, and organic functional groups, on the performance of polyacrylic acid superplasticizer were discussed. According to the differences of chain sections, functional groups, etc, polyacrylic acid superplasticizer could be divided into A, B, C three parts. Among them, A chain section included sulfonic acid groups, B chain section carboxyl groups, C chain section polyester. Polyacrylic acid superplasticizers with different matching of A, B, C chain sections, different length of C chain section and different molecular weights were synthesized by acrylic acid, polyethylene glycol, sodium methyl allylsulfonate; the relation between the molecular structure and performance was also studied. The expetimental results indicate that the water-reduction ratio increases obviously with the increment of the proportion of sodium methyl allylsulfonate chain section in the molecular; the slump retention increases greatly with the increment of the proportion of acrylic acid chain section; the dispersion of cement particles increases with the increment of the chain length of polyethylene glycol; when the molecular weight is in the range of 5000, the dispersion and slump retentibity increase with the increment of the average molecular weight of polymers.

  18. Role of accelerated segment switch in exons to alter targeting (ASSET in the molecular evolution of snake venom proteins

    Kini R Manjunatha

    2009-06-01

    Full Text Available Abstract Background Snake venom toxins evolve more rapidly than other proteins through accelerated changes in the protein coding regions. Previously we have shown that accelerated segment switch in exons to alter targeting (ASSET might play an important role in its functional evolution of viperid three-finger toxins. In this phenomenon, short sequences in exons are radically changed to unrelated sequences and hence affect the folding and functional properties of the toxins. Results Here we analyzed other snake venom protein families to elucidate the role of ASSET in their functional evolution. ASSET appears to be involved in the functional evolution of three-finger toxins to a greater extent than in several other venom protein families. ASSET leads to replacement of some of the critical amino acid residues that affect the biological function in three-finger toxins as well as change the conformation of the loop that is involved in binding to specific target sites. Conclusion ASSET could lead to novel functions in snake venom proteins. Among snake venom serine proteases, ASSET contributes to changes in three surface segments. One of these segments near the substrate binding region is known to affect substrate specificity, and its exchange may have significant implications for differences in isoform catalytic activity on specific target protein substrates. ASSET therefore plays an important role in functional diversification of snake venom proteins, in addition to accelerated point mutations in the protein coding regions. Accelerated point mutations lead to fine-tuning of target specificity, whereas ASSET leads to large-scale replacement of multiple functionally important residues, resulting in change or gain of functions.

  19. Molecular Genetic Characterization of Terreic Acid Pathway in Aspergillus terreus

    Guo, Chun-Jun; Sun, Wei-wen; Bruno, Kenneth S.; Wang, Clay C.

    2014-09-29

    Terreic acid is a natural product derived from 6-methylsalicylic acid (6-MSA). A compact gene cluster for its biosynthesis was characterized. Isolation of the intermediates and shunt products from the mutant strains, in combined with bioinformatic analyses, allowed us to propose a biosynthetic pathway for terreic acid. Defining the pathway and the genes involved will facilitate the engineering of this molecule with interesting antimicrobial and antitumor bioactivities.

  20. Molecular dynamics of sialic acid analogues and their interaction with influenza hemagglutinin

    Blessia T

    2010-01-01

    Full Text Available Synthetic sialic acid analogues with multiple modifications at different positions(C-1/C-2/C-4/C-8/C-9 are investigated by molecular mechanics and molecular dynamics to determine their conformational preferences and structural stability to interact with their natural receptors. Sialic acids with multiple modifications are soaked in a periodic box of water as solvent. Molecular mechanics and a 2 nanosecond molecular dynamics are done using amber force fields with 30 picosecond equilibrium. Direct and water mediated hydrogen bonds existing in the sialic acid analogues, aiding for their structural stabilization are identified in this study. The accessible conformations of side chain linkages of sialic acid analogues holding multiple substituents are determined from molecular dynamics trajectory at every 1ps interval. Transitions between different minimum energy regions in conformational maps are also noticed in C-1, C-2, C-4, C-8 and C-9 substituents. Docking studies were done to find the binding mode of the sialic acid analogues with Influenza hemagglutinin. This finding provides stereo chemical explanation and conformational preference of sialic acid analogues which may be crucial for the design of sialic acid analogues as inhibitors for different sialic acid specific pathogenic proteins such as influenza toxins and neuraminidases.

  1. Study of the effects of dietary polyunsaturated fatty acids: Molecular mechanisms involved intestinal inflammation

    Knoch, B.; Barnett, M. P. G.; Roy, N. C.; McNabb, W. C.

    2009-07-01

    The use of omics techniques in combination with model systems and molecular tools allows to understand how foods and food components act on metabolic pathways to regulate transcriptional processes. Polyunsaturated fatty acids have distinctive nutritional and metabolic effects because they give rise to lipid mediated products and affect the expression of various genes involved in intestinal inflammation. The present review focuses on the molecular effects of dietary polyunsaturated fatty acids on intestinal inflammation. (Author) 74 refs.

  2. Low-molecular-weight carboxylic acids produced from hydrothermal treatment of organic wastes.

    Quitain, Armando T; Faisal, Muhammad; Kang, Kilyoon; Daimon, Hiroyuki; Fujie, Koichi

    2002-07-22

    This article reports production of low-molecular-weight carboxylic acids from the hydrothermal treatment of representative organic wastes and compounds (i.e. domestic sludge, proteinaceous, cellulosic and plastic wastes) with or without oxidant (H(2)O(2)). Organic acids such as acetic, formic, propionic, succinic and lactic acids were obtained in significant amounts. At 623 K (16.5 MPa), acetic acid of about 26 mg/g dry waste fish entrails was obtained. This increased to 42 mg/g dry waste fish entrails in the presence of H(2)O(2). Experiments on glucose to represent cellulosic wastes were also carried out, getting acetic acid of about 29 mg/g glucose. The study was extended to terephthalic acid and glyceraldehyde, reaction intermediates of hydrothermal treatment of polyethylene terephthalate (PET) plastic wastes and glucose, respectively. In addition, production of lactic acid, one of the interesting low-molecular-weight carboxylic acids, was discussed on the viewpoint of resources recovery. Studies on temperature dependence of formation of organic acids showed thermal stability of acetic acid, whereas, formic acid decomposed readily under hydrothermal conditions. In general, results demonstrated that the presence of oxidants favored formation of organic acids with acetic acid being the major product. PMID:12117467

  3. Molecular Determinants of the Response of Tumor Cells to Boswellic Acids

    Thomas Efferth

    2011-08-01

    Full Text Available Frankincense (Boswellia serrata, B. carterii is used as traditional remedy to treat inflammatory diseases. The molecular effects of the active ingredients, the boswellic acids, on the immune system have previously been studied and verified in several clinical studies. Boswellic acids also inhibit cancer cell growth in vitro and in vivo. The molecular basis of the cytotoxicity of boswellic acids is, however, not fully understood as yet. By mRNA-based microarray, COMPARE, and hierarchical cluster analyses, we identified a panel of genes from diverse functional groups, which were significantly associated with sensitivity or resistance of a- or b-boswellic acids, such as transcription factors, signal transducers, growth regulating genes, genes involved in RNA and protein metabolism and others. This indicates that boswellic acids exert profound cytotoxicity on cancer cells by a multiplicity of molecular mechanisms.

  4. Molecular recognition of α-cyclodextrin (CD) to choral amino acids based on methyl orange as a molecular probe

    Yuexian, Fan; Yu, Yang; Shaomin, Shuang; Chuan, Dong

    2005-03-01

    The molecular recognition interaction of α-CD to chiral amino acids was investigated by using spectrophotometry based on methyl orange as a molecular probe. The molecular recognition ability depended on the inclusion formation constants. The molecular recognition of α-CD to aromatic amino acids was the order: DL-tryptophan > L-tryptophan > L-phenylalanine > L-tyrosine ≈ DL-β-3,4-dihydroxy-phenylalanine; whereas for aliphatic amino acids, the order was: L- iso-leucine > L-leucine ≈ L-methionine ≈ DL-mehtionine > D-leucine. The effect of temperature on the inclusion interaction was examined and the thermodynamic parameters of inclusion process, Δ G, Δ H, Δ S, were determined. The experimental results indicated that the inclusion process was an exothermic and enthalpy-driven process accompanied with a negative or minor positive entropic contribution. The inclusion interaction between α-CD and amino acids satisfied the law of enthalpy-entropy compensation. The compensation temperature was 291 K.

  5. Molecular recognition of alpha-cyclodextrin (CD) to choral amino acids based on methyl orange as a molecular probe.

    Yuexian, Fan; Yu, Yang; Shaomin, Shuang; Chuan, Dong

    2005-03-01

    The molecular recognition interaction of alpha-CD to chiral amino acids was investigated by using spectrophotometry based on methyl orange as a molecular probe. The molecular recognition ability depended on the inclusion formation constants. The molecular recognition of alpha-CD to aromatic amino acids was the order: DL-tryptophan > L-tryptophan > L-phenylalanine > L-tyrosine approximately DL-beta-3,4-dihydroxy-phenylalanine; whereas for aliphatic amino acids, the order was: L-iso-leucine > L-leucine approximately L-methionine approximately DL-mehtionine > D-leucine. The effect of temperature on the inclusion interaction was examined and the thermodynamic parameters of inclusion process, delta G, delta H, delta S, were determined. The experimental results indicated that the inclusion process was an exothermic and enthalpy-driven process accompanied with a negative or minor positive entropic contribution. The inclusion interaction between alpha-CD and amino acids satisfied the law of enthalpy-entropy compensation. The compensation temperature was 291 K. PMID:15683802

  6. What are humic substances? : a molecular approach to the study of organic matter in acid soils

    Naafs, Derck Ferdinand Werner

    2004-01-01

    Molecular studies on the composition of organic matter in soils are scarce. In this thesis, a molecular approach to the study of organic matter in acid soils is presented, with a focus on andic, i.e. volcanic, soils. Analyses include both chemical extractions as well as pyrolysis-GC/MS and CPMAS 13C

  7. Isolation and characterisation of high molecular weight ( sup 3 H)hyaluronic acid

    Chabrecek, P. (Slovak Technical Univ., Bratislava (Czechoslovakia). Inst. of Biotechnology); Soltes, L.; Kallay, Z. (Slovenska Akademia Vied, Bratislava (Czechoslovakia). Ustav Experimentalnej Farmakologie); Fugedi, A. (Slovenska Akademia, Bratislava (Czechoslovakia). Computing Centre)

    1990-10-01

    A high-performance gel permeation chromatographic separation method was developed for the isolation and characterisation of high molecular weight ({sup 3}H)hyaluronic acid. The molecular characteristics of the labelled sample were M{sub w}=3.92 x 10{sup 5} Da, M{sub w}/M{sub n}=1.55. (author).

  8. Isolation and characterisation of high molecular weight [3H]hyaluronic acid

    A high-performance gel permeation chromatographic separation method was developed for the isolation and characterisation of high molecular weight [3H]hyaluronic acid. The molecular characteristics of the labelled sample were Mw=3.92 x 105 Da, Mw/Mn=1.55. (author)

  9. A comparative study on efficacy of high and low fluence Q-switched Nd:YAG laser and glycolic acid peel in melasma

    Hemanta Kumar Kar; Lipy Gupta; Amrita Chauhan

    2012-01-01

    Background: Melasma is acquired symmetric hypermelanosis characterized by light-to-deep brown pigmentation over cheeks, forehead, upper lip, and nose. Treatment of this condition is difficult and associated with high recurrence rates. With the advent of newer therapies, there is interest in the use of glycolic acid peels and Q-switched Nd:YAG laser (QSNYL) in high and low fluence for this disorder. Aims: To compare the therapeutic efficacy of low fluence QSNYL, high fluence QSNYL, and glycoli...

  10. A Comparison of Low-Fluence 1064-nm Q-Switched Nd: YAG Laser with Topical 20% Azelaic Acid Cream and their Combination in Melasma in Indian Patients

    Charu Bansal; Hira Naik; Kar, Hemanta K; Amrita Chauhan

    2012-01-01

    Background: Melasma is an acquired symmetric hypermelanosis characterised by irregular light to gray-brown macules on sun-exposed skin with a predilection for the cheeks, forehead, upper lip, nose and chin. The management of melasma is challenging and requires meticulous use of available therapeutic options. Aims: To compare the therapeutic efficacy of low-fluence Q-switched Nd: YAG laser (QSNYL) with topical 20% azelaic acid cream and their combination in melasma in three study groups of 20 ...

  11. INTERRUPTION OF AMINO ACIDS MOLECULAR ASYMMETRY (D/L- ENANTIOMERS DURING NORMAL AGING AND NEURODEGENERATIVE DISEASES

    A.V. Chervyakov

    2010-05-01

    Full Text Available Some facts about D-amino acids, their diffusion in human’s and animal’s organisms, metabolism, identification methods, involving in ageing and pathogenesis of some neurodegenerative diseases are show in this review. Also there is discussing the role of amino acid molecular asymmetry (D and L enantiomers ratio as a fundamental asymmetry of living matter.

  12. Molecular pharmacology of 4-substituted glutamic acid analogues at ionotropic and metabotropic excitatory amino acid receptors

    Bräuner-Osborne, Hans; Nielsen, B; Stensbøl, T B; Johansen, T N; Skjaerbaek, N; Krogsgaard-Larsen, P

    The pharmacology of (2S,4R)-4-methylglutamic acid, (2S,4S)-4-methylglutamic acid and (S)- and (R)-4-methyleneglutamic acids (obtained in high chemical and enantiomeric purity from racemic 4-methyleneglutamic acid by chiral HPLC using a Crownpak CR(+) column), was examined in binding experiments u...

  13. Phosphorus release from phosphate rock and iron phosphate by low-molecular-weight organic acids

    XU Ren-kou; ZHU Yong-guan; David Chittleborough

    2004-01-01

    Low-molecular-weight(LMW) organic acids widely exist in soils, particularly in the rhizosphere. A series of batch experiments were carried out to investigate the phosphorus release from rock phosphate and iron phosphate by Iow-molecular-weight organic acids.Results showed that citric acid had the highest capacity to solubilize P from both rock and iron phosphate. P solubilization from rock phosphate and iron phosphate resulted in net proton consumption. P release from rock phosphate was positively correlated with the pKa values. P release from iron phosphate was positively correlated with Fe-organic acid stability constants except for aromatic acids, but was not correlated with PKa. Increase in the concentrations of organic acids enhanced P solubilization from both rock and iron phosphate almost linearrly. Addition of phenolic compounds further increased the P release from iron phosphate. Initial solution pH had much more substantial effect on P release from rock phosphate than from iron phosphate.

  14. Molecular targets of omega 3 and conjugated linoleic fatty acids – micromanaging cellular response

    Francesco eVisioli

    2012-02-01

    Full Text Available Essential fatty acids cannot be synthesized de novo by mammals and need to be ingested either with the diet or through the use of supplements/functional foods to ameliorate cardiovascular prognosis. This review focus on the molecular targets of omega 3 fatty acids and CLA, as paradigmatic molecules that can be explored both as nutrients and as pharmacological agents, especially as related to cardioprotection. In addition, we indicate novel molecular targets, namely microRNAs that might contribute to the observed biological activities of such essential fatty acids.

  15. Effect of Low-Molecular-Weight Organic Acids on Cl- Adsorption by Variable Charge Soils

    XU Ren-Kou; ANG Ma-Li; WANG Qiang-Sheng; JI Guo-Liang1

    2004-01-01

    Low-molecular-weight (LMW) organic acids exist widely in soils and have been implicated in many soil processes.The objective of the present paper was to evaluate effect of two LMW organic acids, citric acid and oxalic acid, on Cl- adsorption by three variable charge soils, a latosol, a lateritic red soil and a red soil, using a batch method. The results showed that the presence of citric acid and oxalic acid led to a decrease in Cl- adsorption with larger decreases for citric acid. Among the different soils Gl- adsorption in the lateritic red soil and the red soil was more affected by both the LMW organic acids than that in the latosol.

  16. Synthesis, molecular structure, spectroscopic investigations and computational study of a potential molecular switch of 2-([1,1'-biphenyl]-4-yl)-2-methyl-6-(4-nitrophenyl)-4-phenyl-1,3 diazabicyclo [3.1.0]hex-3-ene

    AYOUB KANAANI; DAVOOD AJLOO; HAMZEH I KIYAN; FRESHTE SHAHERI; MAJID AMIRI

    2016-08-01

    This work presents a combined experimental and theoretical study on a photochromic compound, 2-([1,1'-biphenyl]-4-yl)-2-methyl-6-(4-nitrophenyl)-4-phenyl-1,3 diazabicyclo [3.1.0]hex-3-ene, existing in closed form (‘A’) and open form (‘B’). The spectroscopic properties of the title compound have beeninvestigated by using IR, UV–Vis and ¹H NMR techniques. The molecular geometry and spectroscopic data of the title compound have been calculated by using the density functional method (B3LYP) invoking 6-311G(d,p) basis set. UV-Vis spectra of the two forms were recorded. The excitation energies, oscillator strength, etc., were calculated by time-dependent density functional theory (TD-DFT). Furthermore, molecular electrostatic potential map (MEP), frontier molecular orbital analysis (HOMO–LUMO), total density of state (TDOS) and reactivity descriptors were found and discussed. We applied a first-principles computational approach to study a light-sensitive molecular switch. We find that the conductance of the two isomers varies dramatically, which suggests that this system has potential use as a molecular switch.

  17. Potential origin and formation for molecular components of humic acids in soils

    DiDonato, Nicole; Chen, Hongmei; Waggoner, Derek; Hatcher, Patrick G.

    2016-04-01

    Soil humic acids are the base soluble/acid insoluble organic components of soil organic matter. Most of what we know about humic acids comes from studies of their bulk molecular properties or analysis of individual fractions after extraction from soils. This work attempts to better define humic acids and explain similarities and differences for several soils varying in degrees of humification using advanced molecular level techniques. Our investigation using electrospray ionization coupled to Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) and nuclear magnetic resonance spectroscopy (NMR) has given new insight into the distinctive molecular characteristics of humic acids which suggest a possible pathway for their formation. Humic acids from various ecosystems, climate regions and soil textural classes are distinguished by the presence of three predominant molecular components: lignin-like molecules, carboxyl-containing aliphatic molecules and condensed aromatic molecules that bear similarity to black carbon. Results show that humification may be linked to the relative abundance of these three types of molecules as well as the relative abundance of carboxyl groups in each molecular type. This work also demonstrates evidence for lignin as the primary source of soil organic matter, particularly condensed aromatic molecules often categorized as black carbon and is the first report of the non-pyrogenic source for these compounds in soils. We also suggest that much of the carboxyl-containing aliphatic molecules are sourced from lignin.

  18. In-silico design of computational nucleic acids for molecular information processing.

    Ramlan, Effirul Ikhwan; Zauner, Klaus-Peter

    2013-01-01

    Within recent years nucleic acids have become a focus of interest for prototype implementations of molecular computing concepts. During the same period the importance of ribonucleic acids as components of the regulatory networks within living cells has increasingly been revealed. Molecular computers are attractive due to their ability to function within a biological system; an application area extraneous to the present information technology paradigm. The existence of natural information processing architectures (predominately exemplified by protein) demonstrates that computing based on physical substrates that are radically different from silicon is feasible. Two key principles underlie molecular level information processing in organisms: conformational dynamics of macromolecules and self-assembly of macromolecules. Nucleic acids support both principles, and moreover computational design of these molecules is practicable. This study demonstrates the simplicity with which one can construct a set of nucleic acid computing units using a new computational protocol. With the new protocol, diverse classes of nucleic acids imitating the complete set of boolean logical operators were constructed. These nucleic acid classes display favourable thermodynamic properties and are significantly similar to the approximation of successful candidates implemented in the laboratory. This new protocol would enable the construction of a network of interconnecting nucleic acids (as a circuit) for molecular information processing. PMID:23647621

  19. New structure of three-terminal GaAs p(+)-n(-)-delta(p+)-n(-)-n(+) switching device prepared by molecular beam epitaxy

    Wang, Y. H.; Yarn, K. F.; Chang, C. Y.; Jame, M. S.

    1987-08-01

    A new three-terminal GaAs p(+)-n(-)-delta(p+)-n(-)-n(+), voltage-controlled switching device grown by molecular beam epitaxy is presented. A simple method to contact the third terminal is employed by applying the Au-Zn to the delta(p+) barrier using the B-groove etching technique, in which the delta(p+) barrier height can be directly modulated by the external voltage. The device may be more effective than other voltage-controlled devices due to the direct barrier modulation.

  20. Electronic transport properties of indolyl spirooxazine/merooxazine-based light-driven molecular switch: The effect of amino/nitro substituents

    Zhao, H.; Xu, Y. Q.; Zhao, W. K.; Gao, K.; Liu, D. S.

    2014-03-01

    By applying non-equilibrium Green's function formulation combined with first-principles density functional theory, we explore the electronic transport properties of indolinospironaphthoxazine (SO)/indolinomeronaphthoxazine (MO). The results indicate that the MO allows a far larger current than the SO. The substituent group can cause shifts of the energy levels. Higher ON/OFF current ratio can be obtained if either amino or nitro substituent is placed at the position of naphthalene moiety. Our results suggest that such molecular wires can generally display switching function and the efficiency can be increased by adding certain substituent groups to the molecules.

  1. Molecular physiology of weak organic acid stress in Bacillus subtilis

    Brul, S.; Beilen, van, J.W.A.

    2013-01-01

    The mechanism by which weak organic acid (WOA) preservatives inhibit growth of microorganisms may differ between different WOAs and these differences are not well understood. The aim of this thesis has been to obtain a better understanding of the mode of action of these preservatives by which they inhibit the growth of spore-forming bacteria (more specifically Bacillus subtilis).

  2. Molecularly imprinted polymer for caffeic acid by precipitation polymerization and its application to extraction of caffeic acid and chlorogenic acid from Eucommia ulmodies leaves.

    Miura, Chitose; Matsunaga, Hisami; Haginaka, Jun

    2016-08-01

    Molecularly imprinted polymers (MIPs) for caffeic acid (CA) were prepared using 4-vinylpyridine and methacrylamide (MAM) as functional monomers, divinylbenzene as a crosslinker and acetonitrile-toluene (3:1, v/v) as a porogen by precipitation polymerization. The use of MAM as the co-monomer resulted in the formation of microsphere MIPs and non-imprinted polymers (NIPs) with ca. 3- and 5-μm particle diameters, respectively. Binding experiments and Scatchard analyses revealed that the binding capacity and affinity of the MIP to CA are higher than those of the NIP. The retention and molecular-recognition properties of the prepared MIPs were evaluated using water-acetonitrile and sodium phosphate buffer-acetonitrile as mobile phases in hydrophilic interaction chromatography (HILIC) and reversed-phase chromatography, respectively. In HILIC mode, the MIP showed higher molecular-recognition ability for CA than in reversed-phase mode. In addition to shape recognition, hydrophilic interactions seem to work for the recognition of CA on the MIP in HILIC mode, while hydrogen bonding and hydrophobic interactions seem to work for the recognition of CA in reversed-phase mode. The MIP had a specific molecular-recognition ability for CA in HILIC mode, while other structurally related compounds, such as chlorogenic acid (CGA), gallic acid, protocatechuic acid and vanillic acid, could not be recognized by the MIP. Furthermore, the MIP was successfully applied for extraction of CA and CGA in the leaves of Eucommia ulmodies in HILIC mode. PMID:26776340

  3. Palmitic acid interferes with energy metabolism balance by adversely switching the SIRT1-CD36-fatty acid pathway to the PKC zeta-GLUT4-glucose pathway in cardiomyoblasts.

    Chen, Yeh-Peng; Tsai, Chia-Wen; Shen, Chia-Yao; Day, Cecilia-Hsuan; Yeh, Yu-Lan; Chen, Ray-Jade; Ho, Tsung-Jung; Padma, V Vijaya; Kuo, Wei-Wen; Huang, Chih-Yang

    2016-05-01

    Metabolic regulation is inextricably linked with cardiac function. Fatty acid metabolism is a significant mechanism for creating energy for the heart. However, cardiomyocytes are able to switch the fatty acids or glucose, depending on different situations, such as ischemia or anoxia. Lipotoxicity in obesity causes impairments in energy metabolism and apoptosis in cardiomyocytes. We utilized the treatment of H9c2 cardiomyoblast cells palmitic acid (PA) as a model for hyperlipidemia to investigate the signaling mechanisms involved in these processes. Our results show PA induces time- and dose-dependent lipotoxicity in H9c2 cells. Moreover, PA enhances cluster of differentiation 36 (CD36) and reduces glucose transporter type 4 (GLUT4) pathway protein levels following a short period of treatment, but cells switch from CD36 back to the GLUT4 pathway after during long-term exposure to PA. As sirtuin 1 (SIRT1) and protein kinase Cζ (PKCζ) play important roles in CD36 and GLUT4 translocation, we used the SIRT1 activator resveratrol and si-PKCζ to identify the switches in metabolism. Although PA reduced CD36 and increased GLUT4 metabolic pathway proteins, when we pretreated cells with resveratrol to activate SIRT1 or transfected si-PKCζ, both were able to significantly increase CD36 metabolic pathway proteins and reduce GLUT4 pathway proteins. High-fat diets affect energy metabolism pathways in both normal and aging rats and involve switching the energy source from the CD36 pathway to GLUT4. In conclusion, PA and high-fat diets cause lipotoxicity in vivo and in vitro and adversely switch the energy source from the CD36 pathway to the GLUT4 pathway. PMID:27133433

  4. Dissolution of Aluminum in Variably Charged Soils as Affected by Low-Molecular-Weight Organic Acids

    LI Jiu-Yu; XU Ren-Kou; JI Guo-Liang

    2005-01-01

    Low-molecular-weight (LMW) organic acids exist widely in soils and play an important role in soil processes such as mineral weathering, nutrient mobilization and Al detoxification. In this research, a batch experiment was conducted to examine the effects of LMW organic acids on dissolution of aluminum in two variably charged soils, an Ultisol and an Oxisol. The results showed that the LMW organic acids enhanced the dissolution of Al in the two investigated soils in the following order: citric > oxalic > malonic > malic > tartaric > salicylic > lactic > maleic. This was generally in agreement with the magnitude of the stability constants for the Al-organic complexes. The effects of LMW organic acids on Al dissolution were greater in the Ultisol than in the Oxisol as compared to their controls. Also, the accelerating effects of citric and oxalic acids on dissolution of Al increased with an increase in pH, while the effects of lactic and salicylic acids decreased. Additionally, when the organic acid concentration was less than 0.2 mmol L-1, the dissolution of Al changed little with increase in acid concentration. However, when the organic acid concentration was greater than 0.2 mmol L-1,the dissolution of Al increased with increase in acid concentration. In addition to the acid first dissociation constant and stability constant of Al-organic complexes, the promoting effects of LMW organic acids on dissolution of Al were also related to their sorption-desorption equilibrium in the soils.

  5. Molecularly imprinted polymer microspheres for solid-phase extraction of protocatechuic acid in Rhizoma homalomenae.

    Chen, Fang-Fang; Wang, Guo-Ying; Shi, Yan-Ping

    2011-10-01

    Molecularly imprinted polymers (MIPs) had been prepared by precipitation polymerization method using acrylamide as the functional monomer, ethylene glycol dimethacrylate as the cross-linker, acetonitrile as the porogen solvent and protocatechuic acid (PA), one of phenolic acids, as the template molecule. The MIPs were characterized by scanning electron microscopy and Fourier transform infrared, and their performance relative to non-imprinted polymers was assessed by equilibrium binding experiments. Six structurally similar phenolic acids, including p-hydroxybenzoic acid, gallic acid, salicylic acid, syringic acid, vanillic acid, ferulic acid were selected to assess the selectivity and recognition capability of the MIPs. The MIPs were applied to extract PA from the traditional Chinese medicines as a solid-phase extraction sorbent. The resultant cartridge showed that the MIPs have a good extraction performance and were able to selectively extract almost 82% of PA from the extract of Rhizoma homalomenae. Thus, the proposed molecularly imprinted-solid phase extraction-high performance liquid chromatography method can be successfully used to extract and analyse PA in traditional Chinese medicines. PMID:21809445

  6. A molecular switch between the outer and the inner vestibule of the voltage-gated Na+ channel

    conformational change of the inner vestibule generates the IUS state. In order to explain the involvement of both the outer and the inner vestibule in ultra-slow inactivation, we proposed a model in which the mutation K1237E produces a conformational change of the outer vestibule which is transmitted to the internal vestibule through the DIV- S6 segment. The resulting conformational change of the internal vestibule gives rise to the extremely stable IUS state. If this molecular mechanism holds true, then mutations at the location of interaction between the selectivity filter and the adjacent S6 segment should substantially modulate the ultra-slow inactivated state. A homology model of the voltage-gated Na+ channel, based on the crystal structure of the KcsA channel places the domain IV-S6 segment in close proximity to the domain III P-loop (containing the site 1237 which is essential for the generation of IUS). In order to search for experimental evidence for an interaction site between the domain III P-loop and the internal vestibule we generated serial alanine and cysteine replacements of amino acids of the domain DIV- S6 segment in the background of the mutation K1237E. We find that mutations only at the site 1575 substantially decrease the likelihood of entry into IUS or significantly accelerate recovery from IUS, suggesting that this residue represents an interaction site between the domain III p-loop and the domain IV- S6 segment. For the first time these functional data confirm a molecular model in which the turn of the domain III P-loop is in close relationship with the domain IV- S6 segment at the level of I1575. (author)

  7. Charting molecular composition of phosphatidylcholines by fatty acid scanning and ion trap MS3 fragmentation

    Ekroos, Kim; Ejsing, Christer S.; Bahr, Ute;

    2003-01-01

    preliminary separation of lipid classes or of individual molecular species, enzymatic digestion, or chemical derivatization. The approach was validated by the comparative analysis of the molecular composition of PCs from human red blood cells. In the total lipid extract of Madin-Darby canine kidney II cells......The molecular composition of phosphatidylcholines (PCs) in total lipid extracts was characterized by a combination of multiple precursor ion scanning on a hybrid quadrupole time-of-flight mass spectrometer and MS3 fragmentation on an ion trap mass spectrometer. Precursor ion spectra for 50 acyl...... anion fragments of fatty acids (fatty acid scanning) acquired in parallel increased the specificity and the dynamic range of the detection of PCs and identified the fatty acid moieties in individual PC species. Subsequent analysis of detected PC peaks by MS3 fragmentation on an ion trap mass...

  8. An intrinsic propensity of murine peritoneal B1b cells to switch to IgA in presence of TGF-β and retinoic acid.

    Bishnudeo Roy

    Full Text Available AIMS: In the present study we have investigated the comparative switching propensity of murine peritoneal and splenic B cell subpopulations to IgA in presence of retinoic acid (RA and TGF-β. METHODS AND RESULTS: To study the influence of RA and TGF-β on switching of B cell subpopulations to IgA, peritoneal (B1a, B1b and B2 cells and splenic (B1a, marginal zone, and B2 B cells from normal BALB/c mice were FACS purified, cultured for 4 days in presence of RA and TGF-β and the number of IgA producing cells was determined by ELISPOT assay or FACS analysis. In presence of TGF-β, peritoneal B1b cells switched to IgA more potently than other peritoneal B cell subpopulations. When TGF-β was combined with retinoic acid (RA, switching to IgA was even more pronounced. Under these conditions, "innate" B cells like peritoneal and splenic B1 cells and MZ B cells produced IgA more readily than B2 cells. Additionally, high frequency of nucleotide exchanges indicating somatic hypermutation in VH regions was observed. Besides IgA induction, RA treatment of sorted PEC and splenic B cells led to expression of gut homing molecules - α4β7 and CCR9. Intraperitoneal transfer of RA-treated B1 cells into Rag1(-/- recipients resulted in IgA in serum and gut lavage, most efficiently amongst B1b cell recipients. CONCLUSION: Present study demonstrates the differential and synergistic effect of RA and TGF-β on switching of different B cell subpopulations to IgA and establishes the prominence of peritoneal B1b cells in switching to IgA under the influence of these two factors. Our study extends our knowledge about the existing differences among B cell subpopulations with regards to IgA production and indicates towards their differential contribution to gut associated humoral immunity.

  9. Multiscale Reactive Molecular Dynamics for Absolute pK a Predictions and Amino Acid Deprotonation.

    Nelson, J Gard; Peng, Yuxing; Silverstein, Daniel W; Swanson, Jessica M J

    2014-07-01

    Accurately calculating a weak acid's pK a from simulations remains a challenging task. We report a multiscale theoretical approach to calculate the free energy profile for acid ionization, resulting in accurate absolute pK a values in addition to insights into the underlying mechanism. Importantly, our approach minimizes empiricism by mapping electronic structure data (QM/MM forces) into a reactive molecular dynamics model capable of extensive sampling. Consequently, the bulk property of interest (the absolute pK a) is the natural consequence of the model, not a parameter used to fit it. This approach is applied to create reactive models of aspartic and glutamic acids. We show that these models predict the correct pK a values and provide ample statistics to probe the molecular mechanism of dissociation. This analysis shows changes in the solvation structure and Zundel-dominated transitions between the protonated acid, contact ion pair, and bulk solvated excess proton. PMID:25061442

  10. Molecular pharmacology of homologues of ibotenic acid at cloned metabotropic glutamic acid receptors

    Bräuner-Osborne, Hans; Nielsen, B; Krogsgaard-Larsen, P

    We have studied the effects of the enantiomers of 2-amino-3-(3-hydroxyisoxazol-5-yl)propionic acid (homoibotenic acid, HIBO) and analogues substituted with a methyl, bromo or butyl group in the four position of the ring at cloned metabotropic glutamate (mGlu) receptors expressed in Chinese hamste...

  11. Molecular and Functional Characterisation of a new Mammalian Family of Proton-coupled Amino Acid Transporters

    Foltz, Martin

    2006-01-01

    Proton-coupled amino acid transport (PAT) systems in the apical membrane of epithelial cells of the small intestine and the renal tubule have been demonstrated by use of the human intestinal cell line Caco-2 and renal brush border membrane vesicles. The present thesis summarises the revelation of the molecular entity of the PAT system and provides deeper insights into this new mammalian family of proton/amino acid cotransporters. The identified family comprises four structural similar murine ...

  12. Amino acids and proteins at ZnO-water interfaces in molecular dynamics simulations

    Nawrocki, Grzegorz; Cieplak, Marek

    2014-01-01

    We determine potentials of the mean force for interactions of amino acids with four common surfaces of ZnO in aqueous solutions. The method involves all-atom molecular dynamics simulations combined with the umbrella sampling technique. The profiled nature of the density of water with the strongly adsorbed first layer affects the approach of amino acids to the surface and generates either repulsion or weak binding. The largest binding energy is found for tyrosine interacting with the surface i...

  13. Bile acid derivatives as ligands of the farnesoid x receptor: molecular determinants for bile acid binding and receptor modulation.

    Gioiello, Antimo; Cerra, Bruno; Mostarda, Serena; Guercini, Chiara; Pellicciari, Roberto; Macchiarulo, Antonio

    2014-01-01

    Bile acids are a peculiar class of steroidal compounds that never cease to amaze. From being simple detergents with a primary role in aiding the absorption of fats and fat-soluble vitamins, bile acids are now widely considered as crucial hormones endowed with genomic and non-genomic functions that are mediated by their interaction with several proteins including the nuclear receptor Farnesoid X Receptor (FXR). Taking advantages of the peculiar properties of bile acids in interacting with the FXR receptor, several biliary derivatives have been synthesized and tested as FXR ligands. The availability of these compounds has contributed to characterize the receptor from a structural, patho-physiological and therapeutic standpoint. Among these, obeticholic acid is a first-in-class FXR agonist that is demonstrating hepatoprotective effects upon FXR activation in patients with liver diseases such as primary biliary cirrhosis and nonalcoholic steatohepatitis. This review provides an historical overview of the rationale behind the discovery of obeticholic acid and chemical tools generated to depict the molecular features and bio-pharmacological relevance of the FXR receptor, as well as to summarize structure-activity relationships of bile acid-based FXR ligands so far reported. PMID:25388535

  14. Add-on-Statin Extended Release Nicotinic Acid/Laropiprant but Not the Switch to High-Dose Rosuvastatin Lowers Blood Pressure: An Open-Label Randomized Study

    Anastazia Kei

    2011-01-01

    Full Text Available Introduction. Nicotinic acid (NA and statins have been associated with reductions in blood pressure (BP. Patients and Methods. We recruited 68 normotensive and hypertensive dyslipidemic patients who were treated with a conventional statin dose and had not achieved lipid targets. Patients were randomized to switch to high-dose rosuvastatin (40 mg/day or to add-on current statin treatment with extended release (ER NA/laropiprant (1000/20 mg/day for the first 4 weeks followed by 2000/40 mg/day for the next 8 weeks for 3 months. Results. Switching to rosuvastatin 40 mg/day was not associated with significant BP alterations. In contrast, the addition of ER-NA/laropiprant to current statin treatment resulted in a 7% reduction of systolic BP (from 134±12 to 125±10 mmHg, <.001 versus baseline and =.01 versus rosuvastatin group and a 5% reduction of diastolic BP (from 81±9 to 77±6 mmHg, =.009 versus baseline and =.01 versus rosuvastatin group. These reductions were significant only in the subgroup of hypertensives and were independent of the hypolipidemic effects of ER-NA/laropiprant. Conclusions. Contrary to the switch to high-dose rosuvastatin, the addition of ER-NA/laropiprant to statin treatment was associated with significant reductions in both systolic and diastolic BP.

  15. Structure and dynamics studies of the short strong hydrogen bond in the 3,5-dinitrobenzoic acid-nicotinic acid molecular complex.

    Ford, Samantha J.; McIntyre, Garry J.; Johnson, Mark R.; Evans, Ivana Radosavljevic

    2013-01-01

    The molecular complex between 3,5-dinitrobenzoic acid and nicotinic acid (35DBNA) has been studied by variable temperature single crystal X-ray and neutron diffraction (30 to 300 K) and ab initio molecular dynamics, in order to investigate the dynamics and any proton migration in this system, which exhibits structural similarities with the well-known proton migration material 3,5-dicarboxylic acid. The refined structures clearly indicate a significant degree of proton transfer in ...

  16. UPGRADING OF BIO-OIL MOLECULAR DISTILLATION FRACTION WITH SOLID ACID CATALYST

    Zuogang Guo

    2011-05-01

    Full Text Available Molecular distillation technology has been adopted to obtain a bio-oil fraction rich in carboxylic acids and ketones. This unique bio-oil fraction was then upgraded with a La-promoted solid acid catalyst. Three washing pretreatments were used to prepare catalysts A, B, and C, with the intention of reducing the amounts of residual sulfuric acid. Model reactions were used to estimate their catalytic activities and the residual amounts of sulfuric acid. Catalyst B, with washing after calcination, displayed higher catalytic activity (80.83% and lower residual amount of sulfuric acid (50 μmol/g. The catalysts were characterized by techniques such as BET, XRD, and SEM to explain the differences in their catalytic activities. The optimum catalyst B was used in the upgrading of the bio-oil molecular distillation fraction. After upgrading, the corrosivity of the bio-oil fraction declined and its storage stability was improved. The carboxylic acid content in the upgraded bio-oil fraction decreased from 18.39% to 2.70%, while the ester content increased from 0.72% to 31.17%. The conversion of corrosive carboxylic acids to neutral esters reduced the corrosivity of the bio-oil fraction. Moreover, the ketones with unsaturated carbon-carbon double bonds (such as 2-cyclopenten-1-one, 3-methyl-2-cyclopenten-1-one, etc. were converted into saturated compounds, which improved the stability of the bio-oil fraction.

  17. Realization of a four-step molecular switch in scanning tunneling microscope manipulation of single chlorophyll-a molecules

    Iancu, Violeta; Hla, Saw-Wai

    2006-01-01

    Single chlorophyll-a molecules, a vital resource for the sustenance of life on Earth, have been investigated by using scanning tunneling microscope manipulation and spectroscopy on a gold substrate at 4.6 K. Chlorophyll-a binds on Au(111) via its porphyrin unit while the phytyl-chain is elevated from the surface by the support of four CH3 groups. By injecting tunneling electrons from the scanning tunneling microscope tip, we are able to bend the phytyl-chain, which enables the switching of fo...

  18. Identification of Low-Molecular-Weight Nucleic Acid-Related Substances Secreted by Streptomyces aureofaciens

    De Carvalho, Alírio; Molinari, Rubens

    1983-01-01

    Streptomyces aureofaciens growth in chemically defined medium is actively associated with the secretion of low-molecular-weight nucleic acid-related substances and is linked to low availability of phosphate. Thirteen pure compounds were isolated, of which seven were identified.

  19. Relationship between molecular descriptors and the enthalpies of sublimation of natural amino acids

    Badelin, V. G.; Tyunina, V. V.; Girichev, G. V.; Tyunina, E. Yu.

    2016-07-01

    A multiparameter correlation between the enthalpies of sublimation and molecular descriptors of natural amino acids is proposed, based on generalized experimental and literature data on the heat effects of sublimation. The contributions from Van der Waals interactions, hydrogen bond formation, and electrostatic effects into enthalpy of sublimation has been evaluated using regression coefficients.

  20. Comparison of phenotypic and molecular tests to identify lactic acid bacteria

    Paula Mendonça Moraes; Luana Martins Perin; Abelardo Silva Júnior; Luís Augusto Nero

    2013-01-01

    Twenty-nine lactic acid bacteria (LAB) isolates were submitted for identification using Biolog, API50CHL, 16S rDNA sequencing, and species-specific PCR reactions. The identification results were compared, and it was concluded that a polyphasic approach is necessary for proper LAB identification, being the molecular analyzes the most reliable.

  1. Unbinding of Retinoic Acid from its Receptor Studied by Steered Molecular Dynamics

    Kosztin, D; Schulten, K; Kosztin, Dorina; Izrailev, Sergei; Schulten, Klaus

    1999-01-01

    Retinoic acid receptor (RAR) is a ligand-dependent transcription factor that regulates the expression of genes involved in cell growth, differentiation, and development. Binding of the retinoic acid hormone to RAR is accompanied by conformational changes in the protein which induce transactivation or transrepression of the target genes. In this paper we present a study of the hormone binding/unbinding process in order to clarify the role of some of the amino acid contacts and identify possible pathways of the all-trans retinoic acid binding/unbinding to/from human retinoic acid receptor (hRAR)-g. Three possible pathways were explored using steered molecular dynamics simulations. Unbinding was induced on a time scale of 1 ns by applying external forces to the hormone. The simulations suggest that the hormone may employ one pathway for binding and an alternative "back door" pathway for unbinding.

  2. A Metabolic Switch

    Hjorth, Poul G.

    Our muscles are metabolically flexible, i.e., they are capable of `switching' between two types of oxidation: (1) when fasting, a predominantly lipid oxidation with high rates of fatty acid uptake, and (2) when fed, suppression of lipid oxidation in favour of increased glucose uptake, oxidation and...... storage, in response to insulin. One of the many manifestations of obesity and Type 2 diabetes is an insulin resistance of the skeletal muscles, which suppresses this metabolic switch. This talk describes recent development of a low-dimensional system of ODEs that model the metabolic switch, displaying a...

  3. Photoelectron spectroscopy of self-assembled monolayers of molecular switches on noble metal surfaces; Photoelektronenspektroskopie selbstorganisierter Adsorbatschichten aus molekularen Schaltern auf Edelmetalloberflaechen

    Heinemann, Nils

    2012-09-12

    Self-assembled monolayers (SAMs) of butanethiolate (C4) on single crystalline Au(111) surfaces were prepared by adsorption from solution. The thermally activated desorption behaviour of the C4 molecules from the gold substrate was examined by qualitative thermal desorption measurements (TDM), through this a desorption temperature T{sub Des}=473 K could be determined. With this knowledge, it was possible to produce samples of very good surface quality, by thermal treatment T{sub Sample}molecular switch 3-(4-(4-Hexyl-phenylazo)-phenoxy)-propane-1-thiol (ABT), deposited by self-assembly from solution on Au(111), was examined using laser-based photoelectron spectroscopy. Differences in the molecular dipole moment characteristic for the trans and the cis isomer of ABT were observed via changes in the sample work function, accessible by detection of the threshold energy for photoemission. A quantitative

  4. Strong Hydrogen Bonded Molecular Interactions between Atmospheric Diamines and Sulfuric Acid.

    Elm, Jonas; Jen, Coty N; Kurtén, Theo; Vehkamäki, Hanna

    2016-05-26

    We investigate the molecular interaction between methyl-substituted N,N,N',N'-ethylenediamines, propane-1,3-diamine, butane-1,4-diamine, and sulfuric acid using computational methods. Molecular structure of the diamines and their dimer clusters with sulfuric acid is studied using three density functional theory methods (PW91, M06-2X, and ωB97X-D) with the 6-31++G(d,p) basis set. A high level explicitly correlated CCSD(T)-F12a/VDZ-F12 method is used to obtain accurate binding energies. The reaction Gibbs free energies are evaluated and compared with values for reactions involving ammonia and atmospherically relevant monoamines (methylamine, dimethylamine, and trimethylamine). We find that the complex formation between sulfuric acid and the studied diamines provides similar or more favorable reaction free energies than dimethylamine. Diamines that contain one or more secondary amino groups are found to stabilize sulfuric acid complexes more efficiently. Elongating the carbon backbone from ethylenediamine to propane-1,3-diamine or butane-1,4-diamine further stabilizes the complex formation with sulfuric acid by up to 4.3 kcal/mol. Dimethyl-substituted butane-1,4-diamine yields a staggering formation free energy of -19.1 kcal/mol for the clustering with sulfuric acid, indicating that such diamines could potentially be a key species in the initial step in the formation of new particles. For studying larger clusters consisting of a diamine molecule with up to four sulfuric acid molecules, we benchmark and utilize a domain local pair natural orbital coupled cluster (DLPNO-CCSD(T)) method. We find that a single diamine is capable of efficiently stabilizing sulfuric acid clusters with up to four acid molecules, whereas monoamines such as dimethylamine are capable of stabilizing at most 2-3 sulfuric acid molecules. PMID:27128188

  5. Effect on molecular weight of poly (L-lactic acid) by irradiation graft with NVP

    Copolymer of poly (L-lactic acid) (PLLA) grafted with N-vinylpyrrolidone(PLLA-g-PVP) was prepared by γ-irradiation in the presence of methanol as a solvent. The effects of acetic acid (HAc) concentration, monomer concentration and dose rate on molecular weight of PLLA-g-PVP were investigated and the structure of PLLA-g-PVP was characterized by 1H-NMR, FT-IR and TGA, respectively. It shows that, the HAc concentration, monomer concentration and dose rate have an effect on the molecular weight of PLLA-g-PVP at the same absorbed dose. The maximum molecular weight of the copolymers can be obtained in optimum condition of HAc concentration 0.05 mol/L, monomer concentration 30% and dose rate 500 Gy/h, respectively. The two weight loss stages of graft copolymers have been observed more distinctly with the increment of graft ratio. (authors)

  6. New concepts in molecular imaging: non-invasive MRI spotting of proteolysis using an Overhauser effect switch.

    Philippe Mellet

    Full Text Available BACKGROUND: Proteolysis, involved in many processes in living organisms, is tightly regulated in space and time under physiological conditions. However deregulation can occur with local persistent proteolytic activities, e.g. in inflammation, cystic fibrosis, tumors, or pancreatitis. Furthermore, little is known about the role of many proteases, hence there is a need of new imaging methods to visualize specifically normal or disease-related proteolysis in intact bodies. METHODOLOGY/PRINCIPAL FINDINGS: In this paper, a new concept for non invasive proteolysis imaging is proposed. Overhauser-enhanced Magnetic Resonance Imaging (OMRI at 0.2 Tesla was used to monitor the enzymatic hydrolysis of a nitroxide-labeled protein. In vitro, image intensity switched from 1 to 25 upon proteolysis due to the associated decrease in the motional correlation time of the substrate. The OMRI experimental device used in this study is consistent with protease imaging in mice at 0.2 T without significant heating. Simulations show that this enzymatic-driven OMRI signal switch can be obtained at lower frequencies suitable for larger animals or humans. CONCLUSIONS/SIGNIFICANCE: The method is highly sensitive and makes possible proteolysis imaging in three dimensions with a good spatial resolution. Any protease could be targeted specifically through the use of taylor-made cleavable macromolecules. At short term OMRI of proteolysis may be applied to basic research as well as to evaluate therapeutic treatments in small animal models of experimental diseases.

  7. Study of the molecular mobility of methyl-methacrylate and methacrylic acid copolymers by solid state NMR

    Several methyl-methacrylate/methacrylic acid copolymers were prepared in the presence of concentrated nitric acid. The obtained copolymers were characterized by molecular weigh determination and hydrolization degree. The molecular mobility of these copolymers was studied by solid state nuclear magnetic resonance. Results are presented

  8. Separation of phenolic acids from natural plant extracts using molecularly imprinted anion-exchange polymer confined ionic liquids.

    Bi, Wentao; Tian, Minglei; Row, Kyung Ho

    2012-04-01

    Polymer-confined ionic liquids were used for the separation of phenolic acids from natural plant extract by utilizing an anion-exchange mechanism. They were synthesized using molecular imprinting technique to reduce non-directional ion-ion interactions during anion-exchange and other interactions with interference substances that could decrease selectivity. A suitable sorbent for phenolic acid separation could be identified based on the adsorption behaviors of phenolic acids on different polymer-confined ionic liquids. Thus, the developed ionic liquid-based molecularly imprinted anion-exchange polymer (IMAP) achieved high recovery rates by solid-phase extraction of phenolic acids from Salicornia herbacea L. extract: 90.1% for protocatechuic acid, 95.5% for ferulic acid and 96.6% for caffeic acid. Moreover, the phenolic acids were separable from each other by repeated solid phase extraction cycles. The proposed method could be used to separate other phenolic acids or organic acids from complex samples. PMID:21903215

  9. Supra-molecular Association and Polymorphic Behaviour In Systems Containing Bile Acid Salts

    Camillo La Mesa

    2007-08-01

    Full Text Available A wide number of supra-molecular association modes are observed in mixtures containing water and bile salts, BS, (with, eventually, other components. Molecular or micellar solutions transform into hydrated solids, fibres, lyotropic liquid crystals and/or gels by raising the concentration, the temperature, adding electrolytes, surfactants, lipids and proteins. Amorphous or ordered phases may be formed accordingly. The forces responsible for this very rich polymorphism presumably arise from the unusual combination of electrostatic, hydrophobic and hydrogen-bond contributions to the system stability, with subsequent control of the supra-molecular organisation modes. The stabilising effect due to hydrogen bonds does not occur in almost all surfactants or lipids and is peculiar to bile acids and salts. Some supra-molecular organisation modes, supposed to be related to malfunctions and dis-metabolic diseases in vivo, are briefly reported and discussed.

  10. Synthesis of high molecular weight polylactic acid from aqueous lactic acid co-catalyzed by tin(II)chloride dihydrate and succinic anhydride

    LEI Ziqiang; BAI Yanbin; WANG Shoufeng

    2005-01-01

    Polylactic acid was synthesized from commercial available cheap aqueous lactic acid (85%―90% w/w) using succinic anhydride and SnCl2·2H2O as catalyst in the absence of organic solvents. As a result, polylactic acid with a molecular weight of 60000 was prepared in 10 h. The new procedure is much simple, cheap and outstanding in that the start material is aqueous lactic acid; the catalytic system is environmentally benign.

  11. Preparation and characterization of the high molecular weight [3H]hyaluronic acid

    Two methods of preparation were investigated. In the first, hydrogen atoms in the molecule are replaced by tritium. This isotopic substitution was performed in aqueous solution using Pd/CaCO3 as catalyst. In the second method, the high molecular weight hyaluronic acid was alkylated with [3H]methyl bromide in liquid ammonia at a temperature of -33.5 degC. High-performance gel permeation chromatographic separation was used for the separation and characterization of the high molecular weight [3H]hyaluronic acid. Molecular weight parameters for the labelled biopolymers were: M-barw=128 kDa, M-barw/M-barn=1.88 (first method) and M-barw=268 kDa, M-barw/M-barn=1.55 (second method). The high molecular weight [3H]hyaluronic acid with M-barw=268 kDa was degraded further by specific hyaluronidase. Products of the enzymatic depolymerization were observed to be identical for both the labelled and cold biopolymer. This finding indicates that the described labelling procedure using [3H]methyl bromide does not induce any major structural rearrangements in the molecule. (author) 3 figs., 2 tabs., 13 refs

  12. Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations

    Amninder S Virk

    2015-02-01

    Full Text Available Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction. Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.

  13. Evaluating the molecular weight and characteristics of humic acids gradations using gel filtration and radioisotope tracer technique

    The measurement for molecular weight of humic acids gradations in the drab soil showed that the humic acid could be separated into three gradations of molecular weight using gel filtration by G-50 and two gradations by G-100, the molecular weights by G-50 were 78180, 48339, 22863 and molecular weights by G-100 were 63343 and 19870 respectively. While fulvic acid had only one gradation by both G-50 and G-100, the molecular weight was 2300 approximately. The measurement for complexation capacity of cadmium (zinc)-humic acids showed that the contents of Cd(Zn)-humic acid had two peak values with the volume of eluent compounded by cadmium (or zinc). The Cd(or Zn)-fulvic acid had only one peak value. The curve between contents of Cd (Zn)-humic acid and the volume of eluent met with the curve between spectrum and the volume of eluent. The experiment conducted by radioisotope tracer technique indicated that the complexation capacity of 65Zn-humic acids changed with different gradations of humic acids, the complexation curve met with the spectrum curve on the whole, i.e. the value of 65Zn-humic acid had two peak values, while the 65Zn-fulvic acid had only one, indicating that the use of radioisotope tracer technique could eliminate the intervention accompanied by other heavy metal ions

  14. Photochemical alkylation of inorganic selenium in the presence of low molecular weight organic acids.

    Guo, Xuming; Sturgeon, Ralph E; Mester, Zoltán; Gardner, Graeme J

    2003-12-15

    Using a flow-through photochemical reactor and a low pressure mercury lamp as a UV source, alkyl selenium species are formed from inorganic selenium(IV) in the presence of low molecular weight organic acids (LMW acids). The volatile alkyl Se species were cryogenically trapped and identified by GC-MS and GC-ICP-MS. In the presence of formic, acetic, propionic and malonic acids, inorganic selenium(IV) is converted by UV irradiation to volatile selenium hydride and carbonyl, dimethylselenide and diethylselenide, respectively. Se(IV) was successfully removed from contaminated agricultural drainage waters (California, U.S.A.) using a batch photoreactor system Se. Photochemical alkylation may thus offer a promising means of converting toxic selenium salts, present in contaminated water, to less toxic dimethylselenide. The LMW acids and photochemical alkylation process may also be key to understanding the source of atmospheric selenium and are likely involved in its mobility in the natural anaerobic environment. PMID:14717175

  15. High-molecular-weight polymers for protein crystallization: poly-γ-glutamic acid-based precipitants

    Hu, Ting-Chou [Department of Chemistry, University of York, York YO10 5YW (United Kingdom); Korczyńska, Justyna [Department of Chemistry, University of York, York YO10 5YW (United Kingdom); Structural Biology Laboratory, University of York, York YO10 5YW (United Kingdom); Smith, David K. [Department of Chemistry, University of York, York YO10 5YW (United Kingdom); Brzozowski, Andrzej Marek, E-mail: marek@ysbl.york.ac.uk [Department of Chemistry, University of York, York YO10 5YW (United Kingdom); Structural Biology Laboratory, University of York, York YO10 5YW (United Kingdom)

    2008-09-01

    High-molecular-weight poly-γ-glutamic acid-based polymers have been synthesized, tested and adopted for protein crystallization. Protein crystallization has been revolutionized by the introduction of high-throughput technologies, which have led to a speeding up of the process while simultaneously reducing the amount of protein sample necessary. Nonetheless, the chemistry dimension of protein crystallization has remained relatively undeveloped. Most crystallization screens are based on the same set of precipitants. To address this shortcoming, the development of new protein precipitants based on poly-γ-glutamic acid (PGA) polymers with different molecular-weight ranges is reported here: PGA-LM (low molecular weight) of ∼400 kDa and PGA-HM (high molecular weight) of >1000 kDa. It is also demonstrated that protein precipitants can be expanded further to polymers with much higher molecular weight than those that are currently in use. Furthermore, the modification of PGA-like polymers by covalent attachments of glucosamine substantially improved their solubility without affecting their crystallization properties. Some preliminary PGA-based screens are presented here.

  16. High-molecular-weight polymers for protein crystallization: poly-γ-glutamic acid-based precipitants

    High-molecular-weight poly-γ-glutamic acid-based polymers have been synthesized, tested and adopted for protein crystallization. Protein crystallization has been revolutionized by the introduction of high-throughput technologies, which have led to a speeding up of the process while simultaneously reducing the amount of protein sample necessary. Nonetheless, the chemistry dimension of protein crystallization has remained relatively undeveloped. Most crystallization screens are based on the same set of precipitants. To address this shortcoming, the development of new protein precipitants based on poly-γ-glutamic acid (PGA) polymers with different molecular-weight ranges is reported here: PGA-LM (low molecular weight) of ∼400 kDa and PGA-HM (high molecular weight) of >1000 kDa. It is also demonstrated that protein precipitants can be expanded further to polymers with much higher molecular weight than those that are currently in use. Furthermore, the modification of PGA-like polymers by covalent attachments of glucosamine substantially improved their solubility without affecting their crystallization properties. Some preliminary PGA-based screens are presented here

  17. Application of molecular techniques for identification and ennumeration of acetic acid bacteria

    González Benito, Angel

    2005-01-01

    Application of molecular techniques for identification and enumeration of acetic acid bacteria:Los principales objetivos de la tesis son el desarrollo de técnicas de biología molecular rápidas y fiables para caracterizar bacterias acéticas.Las bacterias acéticas son las principales responsables del picado de los vinos y de la producción de vinagre. Sin embargo, existe un desconocimiento importante sobre su comportamiento y evolución. Las técnicas de enumeración y de identificación basadas en ...

  18. Molecular-scale imaging of unstained deoxyribonucleic acid fibers by phase transmission electron microscopy

    The molecular structure of deoxyribonucleic acid (DNA) fibers was observed by a phase reconstruction method called three-dimensional Fourier filtering using a 200 kV transmission electron microscope. The characteristic helical structure and the spacing of adjacent base pairs of DNA were partially resolved due to an improved signal-to-noise ratio and resolution enhancement by the phase reconstruction although the molecular structure was damaged by the electron beam irradiation. In the spherical aberration-free phase images, the arrangements of single atom-sized spots forming sinusoidal curves were sometimes observed, which seem to be the contrast originating in the sulfur atoms along the main chains

  19. Femtosecond Laser Spectroscopy of the Rhodopsin Photochromic Reaction: A Concept for Ultrafast Optical Molecular Switch Creation (Ultrafast Reversible Photoreaction of Rhodopsin

    Olga Smitienko

    2014-11-01

    Full Text Available Ultrafast reverse photoreaction of visual pigment rhodopsin in the femtosecond time range at room temperature is demonstrated. Femtosecond two-pump probe experiments with a time resolution of 25 fs have been performed. The first рump pulse at 500 nm initiated cis-trans photoisomerization of rhodopsin chromophore, 11-cis retinal, which resulted in the formation of the primary ground-state photoproduct within a mere 200 fs. The second pump pulse at 620 nm with a varying delay of 200 to 3750 fs relative to the first рump pulse, initiated the reverse phototransition of the primary photoproduct to rhodopsin. The results of this photoconversion have been observed on the differential spectra obtained after the action of two pump pulses at a time delay of 100 ps. It was found that optical density decreased at 560 nm in the spectral region of bathorhodopsin absorption and increased at 480 nm, where rhodopsin absorbs. Rhodopsin photoswitching efficiency shows oscillations as a function of the time delay between two рump pulses. The quantum yield of reverse photoreaction initiated by the second pump pulse falls within the range 15% ± 1%. The molecular mechanism of the ultrafast reversible photoreaction of visual pigment rhodopsin may be used as a concept for the development of an ultrafast optical molecular switch.

  20. Molecular dynamics simulations data of the twenty encoded amino acids in different force fields.

    Vitalini, F; Noé, F; Keller, B G

    2016-06-01

    We present extensive all-atom Molecular Dynamics (MD) simulation data of the twenty encoded amino acids in explicit water, simulated with different force fields. The termini of the amino acids have been capped to ensure that the dynamics of the Φ and ψ torsion angles are analogues to the dynamics within a peptide chain. We use representatives of each of the four major force field families: AMBER ff-99SBILDN [1], AMBER ff-03 [2], OPLS-AA/L [3], CHARMM27 [4] and GROMOS43a1 [5], [6]. Our data represents a library and test bed for method development for MD simulations and for force fields development. Part of the data set has been previously used for comparison of the dynamic properties of force fields (Vitalini et al., 2015) [7] and for the construction of peptide basis functions for the variational approach to molecular kinetics [8]. PMID:27054161

  1. n-3 Polyunsaturated fatty acids exert immunomodulatory effects on lymphocytes by targeting plasma membrane molecular organization

    Shaikh, Saame Raza; Jolly, Christopher A.; Chapkin, Robert S.

    2011-01-01

    Fish oil, enriched in bioactive n-3 polyunsaturated fatty acids (PUFA), has therapeutic value for the treatment of inflammation-associated disorders. The effects of n-3 PUFAs are pleiotropic and complex; hence, an understanding of their cellular targets and molecular mechanisms of action remains incomplete. Here we focus on recent data indicating n-3 PUFAs exert immunosuppressive effects on the function of effector and regulatory CD4+ T cells. In addition, we also present emerging evidence th...

  2. In vitro evaluation of antiviral and virucidal activity of a high molecular weight hyaluronic acid

    Blasi Elisabetta; Ardizzoni Andrea; Neglia Rachele G; Bettua Clotilde; Scuri Monica; Cuoghi Alessandro; Cermelli Claudio; Iannitti Tommaso; Palmieri Beniamino

    2011-01-01

    Abstract Background hyaluronic acid (HA), a non-sulphated glycosaminoglycan, is present in synovial fluid, vitreous humour serum and many connective tissues. Pharmaceutical preparations of HA are used in clinical practice for wound healing, joint pain, kerato-conjunctivitis, asthma, mouth care, oesophageal-reflux, and gastritis. Moreover, it is used as a filler to counteract ageing and facial lipoatrophy. Our study aims at investigating the in vitro antiviral activity of a high molecular weig...

  3. Neutral molecular cluster formation of sulfuric acid dimethylamine observed in real time under atmospheric conditions

    Kürten, Andreas; Jokinen, Tuija; Simon, Mario; Sipilä, Mikko; Sarnela, Nina; Junninen, Heikki; Adamov, Alexey; Almeida, João; Amorim, Antonio; Bianchi, Federico; Breitenlechner, Martin; Dommen, Josef; Donahue, Neil M.; Duplissy, Jonathan; Ehrhart, Sebastian

    2015-01-01

    For atmospheric sulfuric acid (SA) concentrations the presence of dimethylamine (DMA) at mixing ratios of several parts per trillion by volume can explain observed boundary layer new particle formation rates. However, the concentration and molecular composition of the neutral (uncharged) clusters have not been reported so far due to the lack of suitable instrumentation. Here we report on experiments from the Cosmics Leaving Outdoor Droplets chamber at the European Organization for Nuclear Res...

  4. Molecular characterization of lactic acid bacteria recovered from natural fermentation of beet root and carrot Kanji

    Kingston, J. J.; Radhika, M.; Roshini, P. T.; Raksha, M. A.; H.S. Murali; Batra, H. V.

    2010-01-01

    The lactic acid bacteria (LAB) play an important role in the fermentation of vegetables to improve nutritive value, palatability, acceptability, microbial quality and shelf life of the fermented produce. The LAB associated with beetroot and carrot fermentation were identified and characterized using different molecular tools. Amplified ribosomal DNA restriction analysis (ARDRA) provided similar DNA profile for the 16 LAB strains isolated from beetroot and carrot fermentation while repetitive ...

  5. Molecular dynamics study of solvation effects on acid dissociation in aprotic media

    Laria, Daniel; Kapral, Raymond; Estrin, Dario; Ciccotti, Giovanni

    1996-01-01

    Acid ionization in aprotic media is studied using Molecular Dynamics techniques. In particular, models for HCl ionization in acetonitrile and dimethylsulfoxide are investigated. The proton is treated quantum mechanically using Feynman path integral methods and the remaining molecules are treated classically. Quantum effects are shown to be essential for the proper treatment of the ionization. The potential of mean force is computed as a function of the ion pair separation and the local solven...

  6. Ancient low–molecular-weight organic acids in permafrost fuel rapid carbon dioxide production upon thaw

    Drake, Travis W.; Wickland, Kimberly P.; Spencer, Robert G.M.; McKnight, Diane M.; Striegl, Robert G.

    2015-01-01

    To our knowledge, this study is the first to directly link rapid microbial consumption of ancient permafrost-derived dissolved organic carbon (DOC) to CO2 production using a novel bioreactor. Rapid mineralization of the freshly thawed DOC was attributed to microbial decomposition of low–molecular-weight organic acids, which were completely consumed during the experiments. Our results indicate that substantial biodegradation of permafrost DOC occurs immediately after thaw and before downstream...

  7. Molecular assessment of complex microbial communities degrading long chain fatty acids in methanogenic bioreactors

    Sousa, D.Z.; Pereira, M.A.; Smidt, Hauke; Stams, A.J.M.; Alves, M. M.

    2007-01-01

    Microbial diversity of anaerobic sludge after extended contact with long chain fatty acids (LCFA) was studied using molecular approaches. Samples containing high amounts of accumulated LCFA were obtained after continuous loading of two bioreactors with oleate or with palmitate. These sludge samples were then incubated in batch assays to allow degradation of the biomass-associated LCFA. In addition, sludge used as inoculum for the reactors was also characterized. Predominant ...

  8. Molecular characterization of lactic acid bacteria isolated from industrially fermented Greek table olives

    Doulgeraki, Agapi; Pramateftaki, Paraskevi; Argyri, Anthoula; Nychas, George John; Tassou, Chrysoula; Panagou, Efstathios

    2012-01-01

    A total of 145 lactic acid bacteria (LAB) isolates have been recovered from fermented table olives and brine and characterized at strain level with molecular tools. Pulsed-Field Gel Electrophoresis (PFGE) of ApaI macrorestriction fragments was applied for strain differentiation. Species differentiation was based either on Denaturing Gradient Gel Electrophoresis (PCR-DGGE) (black olives) or on restriction analysis of the amplified 16S rRNA gene (PCR-ARDRA) (brine and green olives). Species ide...

  9. Photoinduced switching to metallic states in the two-dimensional organic Mott insulator dimethylphenazine-tetrafluorotetracyanoquinodimethane with anisotropic molecular stacks

    Matsuzaki, Hiroyuki; Ohkura, Masa-aki; Ishige, Yu; Nogami, Yoshio; Okamoto, Hiroshi

    2015-06-01

    A photoinduced phase transition was investigated in an organic charge-transfer (CT) complex M2P -TCNQ F4 , [M2P : 5,10-dihydro-5,10-dimethylphenazine, donor (D) molecule; TCNQ F4 : 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane, acceptor (A) molecule] by means of femtosecond pump-probe reflection spectroscopy. This is an ionic compound and has a peculiar two-dimensional (2D) molecular arrangement; the same A (or D) molecules arrange along the [100] direction, and A and D molecules alternately arrange along the [111] direction. It results in a strongly anisotropic two-dimensional electronic structure. This compound shows a structural and magnetic phase transition at 122 K below which the two neighboring molecules are dimerized along both the [100] and [111] directions. We demonstrate that two kinds of photoinduced phase transitions occur by irradiation of a femtosecond laser pulse; in the high-temperature lattice-uniform phase, a quasi-one-dimensional (1D) metallic state along the AA(DD) stack is generated, and in the low-temperature lattice-dimerized phase, a quasi-2D metallic state is initially produced and molecular dimerizations are subsequently released. Mixed-stack CT compounds consisting of DA stacks are generally insulators or semiconductors in the ground state. Here, such a dynamical metallization in the DA stack is demonstrated. The release of the dimerizations drives several kinds of coherent oscillations which play an important role in the stabilization of the lattice-dimerized phase. The mechanisms of those photoinduced phase transitions are discussed in terms of the magnitudes of the anisotropic bandwidths and molecular dimerizations along two different directions of the molecular stacks.

  10. Molecular Structures and Dynamics of the Stepwise Activation Mechanism of a Matrix Metalloproteinase Zymogen: Challenging the Cysteine Switch Dogma

    Rosenblum,G.; Meroueh, S.; Toth, M.; Fisher, J.; Fridman, R.; Mobashery, S.; Sagi, I.

    2007-01-01

    Activation of matrix metalloproteinase zymogen (pro-MMP) is a vital homeostatic process, yet its molecular basis remains unresolved. Using stopped-flow X-ray spectroscopy of the active site zinc ion, we determined the temporal sequence of pro-MMP-9 activation catalyzed by tissue kallikrein protease in milliseconds to several minutes. The identity of three intermediates seen by X-ray spectroscopy was corroborated by molecular dynamics simulations and quantum mechanics/molecular mechanics calculations. The cysteine-zinc interaction that maintains enzyme latency is disrupted via active-site proton transfers that mediate transient metal-protein coordination events and eventual binding of water. Unexpectedly, these events ensue as a direct result of complexation of pro-MMP-9 and kallikrein and occur before proteolysis and eventual dissociation of the pro-peptide from the catalytic site. Here we demonstrate the synergism among long-range protein conformational transitions, local structural rearrangements, and fine atomic events in the process of zymogen activation.