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Sample records for liquid crystal-forming molecules

  1. Room temperature supramolecular columnar liquid crystals formed by hydrogen bonding of isoquinoline derivatives

    NASA Astrophysics Data System (ADS)

    Hyup Lee, Jun; Lee, Seung Jun; Jho, Jae Young

    2014-07-01

    We report new self-assembled discotic liquid crystals exhibiting columnar mesophases at room temperature, which are constructed by intermolecular hydrogen bonding between the core of 1,3,5-trihydroxybenzene or 1,3,5-cyclohexanetricarboxylic acid and the peripheral molecules of isoquinoline derivatives. The mesomorphic properties of supramolecular liquid crystals were investigated by differential scanning calorimetry, polarized optical microscopy, and X-ray diffraction studies. The self-assembled liquid crystals exhibited rectangular columnar phases (Colro) with an ordered stacking structure of the mesogens in a column at room temperature, regardless of the type of the core molecule, due probably to the close-packed aromatic rings around a core molecule and the angular structure in three arms of the discotic mesogen. These room temperature columnar phases are rare examples for the discotic liquid crystals, and our findings in the present study provide a new way to prepare low melting columnar liquid crystalline materials for molecular electronics.

  2. Metallotropic liquid crystals formed by surfactant templating of molten metal halides.

    PubMed

    Martin, James D; Keary, Cristin L; Thornton, Todd A; Novotnak, Mark P; Knutson, Jeremey W; Folmer, Jacob C W

    2006-04-01

    Liquid crystals consist of anisotropic molecular units, and most are organic molecules. Materials incorporating metals into anisotropic molecules, described as metallomesogens, have been prepared. Anisotropic structures such as one-dimensional chains and two-dimensional layers are frequently observed in solid-state inorganic materials, however, little is understood about structural organization in melts of such materials. Achieving liquid-crystalline behaviour in inorganic fluids should be possible if the anisotropic structure can be retained or designed into the molten phase. We demonstrated the ability to engineer zeolite-type structures into metal halide glasses and liquids. In this work we have engineered lamellar, cubic and hexagonal liquid-crystalline structure in metal-halide melts by controlling the volume fraction and nature of the inorganic block (up to 80 mol%) with respect to alkylammonium surfactants. The high metal content of these liquid-crystalline systems significantly advances the field of metallomesogens, which seeks to combine magnetic, electronic, optical, redox and catalytic properties common to inorganic materials with the fluid properties of liquid crystals. PMID:16547520

  3. Self-assembled molecular wires of discotic liquid crystal formed with the crucial contribution of solvents

    NASA Astrophysics Data System (ADS)

    Park, Ji Hyun; Kim, Kyung Ho; Sosa Vargas, Lydia; Takanishi, Yoichi; Kim, Youn Sang; Yamamoto, Jun; Shimizu, Yo; Park, Yung Woo; Lagerwall, Jan Pf; Scalia, Giusy

    The self-organization of discotic liquid crystal molecules allows the spontaneous formation of well-aligned and tens of micrometer long molecular wires. In this work, we present a study based on hexapentyloxytriphenylene (HAT5) to investigate the molecular wire formation mechanism induced by solvents with selected characteristics, including chemical structure, boiling point, vapor pressure, and surface tension. The aromaticity in solvents such as toluene and benzene promotes the assembly into very long and thin wires entering into the structures, while chain-like solvents promotes more disordered structures. This finding allows a guided formation of different nanostructures from the same type of molecules just by choosing the type of solvent according to the need. Raman spectroscopy supports the idea of an active role of aromatic solvents entering into the molecular structure between discotic molecules with good quality intermolecular order. Highly aligned molecular wires bridging electrodes on SiO2 substrate show a clearly higher electrical conductivity compared to disorganized aggregates and bare HAT5. DLS and X-ray scattering were also used to investigate films and solutions. We finally discuss possible mechanisms behind the hierarchical assembly of the nanowires. NRF.

  4. A new crystal form of beta-cyclodextrin-ethanol inclusion complex: channel-type structure without long guest molecules.

    PubMed

    Aree, Thammarat; Chaichit, Narongsak

    2003-07-22

    A new crystal form of beta-cyclodextrin (beta-CD)[bond]ethanol[bond]dodecahydrate inclusion complex [(C(6)H(10)O(5))(7).0.3C(2)H(5)OH.12H(2)O] belongs to monoclinic space group C2 (form II) with unit cell constants a=19.292(1), b=24.691(1), c=15.884(1) A, beta=109.35(1) degrees. The beta-CD macrocycle is more circular than that of the complex in space group P2(1) [form I: J. Am. Chem. Soc. 113 (1991) 5676]. In form II, a disordered ethanol molecule (occupancy 0.3) is placed in the upper part of beta-CD cavity (above the O-4 plane) and is sustained by hydrogen bonding to water site W-2. In form I, an ethanol molecule located below the O-4-plane is well ordered because it hydrogen bonds to surrounding O-3[bond]H, O-6[bond]H groups of the symmetry-related beta-CD molecules. In the crystal lattice of form I, beta-CD macrocycles are stacked in a typical herringbone cage structure. By contrast, the packing structure of form II is a head-to-head channel that is stabilized at both O-2/O-3 and O-6 sides of each beta-CD by direct O(CD)...O(CD) and indirect O(CD)...O(W)...(O(W))...O(CD) hydrogen bonds. The 12 water molecules are disordered in 18 positions both inside the channel-like cavity of beta-CD dimer (W-1[bond]W-6) and in the interstices between the beta-CD macrocycles (W-7[bond]W-18). The latter forms a cluster that is hydrogen bonded together and to the neighboring beta-CD O[bond]H groups. PMID:12860429

  5. Instability of a Biaxial Nematic Liquid Crystal Formed by Homeotropic Anchoring on Surface Grooves

    NASA Astrophysics Data System (ADS)

    Zhang, Zhi-Dong; Xuan, Li

    2011-10-01

    A method used to treat the elastic distortion of a uniaxial nematic liquid crystal induced by homogeneous anchoring on the surface grooves is generalized to biaxial nematic liquid crystals under the homeotropic anchoring condition. Employing some approximations for the elastic constants, we obtain an additional term in the elastic energy per unit area which depends on the angle between the minor director at infinity and the direction of the grooves, with a period of π/2. This leads to instability on the surface grooves so that two states with crossed minor directors are energetically indistinguishable. Our theoretical study explains why the homeotropic alignment method developed for uniaxial liquid crystals loses efficacy for biaxial nematics.

  6. Studying how protein crystals form

    NASA Technical Reports Server (NTRS)

    2000-01-01

    Watching molecules of the iron-storing protein apoferritin come together to form a nucleus reveals some interesting behavior. In this series of images, researchers observed clusters of four molecules at the corners of a diamond shape (top). As more molecules attach to the cluster, they arrange themselves into rods (second from top), and a raft-like configuration of molecules forms the critical nucleus (third from top), suggesting that crystal growth is much slower than it could be were the molecules arranged in a more compact formation. In the final image, a crystallite consisting of three layers containing approximately 60 to 70 molecules each is formed. Atomic force microscopy made visualizing the process of nucleation possible for the first time. The principal investigator is Peter Vekilov, of the University of Alabama in Huntsville. Vekilov's team at UAH studies protein solutions as they change phases from liquids to crystalline solids. They want to know if the molecules in the solution interact with one another, and if so, how, from the perspectives of thermodynamics and kinetics. They want to understand which forces -- electrical, electrostatic, hydrodynamic, or other kinds of forces -- are responsible for the interactions. They also study nucleation, the begirning stage of crystallization. This process is important to understand because it sets the stage for crystal growth in all kinds of solutions and liquid melts that are important in such diverse fields as agriculture, medicine, and the fabrication of metal components. Nucleation can determine the rate of crystal growth, the number of crystals that will be formed, and the quality and size of the crystals.

  7. Gypsum crystals formed on decomposing calcium citrate

    NASA Astrophysics Data System (ADS)

    Söhnel, O.; Křivánková, I.; Krčmář, S.; Jurčová, M.

    1991-06-01

    Particle size and the specific surface area of gypsum crystals formed on decomposing an aqueous suspension of solid calcium citrate tetrahydrate by diluted 50% sulphuric acid at 25, 40, 60, 80 and 100°C was studied. The size of the gypsum crystals increases with increasing temperature of decomposition. At a constant temperature within the range of 25 to 100°C the median of gypsum crystal size distribution (PSD) increases for approximately 4 h after commencing decomposition and then reaches a virtually constant value. The specific surface area of gypsum crystals decreases after commencement of the reaction for approximately 6 h before reaching a constant value. Gypsum crystal growth by solute deposition from the liquid is responsible for PSD changes for approximately one hour at the commencement of reaction. Then the growth of larger crystals at the expense of smaller crystals, i.e. ripening, is apparently responsible for further changes in the PSD.

  8. Four crystal forms of a Bence-Jones protein

    SciTech Connect

    Makino, Debora L.; Henschen-Edman, Agnes H.; McPherson, Alexander

    2005-01-01

    Four crystal forms have been grown and characterized by X-ray diffraction of a Bence-Jones protein collected from the urine of a multiple myeloma patient more than 40 y ago. The trigonal crystal form may shed some light on the formation of fibrils common to certain storage diseases. Four crystal forms have been grown and characterized by X-ray diffraction of a Bence-Jones protein collected from the urine of a multiple myeloma patient more than 40 years ago. Closely related tetragonal and orthorhombic forms belonging to space groups P4{sub 3}2{sub 1}2 and P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = b = 68.7, c = 182.1 and a = 67.7, b = 69.4, c = 87.3 Å, diffract to 1.5 and 1.9 Å, respectively. Two closely related trigonal forms, both belonging to space group P3{sub 1}21 with unit-cell parameters a = b = 154.3 Å but differing by a doubling of the c axis, one 46.9 Å and the other 94.0 Å, diffract to 2.9 and 2.6 Å resolution, respectively. The trigonal crystal of short c-axis length shows a positive indication of twinning. The trigonal crystal of longer c axis, which appeared only after eight months of incubation at room temperature, is likely to be composed of proteolytically degraded molecules and unlike the other crystal forms contains two entire Bence-Jones dimers in the asymmetric unit. This latter crystal form may shed some light on the formation of fibrils common to certain storage diseases.

  9. Single Molecule Studies on Dynamics in Liquid Crystals

    PubMed Central

    Täuber, Daniela; von Borczyskowski, Christian

    2013-01-01

    Single molecule (SM) methods are able to resolve structure related dynamics of guest molecules in liquid crystals (LC). Highly diluted small dye molecules on the one hand explore structure formation and LC dynamics, on the other hand they report about a distortion caused by the guest molecules. The anisotropic structure of LC materials is used to retrieve specific conformation related properties of larger guest molecules like conjugated polymers. This in particular sheds light on organization mechanisms within biological cells, where large molecules are found in nematic LC surroundings. This review gives a short overview related to the application of highly sensitive SM detection schemes in LC. PMID:24077123

  10. Insertion of liquid crystal molecules into hydrocarbon monolayers.

    PubMed

    Popov, Piotr; Lacks, Daniel J; Jákli, Antal; Mann, Elizabeth K

    2014-08-01

    Atomistic molecular dynamics simulations were carried out to investigate the molecular mechanisms of vertical surface alignment of liquid crystals. We study the insertion of nCB (4-Cyano-4'-n-biphenyl) molecules with n = 0,…,6 into a bent-core liquid crystal monolayer that was recently found to provide good vertical alignment for liquid crystals. The results suggest a complex-free energy landscape for the liquid crystal within the layer. The preferred insertion direction of the nCB molecules (core or tail first) varies with n, which can be explained by entropic considerations. The role of the dipole moments was found to be negligible. As vertical alignment is the leading form of present day liquid crystal displays (LCD), these results will help guide improvement of the LCD technology, as well as lend insight into the more general problem of insertion of biological and other molecules into lipid and surfactant layers. PMID:25106607

  11. Insertion of liquid crystal molecules into hydrocarbon monolayers

    SciTech Connect

    Popov, Piotr Mann, Elizabeth K.; Lacks, Daniel J.; Jákli, Antal

    2014-08-07

    Atomistic molecular dynamics simulations were carried out to investigate the molecular mechanisms of vertical surface alignment of liquid crystals. We study the insertion of nCB (4-Cyano-4{sup ′}-n-biphenyl) molecules with n = 0,…,6 into a bent-core liquid crystal monolayer that was recently found to provide good vertical alignment for liquid crystals. The results suggest a complex-free energy landscape for the liquid crystal within the layer. The preferred insertion direction of the nCB molecules (core or tail first) varies with n, which can be explained by entropic considerations. The role of the dipole moments was found to be negligible. As vertical alignment is the leading form of present day liquid crystal displays (LCD), these results will help guide improvement of the LCD technology, as well as lend insight into the more general problem of insertion of biological and other molecules into lipid and surfactant layers.

  12. Ribosome engineering to promote new crystal forms

    SciTech Connect

    Selmer, Maria; Gao, Yong-Gui; Weixlbaumer, Albert; Ramakrishnan, V.

    2012-05-01

    Truncation of ribosomal protein L9 in T. thermophilus allows the generation of new crystal forms and the crystallization of ribosome–GTPase complexes. Crystallographic studies of the ribosome have provided molecular details of protein synthesis. However, the crystallization of functional complexes of ribosomes with GTPase translation factors proved to be elusive for a decade after the first ribosome structures were determined. Analysis of the packing in different 70S ribosome crystal forms revealed that regardless of the species or space group, a contact between ribosomal protein L9 from the large subunit and 16S rRNA in the shoulder of a neighbouring small subunit in the crystal lattice competes with the binding of GTPase elongation factors to this region of 16S rRNA. To prevent the formation of this preferred crystal contact, a mutant strain of Thermus thermophilus, HB8-MRCMSAW1, in which the ribosomal protein L9 gene has been truncated was constructed by homologous recombination. Mutant 70S ribosomes were used to crystallize and solve the structure of the ribosome with EF-G, GDP and fusidic acid in a previously unobserved crystal form. Subsequent work has shown the usefulness of this strain for crystallization of the ribosome with other GTPase factors.

  13. The Dipole Polarizability of a Water Molecule in Liquid Water

    NASA Astrophysics Data System (ADS)

    Distasio, Robert; Maitra, Rahul

    The dipole polarizability, α, provides a measure of the tendency of a molecule or material to deform (or polarize) in the presence of an electric field. Within the framework of density functional theory (DFT), we present a hierarchy of first principles based approaches for computing α of a molecule located in the condensed phase. This hierarchy includes a successive treatment of both short-range (hybridization, Pauli exchange-repulsion, etc.) and long-range (Coulomb) electrodynamical response screening in the computation of α, while simultaneously accounting for the surrounding condensed-phase environment. Utilizing highly accurate liquid water configurations generated from van der Waals inclusive hybrid DFT based ab initio molecular dynamics, we computed α for a given water molecule in liquid water as a first application of this approach. Our findings will be compared and contrasted with α computed for an isolated gas-phase water molecule.

  14. A new crystal form of a hyperthermophilic endocellulase

    SciTech Connect

    Kataoka, Misumi; Ishikawa, Kazuhiko

    2014-06-18

    The hyperthermostable endocellulase from P. furiosus was crystallized at pH 5.5. The new crystal form has symmetry consistent with space group C2 and exhibits a structure different from that of the protein crystallized at pH 9.0. The hyperthermophilic glycoside hydrolase family endocellulase 12 from the archaeon Pyrococcus furiosus (EGPf; Gene ID PF0854; EC 3.2.1.4) catalyzes the hydrolytic cleavage of the β-1,4-glucosidic linkage in β-glucan in lignocellulose biomass. A crystal of EGPf was previously prepared at pH 9.0 and its structure was determined at an atomic resolution of 1.07 Å. This article reports the crystallization of EGPf at the more physiologically relevant pH of 5.5. Structure determination showed that this new crystal form has the symmetry of space group C2. Two molecules of the enzyme are observed in the asymmetric unit. Crystal packing is weak at pH 5.5 owing to two flexible interfaces between symmetry-related molecules. Comparison of the EGPf structures obtained at pH 9.0 and pH 5.5 reveals a significant conformational difference at the active centre and in the surface loops. The interfaces in the vicinity of the flexible surface loops impact the quality of the EGPf crystal.

  15. Attosecond dynamics of electrons in molecules and liquids

    NASA Astrophysics Data System (ADS)

    Woerner, Hans Jakob

    2016-05-01

    The ultrafast motion of electrons and holes following light-matter interaction is fundamental to a broad range of chemical and biophysical processes. In this lecture, I will discuss two recent experiments carried out in our group that measure the atomic-scale motion of charge with attosecond temporal resolution (1 as = 10-18 s). The first experiment is carried out on isolated, spatially oriented molecules in the gas phase. We advance high-harmonic spectroscopy to resolve spatially and temporally the migration of an electron hole immediately following ionization of iodoacetylene, while simultaneously demonstrating extensive control over the process. A multidimensional approach, based on the measurement of both even and odd harmonic orders, enables us to reconstruct both quantum amplitudes and phases of the electronic states with a resolution of ~ 100 as. We separately reconstruct quasi-field-free and laser-controlled charge migration as a function of the spatial orientation of the molecule and determine the shape of the hole created by ionization. The second experiment is carried out on a free-flowing microjet of liquid water. We use an attosecond pulse train synchronized with a near-infrared laser pulse to temporally resolve the process of photoemission from liquid water using the RABBIT technique. We measure a delay on the order of 50 as between electrons emitted from the HOMO of liquid water compared to that of gas-phase water and a substantially reduced modulation contrast of the corresponding sidebands. Since our measurements on solvated water molecules are referenced to isolated ones, the measured delays reflect (i) the photoionization delays caused by electron transport through the aqueous environment and (ii) the effect of solvation on the parent molecule. The relative modulation contrast, in turn, contains information on (iii) the modification of transition amplitudes and (iv) dephasing processes. These experiments make the liquid phase and its fascinating

  16. Single Molecule Electrochemical Detection in Aqueous Solutions and Ionic Liquids.

    PubMed

    Byers, Joshua C; Paulose Nadappuram, Binoy; Perry, David; McKelvey, Kim; Colburn, Alex W; Unwin, Patrick R

    2015-10-20

    Single molecule electrochemical detection (SMED) is an extremely challenging aspect of electroanalytical chemistry, requiring unconventional electrochemical cells and measurements. Here, SMED is reported using a "quad-probe" (four-channel probe) pipet cell, fabricated by depositing carbon pyrolytically into two diagonally opposite barrels of a laser-pulled quartz quadruple-barreled pipet and filling the open channels with electrolyte solution, and quasi-reference counter electrodes. A meniscus forms at the end of the probe covering the two working electrodes and is brought into contact with a substrate working electrode surface. In this way, a nanogap cell is produced whereby the two carbon electrodes in the pipet can be used to promote redox cycling of an individual molecule with the substrate. Anticorrelated currents generated at the substrate and tip electrodes, at particular distances (typically tens of nanometers), are consistent with the detection of single molecules. The low background noise realized in this droplet format opens up new opportunities in single molecule electrochemistry, including the use of ionic liquids, as well as aqueous solution, and the quantitative assessment and analysis of factors influencing redox cycling currents, due to a precisely known gap size. PMID:26398675

  17. Macroscopic chirality of a liquid crystal from nonchiral molecules

    NASA Astrophysics Data System (ADS)

    Jákli, A.; Nair, G. G.; Lee, C. K.; Sun, R.; Chien, L. C.

    2001-06-01

    The transfer of chirality from nonchiral polymer networks to the racemic B2 phase of nonchiral banana-shaped molecules is demonstrated. This corresponds to the transfer of chirality from an achiral material to another achiral material. There are two levels of chirality transfers. (a) On a microscopic level the presence of a polymer network (chiral or nonchiral) favors a chiral state over a thermodynamically stable racemic state due to the inversion symmetry breaking at the polymer-liquid crystal interfaces. (b) A macroscopically chiral (enantimerically enriched) sample can be produced if the polymer network has a helical structure, and/or contains chemically chiral groups. The chirality transfer can be locally suppressed by exposing the liquid crystal to a strong electric field treatment.

  18. Two dimensional NMR of liquids and oriented molecules

    SciTech Connect

    Gochin, M.

    1987-02-01

    Chapter 1 discusses the quantum mechanical formalism used for describing the interaction between magnetic dipoles that dictates the appearance of a spectrum. The NMR characteristics of liquids and liquid crystals are stressed. Chapter 2 reviews the theory of multiple quantum and two dimensional NMR. Properties of typical spectra and phase cycling procedures are discussed. Chapter 3 describes a specific application of heteronuclear double quantum coherence to the removal of inhomogeneous broadening in liquids. Pulse sequences have been devised which cancel out any contribution from this inhomogeneity to the final spectrum. An interpretation of various pulse sequences for the case of /sup 13/C and /sup 1/H is given, together with methods of spectral editing by removal or retention of the homo- or heteronuclear J coupling. The technique is applied to a demonstration of high resolution in both frequency and spatial dimensions with a surface coil. In Chapter 4, multiple quantum filtered 2-D spectroscopy is demonstrated as an effective means of studying randomly deuterated molecules dissolved in a nematic liquid crystal. Magnitudes of dipole coupling constants have been determined for benzene and hexane, and their signs and assignments found from high order multiple quantum spectra. For the first time, a realistic impression of the conformation of hexane can be estimated from these results. Chapter 5 is a technical description of the MDB DCHIB-DR11W parallel interface which has been set up to transfer data between the Data General Nova 820 minicomputer, interfaced to the 360 MHz spectrometer, and the Vax 11/730. It covers operation of the boards, physical specifications and installation, and programs for testing and running the interface.

  19. Long DNA Molecules at Liquid-Solid Interfaces

    NASA Astrophysics Data System (ADS)

    Samuilov, Vladimir; Li, B.; Sokolov, J.; Rafailovich, M.; Chu, B.

    2006-03-01

    The electrophoresis of long DNA molecules was studied using a newly developed method of electrophoresis on flat surfaces [1] in the regime of strong electrostatic interaction. The mobility of lambda- DNA molecules on this surface was found to scale as the square root of the persistent length with the ionic strength at high buffer. This experimental result indicates that at high buffer concentration the separation mechanism of solid-liquid interface electrophoresis is expected to be due to surface friction rather than biased reptation [2-4]. At low buffer concentrations the DNA chains are stretched .The electric double layer is responsible for a velocity profile of the electroosmotic flow. The net electrophoretic mobility of longer DNA, being trapped closer to the surface as found to be higher then for the shorter ones in the electric field. [1]. N. Pernodet, V. Samuilov, K. Shin, et al. Physical Review Letters, 85 (2000) 5651-5654. [2] Y.-S. Seo, V.A. Samuilov, J. Sokolov, et al. Electrophoresis, 23 (2002) 2618-2625. [3] Y.-S. Seo, H.. Luo, V. A. Samuilov, et al. DNA Electrophoresis on nanopatterned surfaces, Nano Letters, 4, 2004, 659-664.

  20. NMR studies of molecules in liquid crystals and graphite

    SciTech Connect

    Rosen, M.E.

    1992-06-01

    NMR experiments to measure proton dipole couplings were performed on a series of n-alkanes (n-hexane through n-decane) dissolved in nematic liquid crystals. Computer modeling of the experimental NMR-spectra was done using several different models for intermolecular interactions in these systems. The model of Photinos et al. was found to be best in describing the intermolecular interactions in these systems and can provide a statistical picture of the conformation and orientation of the alkane molecules in their partially-oriented environment. Order parameters and conformational distributions for the alkanes can be calculated from the modeling. The alkanes are found to have conformational distributions very much like those found in liquid alkanes. Proton NMR spectra of tetrahydrofuran (THF) intercalated in two graphite intercalation compounds were also measured. Computer simulations of these spectra provide a picture of THF in the constrained environment between the graphene layers where the THF is oriented at a particular angle, can translate and rotate freely, but does not appear to pseudorotate.

  1. Preliminary crystallographic studies of four crystal forms of serum albumin

    NASA Technical Reports Server (NTRS)

    Carter, D. C.; Chang, B.; Ho, J. X.; Keeling, K.; Krishnasami, Z.

    1994-01-01

    Several crystal forms of serum albumin suitable for three-dimensional structure determination have been grown. These forms include crystals of recombinant and wild-type human serum albumin, baboon serum albumin, and canine serum albumin. The intrinsic limits of X-ray diffraction for these crystals are in the range 0.28-0.22 nm. Two of the crystal forms produced from human and canine albumin include incorporated long-chain fatty acids. Molecular replacement experiments have been successfully conducted on each crystal form using the previously determined atomic coordinates of human serum albumin illustrating the conserved tertiary structure.

  2. Preliminary crystallographic studies of four crystal forms of serum albumin.

    PubMed

    Carter, D C; Chang, B; Ho, J X; Keeling, K; Krishnasami, Z

    1994-12-15

    Several crystal forms of serum albumin suitable for three-dimensional structure determination have been grown. These forms include crystals of recombinant and wild-type human serum albumin, baboon serum albumin, and canine serum albumin. The intrinsic limits of X-ray diffraction for these crystals are in the range 0.28-0.22 nm. Two of the crystal forms produced from human and canine albumin include incorporated long-chain fatty acids. Molecular replacement experiments have been successfully conducted on each crystal form using the previously determined atomic coordinates of human serum albumin illustrating the conserved tertiary structure. PMID:7813459

  3. Deterministically Polarized Fluorescence from Single Dye Molecules Aligned in Liquid Crystal Host

    SciTech Connect

    Lukishova, S.G.; Schmid, A.W.; Knox, R.; Freivald, P.; Boyd, R. W.; Stroud, Jr., C. R.; Marshall, K.L.

    2005-09-30

    We demonstrated for the first time to our konwledge deterministically polarized fluorescence from single dye molecules. Planar aligned nematic liquid crystal hosts provide deterministic alignment of single dye molecules in a preferred direction.

  4. Mirror Symmetry Breaking by Chirality Synchronisation in Liquids and Liquid Crystals of Achiral Molecules.

    PubMed

    Tschierske, Carsten; Ungar, Goran

    2016-01-01

    Spontaneous mirror symmetry breaking is an efficient way to obtain homogeneously chiral agents, pharmaceutical ingredients and materials. It is also in the focus of the discussion around the emergence of uniform chirality in biological systems. Tremendous progress has been made by symmetry breaking during crystallisation from supercooled melts or supersaturates solutions and by self-assembly on solid surfaces and in other highly ordered structures. However, recent observations of spontaneous mirror symmetry breaking in liquids and liquid crystals indicate that it is not limited to the well-ordered solid state. Herein, progress in the understanding of a new dynamic mode of symmetry breaking, based on chirality synchronisation of transiently chiral molecules in isotropic liquids and in bicontinuous cubic, columnar, smectic and nematic liquid crystalline phases is discussed. This process leads to spontaneous deracemisation in the liquid state under thermodynamic control, giving rise to long-term stable symmetry-broken fluids, even at high temperatures. These fluids form conglomerates that are capable of extraordinary strong chirality amplification, eventually leading to homochirality and providing a new view on the discussion of emergence of uniform chirality in prebiotic systems. PMID:26416335

  5. NMR STUDIES OF LIQUID CRYSTALS AND MOLECULES DISSOLVED IN LIQUID CRYSTAL SOLVENTS

    SciTech Connect

    Drobny, G.P.

    1982-11-01

    This thesis describes several studies in which nuclear magnetic resonance (nmr) spectroscopy has been used to probe the structure, orientation and dynamics of liquid crystal mesogens and molecules dissolved in liquid crystalline phases. In addition, a modern high field nmr spectrometer is described which has been used to perform such nmr studies. Chapter 1 introduces the quantum mechanical formalisms used throughout this thesis and briefly reviews the fundamentals of nuclear spin physics and pulsed nmr spectroscopy. First the density operator is described and a specific form for the canonical ensemble is derived. Then Clebsch-Gordon coefficients, Wigner rotation matrices, and irreducible tensor operators are reviewed. An expression for the equilibrium (Curie) magnetization is obtained and the linear response of a spin system to a strong pulsed r.f. irradiation is described. Finally, the spin interaction Hamiltonians relevant to this work are reviewed together with their truncated forms. Chapter 2 is a deuterium magnetic resonance study of two 'nom' liquid crystals which possess several low temperature mesomorphic phases. Specifically, deuterium quadrupolar echo spectroscopy is used to determine the orientation of the liquid crystal molecules in smectic phases, the changes in molecular orientation and motion that occur at smectic-smectic phase transitions, and the order of the phase transitions. For both compounds, the phase sequence is determined to be isotropic, nematic, smectic A, smectic C, smectic B{sub A}, smectic B{sub C}, and crystalline. The structure of the smectic A phase is found to be consistent with the well-known model of a two dimensional liquid in which molecules are rapidly rotating about their long axes and oriented at right angles to the plane of the layers. Molecules in the smectic C phase are found to have their long axes tilted with respect to the layer normal, and the tilt angle is temperature dependent, increasing from zero at the smectic A

  6. Detection of liquid hazardous molecules using linearly focused Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Cho, Soo Gyeong; Chung, Jin Hyuk

    2013-05-01

    In security, it is an important issue to analyze hazardous materials in sealed bottles. Particularly, prompt nondestructive checking of sealed liquid bottles in a very short time at the checkpoints of crowded malls, stadiums, or airports is of particular importance to prevent probable terrorist attack using liquid explosives. Aiming to design and fabricate a detector for liquid explosives, we have used linearly focused Raman spectroscopy to analyze liquid materials in transparent or semi-transparent bottles without opening their caps. Continuous lasers with 532 nm wavelength and 58 mW/130 mW beam energy have been used for the Raman spectroscopy. Various hazardous materials including flammable liquids and explosive materials have successfully been distinguished and identified within a couple of seconds. We believe that our technique will be one of suitable methods for fast screening of liquid materials in sealed bottles.

  7. Crystallization from microemulsions ? a novel method for the preparation of new crystal forms of aspartame

    NASA Astrophysics Data System (ADS)

    Füredi-Milhofer, Helga; Garti, N.; Kamyshny, A.

    1999-03-01

    Solubilization and crystallization of the artificial sweetener aspartame (APM), in water/isooctane microemulsions stabilized with sodium diisooctyl sulfosuccinate (AOT) has been investigated. The amount of aspartame that could be solubilized depended primarily on the amount of surfactant and on the temperature. The maximum AOT/aspartame molar ratio at the w/o interface is shown to be 6.2 at 25°C. It was concluded that the dipeptide is located at the w/o interface interspersed between surfactant molecules and that it acts as a cosurfactant. A new crystal form, APM III, was obtained by cooling of hot w/isooctane/AOT microemulsions containing solubilized aspartame. The new crystal form exhibits a distinct X-ray diffraction powder pattern, as well as changes in the FTIR spectra, thermogravimetric and DSC patterns. H-NMR spectra of APM III dissolved in D 2O were identical to the spectrum of commercial aspartame recorded under the same conditions. The new crystal form has greatly improved dissolution kinetics.

  8. Imposed Orientation of Dye Molecules by Liquid Crystals and an Electric Field.

    ERIC Educational Resources Information Center

    Sadlej-Sosnowska, Nina

    1980-01-01

    Describes experiments using dye solutions in liquid crystals in which polar molecules are oriented in an electrical field and devices are constructed to change their color in response to an electric signal. (CS)

  9. Isotropic rotation vs. shear relaxation in supercooled liquids with globular cage molecules.

    PubMed

    Kaseman, Derrick C; Gulbiten, Ozgur; Aitken, Bruce G; Sen, Sabyasachi

    2016-05-01

    The temperature dependence of the rotational dynamics of P4Se3 molecules in the glass-forming molecular liquid P5Se3 is studied using two-dimensional (31)P nuclear magnetic resonance spectroscopy. Unlike typical molecular glass-forming liquids, the constituent molecules in the P5Se3 liquid perform rapid isotropic rotation without significant translational diffusion in the supercooled regime and this rotational process shows a decoupling in time scale from shear relaxation by nearly six orders of magnitude at the glass transition. This dynamical behavior of liquid-like rotation and localized translation appears to be universal to glass-forming liquids with high-symmetry globular molecules that are characterized by an underlying thermodynamically stable plastic crystal phase. PMID:27155639

  10. Isotropic rotation vs. shear relaxation in supercooled liquids with globular cage molecules

    NASA Astrophysics Data System (ADS)

    Kaseman, Derrick C.; Gulbiten, Ozgur; Aitken, Bruce G.; Sen, Sabyasachi

    2016-05-01

    The temperature dependence of the rotational dynamics of P4Se3 molecules in the glass-forming molecular liquid P5Se3 is studied using two-dimensional 31P nuclear magnetic resonance spectroscopy. Unlike typical molecular glass-forming liquids, the constituent molecules in the P5Se3 liquid perform rapid isotropic rotation without significant translational diffusion in the supercooled regime and this rotational process shows a decoupling in time scale from shear relaxation by nearly six orders of magnitude at the glass transition. This dynamical behavior of liquid-like rotation and localized translation appears to be universal to glass-forming liquids with high-symmetry globular molecules that are characterized by an underlying thermodynamically stable plastic crystal phase.

  11. Three crystal forms of the bifunctional enzyme proline utilization A (PutA) from Bradyrhizobium japonicum.

    PubMed

    Schuermann, Jonathan P; White, Tommi A; Srivastava, Dhiraj; Karr, Dale B; Tanner, John J

    2008-10-01

    Proline utilization A proteins (PutAs) are large (1000-1300 residues) membrane-associated bifunctional flavoenzymes that catalyze the two-step oxidation of proline to glutamate by the sequential action of proline dehydrogenase and Delta(1)-pyrroline-5-carboxylate dehydrogenase domains. Here, the first successful crystallization efforts for a PutA protein are described. Three crystal forms of PutA from Bradyrhizobium japonicum are reported: apparent tetragonal, hexagonal and centered monoclinic. The apparent tetragonal and hexagonal crystals were grown in the presence of PEG 3350 and sodium formate near pH 7. The apparent tetragonal form diffracted to 2.7 A resolution and exhibited pseudo-merohedral twinning such that the true space group is P2(1)2(1)2(1) with four molecules in the asymmetric unit. The hexagonal form diffracted to 2.3 A resolution and belonged to space group P6(2)22 with one molecule in the asymmetric unit. Centered monoclinic crystals were grown in ammonium sulfate, diffracted to 2.3 A resolution and had two molecules in the asymmetric unit. Removing the histidine tag was important in order to obtain the C2 crystal form. PMID:18931443

  12. Three crystal forms of the bifunctional enzyme proline utilization A (PutA) from Bradyrhizobium japonicum

    PubMed Central

    Schuermann, Jonathan P.; White, Tommi A.; Srivastava, Dhiraj; Karr, Dale B.; Tanner, John J.

    2008-01-01

    Proline utilization A proteins (PutAs) are large (1000–1300 residues) membrane-associated bifunctional flavoenzymes that catalyze the two-step oxidation of proline to glutamate by the sequential action of proline dehydrogenase and Δ1-pyrroline-5-carboxylate dehydrogenase domains. Here, the first successful crystallization efforts for a PutA protein are described. Three crystal forms of PutA from Bradyrhizobium japonicum are reported: apparent tetragonal, hexagonal and centered monoclinic. The apparent tetragonal and hexagonal crystals were grown in the presence of PEG 3350 and sodium formate near pH 7. The apparent tetragonal form diffracted to 2.7 Å resolution and exhibited pseudo-merohedral twinning such that the true space group is P212121 with four molecules in the asymmetric unit. The hexagonal form diffracted to 2.3 Å resolution and belonged to space group P6222 with one molecule in the asymmetric unit. Centered monoclinic crystals were grown in ammonium sulfate, diffracted to 2.3 Å resolution and had two molecules in the asymmetric unit. Removing the histidine tag was important in order to obtain the C2 crystal form. PMID:18931443

  13. Measuring the internal energy content of molecules transported across the liquid-gas interface

    NASA Astrophysics Data System (ADS)

    Maselli, Olivia J.; Gascooke, Jason R.; Lawrance, Warren D.; Buntine, Mark A.

    2009-09-01

    Many details concerning the mechanism associated with the liberation of molecules from a liquid surface remain to be elucidated. We use the liquid microjet technique coupled with laser spectroscopy to measure the rotational and vibrational energy content of benzene spontaneously evaporating from a water-ethanol solution. These measurements provide molecular level insight into the mass and energy transfer processes associated with evaporation.

  14. Extended orientational correlation study for molecular liquids containing distorted tetrahedral molecules: application to methylene halides.

    PubMed

    Pothoczki, Szilvia; Temleitner, László; Pusztai, László

    2010-04-28

    The method of Rey [Rey, J. Chem. Phys. 126, 164506 (2007)] for describing how molecules orient toward each other in systems with perfect tetrahedral molecules is extended to the case of distorted tetrahedral molecules of c(2v) symmetry by means of introducing 28 subgroups. Additionally, the original analysis developed for perfect tetrahedral molecules, based on six groups, is adapted for molecules with imperfect tetrahedral shape. Deriving orientational correlation functions have been complemented with detailed analyses of dipole-dipole correlations. This way, (up to now) the most complete structure determination can be carried out for such molecular systems. In the present work, these calculations have been applied for particle configurations resulting from reverse Monte Carlo computer modeling. These particle arrangements are fully consistent with structure factors from neutron and x-ray diffraction measurements. Here we present a complex structural study for methylene halide (chloride, bromide, and iodide) molecular liquids, as possibly the best representative examples. It has been found that the most frequent orientations of molecules are of the 2:2 type over the entire distance range in these liquids. Focusing on the short range orientation, neighboring molecules turn toward each other with there "H,Y"-"H,Y" (Y: Cl, Br, I) edges, apart from CH(2)Cl(2) where the H,H-H,Cl arrangement is the most frequent. In general, the structure of methylene chloride appears to be different from the structure of the other two liquids. PMID:20441292

  15. Piezoelectric properties of polymers containing bent-shape liquid crystal molecules

    NASA Astrophysics Data System (ADS)

    Diorio, N.; Varga, M.; Carif, A.; Puskas, J. E.; Fodor-Csorba, K.; Sprunt, S.; Gleeson, J. T.; Jakli, A.

    2013-03-01

    Recently, bent-core liquid crystal elastomers have shown to exhibit large values of flexoelectricity as many as 3 orders of magnitude larger than liquid crystal elastomers containing rod-shaped molecules. These unusual high responses are attributed to have piezoelectric origin. Motivated by this, in this study, two bent-core liquid crystals were used to make various types of materials; low molecular weight bent-core nematic fluid, side chain bent-core liquid crystal polymer, low molecular liquid crystal dispersed in a polyisobutylene-based thermoplastic elastomer, and side-chain bent-core elastomers. Liquid crystal elastomers combine elasticity and flexibility inherent to rubbers and the optical and electrical properties of liquid crystals, and are promising materials for applications such as electro-optics, flexible electronics and actuator technologies for biomedical applications. Most conventional liquid crystal elastomers have rod-shaped liquid crystal molecules chemically attached to a crosslinked polymer network. Converse piezoelectric responses were measured by a Mirau interferometer and the direct piezoelectric signals were studied by home-made device where the stress is provided by an audio speaker. The results will be analyzed in terms of ferroelectric clusters of the materials in the nematic phase and will be compared with other piezoelectric materials. Supported by Grants NSF-DMR -0964765 and NSF-DMR -0804878.

  16. Redistribution of fluorescent molecules at the solid/liquid interface with total internal reflection illumination.

    PubMed

    Wei, Lin; Ye, Zhongju; Luo, Wenjuan; Chen, Bo; Xiao, Lehui

    2016-08-01

    Many intriguing physical and chemical processes commonly take place at the solid/liquid interface. Total internal reflection illumination, together with single molecule spectroscopy, provides a robust platform for the selective exploration of kinetic processes close the interface. With these techniques, it was observed that the distribution of Rhodamine B molecules close to a solid/liquid interface could be regulated in a photo-induced route. The laser-induced repulsion force at this interface is enough to compromise the Brownian diffusion of single molecules in a range of several hundred nanometers normal to the solid/liquid interface. This observation is fundamentally and practically interesting because moderate laser intensity is enough to initiate this repulsion effect. Therefore, it might display extensive applications in the development of photo-modulation technique with high throughput capability. PMID:27216678

  17. Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid-vapor interface

    NASA Astrophysics Data System (ADS)

    Nagayama, Gyoko; Takematsu, Masaki; Mizuguchi, Hirotaka; Tsuruta, Takaharu

    2015-07-01

    The structure and thermodynamic properties of the liquid-vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid-vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid-vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid-vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid-vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.

  18. The Analysis of the Human High Affinity IgE Receptor FceRIa from Multiple Crystal Forms

    SciTech Connect

    Garman, S.C.; Sechi, S.; Kinet, J.-P.; Jardetzky, T.S.

    2010-03-05

    We have solved the structure of the human high affinity IgE receptor, Fc{var_epsilon}RI{alpha}, in six different crystal forms, showing the structure in 15 different chemical environments. This database of structures shows no change in the overall shape of the molecule, as the angle between domains 1 and 2 (D1 and D2) varies little across the ensemble. However, the receptor has local conformational variability in the C' strand of D2 and in the BC loop of D1. In every crystal form, a residue inserts between tryptophan residues 87 and 110, mimicking the position of a proline from the IgE ligand. The different crystal forms reveal a distribution of carbohydrates lining the front and back surfaces of the structure. An analysis of crystal contacts in the different forms indicates regions where the molecule interacts with other proteins, and reveals a potential new binding site distal to the IgE binding site. The results of this study point to new directions for the design of molecules to inhibit the interaction of Fc{var_epsilon}RI{alpha} with its natural ligand and thus to prevent a primary step in the allergic response.

  19. Spontaneous Mirror-Symmetry Breaking in Isotropic Liquid Phases of Photoisomerizable Achiral Molecules.

    PubMed

    Alaasar, Mohamed; Prehm, Marko; Cao, Yu; Liu, Feng; Tschierske, Carsten

    2016-01-01

    Spontaneous mirror-symmetry breaking is of fundamental importance in science as it contributes to the development of chiral superstructures and new materials and has a major impact on the discussion around the emergence of uniform chirality in biological systems. Herein we report chirality synchronization, leading to spontaneous chiral conglomerate formation in isotropic liquids of achiral and photoisomerizable azobenzene-based rod-like molecules. The position of fluorine substituents at the aromatic core is found to have a significant effect on the stability and the temperature range of these chiral liquids. Moreover, these liquid conglomerates occur in a new phase sequence adjacent to a 3D tetragonal mesophase. PMID:26490058

  20. Hydrodynamics of Liquids of Chiral Molecules and Suspensions Containing Chiral Particles

    NASA Astrophysics Data System (ADS)

    Andreev, A. V.; Son, D. T.; Spivak, B.

    2010-05-01

    We obtain hydrodynamic equations describing a fluid consisting of chiral molecules or a suspension of chiral particles in a Newtonian fluid. The hydrodynamic velocity and stresses arising in a flowing chiral liquid have components that are forbidden by symmetry in a Newtonian liquid. For example, a chiral liquid in a Poiseuille flow between parallel plates exerts forces on the plates, which are perpendicular to the flow. A generic flow results in spatial separation of particles of different chirality. Thus even a racemic suspension will exhibit chiral properties in a generic flow. A suspension of particles of random shape in a Newtonian liquid is described by equations which are similar to those describing a racemic mixture of chiral particles in a liquid.

  1. Small Molecule-Assisted Exfoliation of Layered Zirconium Phosphate Nanoplatelets by Ionic Liquids.

    PubMed

    Xia, Fangqing; Yong, Huaisong; Han, Xiao; Sun, Dazhi

    2016-12-01

    Exfoliation of layered inorganic nanomaterials into single-layered sheets has been widely interested in materials chemistry and composite fabrication. Here, we report the exfoliation of layered zirconium phosphate nanoplatelets by using small molecule intercalating agents in ionic liquids, which opens a new platform for fabricating single-layered inorganic materials from synthetic layered compounds. PMID:27460596

  2. Dielectric relaxations of small carbohydrate molecules in the liquid and glassy states

    SciTech Connect

    Noel, T.R.; Ring, S.G.; Whittam, M.A.

    1992-06-25

    Dielectric relaxations of several vitreous and liquid monosaccharides were measured at 100 - 10{sup 5} Hz and -100 to 150 {degrees}C. Depending upon the molecule, one or two relaxations were observed. Primary alcohol moieties on the monosaccharide conferred higher activation energies than those without, such as xylitol and glucitol. 19 refs., 7 figs., 2 tabs.

  3. Small Molecule-Assisted Exfoliation of Layered Zirconium Phosphate Nanoplatelets by Ionic Liquids

    NASA Astrophysics Data System (ADS)

    Xia, Fangqing; Yong, Huaisong; Han, Xiao; Sun, Dazhi

    2016-07-01

    Exfoliation of layered inorganic nanomaterials into single-layered sheets has been widely interested in materials chemistry and composite fabrication. Here, we report the exfoliation of layered zirconium phosphate nanoplatelets by using small molecule intercalating agents in ionic liquids, which opens a new platform for fabricating single-layered inorganic materials from synthetic layered compounds.

  4. Zirconium fluoride glass - Surface crystals formed by reaction with water

    NASA Technical Reports Server (NTRS)

    Doremus, R. H.; Bansal, N. P.; Bradner, T.; Murphy, D.

    1984-01-01

    The hydrated surfaces of a zirconium barium fluoride glass, which has potential for application in optical fibers and other optical elements, were observed by scanning electron microscopy. Crystalline zirconium fluoride was identified by analysis of X-ray diffraction patterns of the surface crystals and found to be the main constituent of the surface material. It was also found that hydrated zirconium fluorides form only in highly acidic fluoride solutions. It is possible that the zirconium fluoride crystals form directly on the glass surface as a result of its depletion of other ions. The solubility of zirconium fluoride is suggested to be probably much lower than that of barium fluoride (0.16 g/100 cu cm at 18 C). Dissolution was determined to be the predominant process in the initial stages of the reaction of the glass with water. Penetration of water into the glass has little effect.

  5. Homeotropic orientation of a nematic liquid crystal by bent-core molecules adsorbed on its surface

    NASA Astrophysics Data System (ADS)

    Hwang, Jiyong; Yang, Seungbin; Lee, Hyojin; Kim, Jongyoon; Lee, Ji-Hoon; Kang, Shin-Woong; Choi, E.-Joon

    2015-06-01

    We reported the promotion of a homeotropic alignment of a nematic liquid crystal (NLC) by bent-core liquid-crystal (BLC) Molecules adsorbed its surface. The BLC was mixed at various concentrations with the NLC, and the mixtures were injected into an empty cell with a cell gap of 13 μm. Although the pure NLC showed a heterogeneous orientation, the BLC-NLC mixture was gradually transformed to a homeotropic alignment with increasing concentration of the BLC. We investigated the surface topography of the samples by using an atomic force microscopy (AFM) and found that the BLC molecules were segregated into a polyimide (PI) surface and formed protrusion domains with diameters of 50-100 nm. The BLC protrusions might promote the homeotropic orientation of the NLC molecules.

  6. Use of Rigid Liquid Crystalline Polypeptides as Alignment Matrices for Organic Nonlinear Optical Molecules.

    NASA Astrophysics Data System (ADS)

    Tokarski, Zbigniew

    The orientation of nonlinear optical (NLO) organic molecules is crucial for the existence of high values for the macroscopic susceptibilities. The orientation and interaction of several smaller NLO active molecules with an easily alignable polypeptide host was investigated to determine which functional groups and molecular shapes would produce the largest orientation with the host material; these parameters included aromatic vs aliphatic, polar vs nonpolar, saturate vs unsaturated hydrocarbons and the length of the guest molecule. The host materials were either poly ( gamma-benzyl-l-glutamate) (PBLG) or poly ( gamma-ethyl-l-glutamate) (PELG) lyotropic liquid crystals. These host polymers formed pseudo-hexagonal crystalline structures with long rigid alpha -helical backbones. The interstitial alignment of the guest molecules was dictated by the overall alignment of the host polypeptide rigid rods. Within these films many of the guest molecules existed in a metastable state that delayed phase separation for several hours. The rate of phase separation was influenced by the concentration of the guest molecule and on the side chain moiety of the polypeptide. Guest phase separation to a solid or a liquid occurred at a faster rate in PELG films, due to the lack of the side chain induced hindrance, than in PBLG films. An indicator of the occurrence of phase separation was with the onset of opaqueness in the films. The thin polypeptide films containing the aligned guest molecules became optically opaque as the incompatibilities between the side chains of the polypeptides and the guest molecules increased. The nonlinear optical susceptibility measurements were hampered by either the low guest solubility or the low concentration level required to avoid the guest -host incompatibility. Electro-optic and degenerate two and four wave mixing were done and produced signals in solutions but not in the doped films. The semiflexible aromatic guest molecules, such as the derivatives

  7. The inherent dynamics of a molecular liquid: Geodesic pathways through the potential energy landscape of a liquid of linear molecules

    NASA Astrophysics Data System (ADS)

    Jacobson, Daniel; Stratt, Richard M.

    2014-05-01

    Because the geodesic pathways that a liquid follows through its potential energy landscape govern its slow, diffusive motion, we suggest that these pathways are logical candidates for the title of a liquid's "inherent dynamics." Like their namesake "inherent structures," these objects are simply features of the system's potential energy surface and thus provide views of the system's structural evolution unobstructed by thermal kinetic energy. This paper shows how these geodesic pathways can be computed for a liquid of linear molecules, allowing us to see precisely how such molecular liquids mix rotational and translational degrees of freedom into their dynamics. The ratio of translational to rotational components of the geodesic path lengths, for example, is significantly larger than would be expected on equipartition grounds, with a value that scales with the molecular aspect ratio. These and other features of the geodesics are consistent with a picture in which molecular reorientation adiabatically follows translation—molecules largely thread their way through narrow channels available in the potential energy landscape.

  8. Experimental and Computational Characterization of Biological Liquid Crystals: A Review of Single-Molecule Bioassays

    PubMed Central

    Eom, Kilho; Yang, Jaemoon; Park, Jinsung; Yoon, Gwonchan; Soo Sohn, Young; Park, Shinsuk; Yoon, Dae Sung; Na, Sungsoo; Kwon, Taeyun

    2009-01-01

    Quantitative understanding of the mechanical behavior of biological liquid crystals such as proteins is essential for gaining insight into their biological functions, since some proteins perform notable mechanical functions. Recently, single-molecule experiments have allowed not only the quantitative characterization of the mechanical behavior of proteins such as protein unfolding mechanics, but also the exploration of the free energy landscape for protein folding. In this work, we have reviewed the current state-of-art in single-molecule bioassays that enable quantitative studies on protein unfolding mechanics and/or various molecular interactions. Specifically, single-molecule pulling experiments based on atomic force microscopy (AFM) have been overviewed. In addition, the computational simulations on single-molecule pulling experiments have been reviewed. We have also reviewed the AFM cantilever-based bioassay that provides insight into various molecular interactions. Our review highlights the AFM-based single-molecule bioassay for quantitative characterization of biological liquid crystals such as proteins. PMID:19865530

  9. Evidence for Triclinic Symmetry in Smectic Liquid Crystals of Bent-Shape Molecules

    SciTech Connect

    Jakli, A.; Kruerke, D.; Sawade, H.; Heppke, G.

    2001-06-18

    The first experimental evidence for triclinic symmetry of bulk smectic liquid-crystal samples of achiral banana-shaped molecules is presented. This phase corresponds to the so-called Sm-C{sub G} phase consisting of biaxial molecules and characterized by two tilt directions with respect to the layer normal: tilt of the molecular plane (clinic) and tilt of the molecular kink direction (leaning). Each smectic layer has a polarization component normal to the smectic layers (C{sub 1} symmetry). The observations suggest that the phase tentatively labeled as B{sub 7} is identical with the Sm-C{sub G} phase.

  10. Quantum Phase Transition Between a Luttinger Liquid and a Gas of Cold Molecules

    SciTech Connect

    Law, K. T.; Feldman, D. E.

    2008-08-29

    We consider cold polar molecules confined in a helical optical lattice similar to those used in holographic microfabrication. An external electric field polarizes molecules along the axis of the helix. The large-distance intermolecular dipolar interaction is attractive but the short-scale interaction is repulsive due to geometric constraints and thus prevents collapse. The interaction strength depends on the electric field. We show that a zero-temperature second-order liquid-gas transition occurs at a critical field. It can be observed under experimentally accessible conditions.

  11. Langmuir Fiilms of Anthracene Derivatives on Liquid Mercury I: Symmetric Molecules

    SciTech Connect

    Tamam,L.; Kraack, H.; Sloutskin, E.; Ocko, B.; Pershan, P.; Ofer, E.; Deutsch, M.

    2007-01-01

    The structure and phase sequence of liquid-mercury-supported Langmuir films (LFs) of two symmetric acenes, anthracene and anthraquinone, were studied by surface tensiometry and X-ray diffraction. At low coverage, both form a monolayer of surface-parallel, flat-lying, molecules. At high coverage, we find a monolayer of side-lying molecules, where the molecular plane is surface-normal, and the molecular long axis is surface-parallel. None of these phases exhibit long-range in-plane order.

  12. A new strategy of transforming pharmaceutical crystal forms.

    PubMed

    Tian, Jian; Dalgarno, Scott J; Atwood, Jerry L

    2011-02-01

    The robust nature of network materials allows them to (for example) respond to external stimuli such as pressure, temperature, light, or gas/solvent adsorption and desorption. There is difficulty in retaining long-range order in purely molecular organic solids, due to weak intermolecular interactions such as van der Waals forces. Here, we show gas-induced transformations of the well-known pharmaceuticals clarithromycin and lansoprazole. For clarithromycin, the stimulus is capable of converting the kinetic solvate and guest-free crystal forms to the commercial thermodynamically stable polymorph with a huge saving in energy cost relative to industrially employed methods. The synthesis of the marketing form of lansoprazole involves a solvate that readily decomposes and that is stirred in water, filtered, and dried intensively. Our method readily circumvents such synthetic problems and transforms the sensitive solvate to the marketed drug substance with ease. Such expedient transformations hold great implications for the pharmaceutical industry in general when considering the ease of transformation and mild conditions employed. PMID:21207977

  13. Projection structure of frog rhodopsin in two crystal forms.

    PubMed Central

    Schertler, G F; Hargrave, P A

    1995-01-01

    Rhodopsin is the G protein-coupled receptor that upon light activation triggers the visual transduction cascade. Rod cell outer segment disc membranes were isolated from dark-adapted frog retinas and were extracted with Tween detergents to obtain two-dimensional rhodopsin crystals for electron crystallography. When Tween 80 was used, tubular structures with a p2 lattice (a = 32 A, b = 83 A, gamma = 91 degrees) were formed. The use of a Tween 80/Tween 20 mixture favored the formation of larger p22(1)2(1) lattices (a = 40 A, b = 146 A, gamma = 90 degrees). Micrographs from frozen hydrated frog rhodopsin crystals were processed, and projection structures to 7-A resolution for the p22(1)2(1) form and to 6-A resolution for the p2 form were calculated. The maps of frog rhodopsin in both crystal forms are very similar to the 9-A map obtained previously for bovine rhodopsin and show that the arrangement of the helices is the same. In a tentative topographic model, helices 4, 6, and 7 are nearly perpendicular to the plane of the membrane. In the higher-resolution projection maps of frog rhodopsin, helix 5 looks more tilted than it appeared previously. The quality of the two frog rhodopsin crystals suggests that they would be suitable to obtain a three-dimensional structure in which all helices would be resolved. Images Fig. 1 Fig. 2 Fig. 6 PMID:8524807

  14. Distribution of binding energies of a water molecule in the water liquid-vapor interface

    SciTech Connect

    Chempath, Shaji; Pratt, Lawrence R

    2008-01-01

    Distributions of binding energies of a water molecule in the water liquid-vapor interface are obtained on the basis of molecular simulation with the SPC/E model of water. These binding energies together with the observed interfacial density profile are used to test a minimally conditioned Gaussian quasi-chemical statistical thermodynamic theory. Binding energy distributions for water molecules in that interfacial region clearly exhibit a composite structure. A minimally conditioned Gaussian quasi-chemical model that is accurate for the free energy of bulk liquid water breaks down for water molecules in the liquid-vapor interfacial region. This breakdown is associated with the fact that this minimally conditioned Gaussian model would be inaccurate for the statistical thermodynamics of a dilute gas. Aggressive conditioning greatly improves the performance of that Gaussian quasi-chemical model. The analogy between the Gaussian quasi-chemical model and dielectric models of hydration free energies suggests that naive dielectric models without the conditioning features of quasi-chemical theory will be unreliable for these interfacial problems. Multi-Gaussian models that address the composite nature of the binding energy distributions observed in the interfacial region might provide a mechanism for correcting dielectric models for practical applications.

  15. Conformational flexibility in the apolipoprotein E amino-terminal domain structure determined from three new crystal forms: implications for lipid binding.

    PubMed Central

    Segelke, B. W.; Forstner, M.; Knapp, M.; Trakhanov, S. D.; Parkin, S.; Newhouse, Y. M.; Bellamy, H. D.; Weisgraber, K. H.; Rupp, B.

    2000-01-01

    An amino-terminal fragment of human apolipoprotein E3 (residues 1-165) has been expressed and crystallized in three different crystal forms under similar crystallization conditions. One crystal form has nearly identical cell dimensions to the previously reported orthorhombic (P2(1)2(1)2(1)) crystal form of the amino-terminal 22 kDa fragment of apolipoprotein E (residues 1-191). A second orthorhombic crystal form (P2(1)2(1)2(1) with cell dimensions differing from the first form) and a trigonal (P3(1)21) crystal form were also characterized. The structures of the first orthorhombic and the trigonal form were determined by seleno-methionine multiwavelength anomalous dispersion, and the structure of the second orthorhombic form was determined by molecular replacement using the structure from the trigonal form as a search model. A combination of modern experimental and computational techniques provided high-quality electron-density maps, which revealed new features of the apolipoprotein E structure, including an unambiguously traced loop connecting helices 2 and 3 in the four-helix bundle and a number of multiconformation side chains. The three crystal forms contain a common intermolecular, antiparallel packing arrangement. The electrostatic complimentarity observed in this antiparallel packing resembles the interaction of apolipoprotein E with the monoclonal antibody 2E8 and the low density lipoprotein receptor. Superposition of the model structures from all three crystal forms reveals flexibility and pronounced kinks in helices near one end of the four-helix bundle. This mobility at one end of the molecule provides new insights into the structural changes in apolipoprotein E that occur with lipid association. PMID:10850798

  16. Cold crystallisation behaviour of water molecules in ionic liquids as a screening method to evaluate biocompatibility of the hydrated ionic liquids.

    PubMed

    Fujita, Kyoko; Nikawa, Yohsuke; Ohno, Hiroyuki

    2013-04-21

    Hydrated ionic liquids, exhibiting cold crystallisation behaviour of water molecules in a certain range of water contents, successfully dissolved cytochrome c maintaining the original spin state of heme. PMID:23486783

  17. Single-Photon Source for Quantum Information Based on Single Dye Molecule Fluorescence in Liquid Crystal Host

    SciTech Connect

    Lukishova, S.G.; Knox, R.P.; Freivald, P.; McNamara, A.; Boyd, R.W.; Stroud, Jr., C.R.; Schmid, A.W.; Marshall, K.L.

    2006-08-18

    This paper describes a new application for liquid crystals: quantum information technology. A deterministically polarized single-photon source that efficiently produces photons exhibiting antibunching is a pivotal hardware element in absolutely secure quantum communication. Planar-aligned nematic liquid crystal hosts deterministically align the single dye molecules which produce deterministically polarized single (antibunched) photons. In addition, 1-D photonic bandgap cholesteric liquid crystals will increase single-photon source efficiency. The experiments and challenges in the observation of deterministically polarized fluorescence from single dye molecules in planar-aligned glassy nematic-liquid-crystal oligomer as well as photon antibunching in glassy cholesteric oligomer are described for the first time.

  18. The importance of dynamic light scattering in obtaining multiple crystal forms of Trypanosoma brucei PGK.

    PubMed Central

    Bernstein, B. E.; Michels, P. A.; Kim, H.; Petra, P. H.; Hol, W. G.

    1998-01-01

    Phosphoglycerate kinase (PGK) catalyzes the phosphoryl transfer between 1,3 bis-phosphoglycerate and ADP to form 3-phosphoglycerate and ATP, undergoing significant conformational changes during catalysis. To more precisely document this reaction and the corresponding conformational changes, we have crystallized Trypanosoma brucei PGK in several crystal forms: (1) in the presence of 3-phosphoglycerate and MgADP, PGK crystallizes with four molecules in the asymmetric unit; (2) in the presence of the ATP analog, AMP-PNP, PGK crystallizes in a similar form; (3) in the presence of the bisubstrate analog, adenylyl 1,1,5,5-tetrafluoropentane-1,5-bisphosphonate, PGK crystals grow with one molecule in the asymmetric unit. Large scale expression and purification of T. brucei PGK from an E. coli overexpression system was required to obtain sufficient enzyme yields. Results from dynamic light scattering experiments allowed us to identify substrates and analogs which were amenable for crystallization. Ease of crystal growth and diffraction quality for a particular PGK-ligand complex is highly consistent with the apparent monodispersity of the complex in solution as judged by dynamic light scattering. The three-dimensional structures of the various enzyme-ligand complexes are currently being exploited to obtain a better understanding of PGK catalysis, as well as for structure based design of enzyme inhibitors to be used in the development of anti-trypanosomal agents. PMID:9521128

  19. Viscosity of liquid mixtures: The Vesovic-Wakeham method for chain molecules

    NASA Astrophysics Data System (ADS)

    de Wijn, Astrid S.; Riesco, Nicolas; Jackson, George; Martin Trusler, J. P.; Vesovic, Velisa

    2012-02-01

    New expressions for the viscosity of liquid mixtures, consisting of chain-like molecules, are derived by means of Enskog-type analysis. The molecules of the fluid are modelled as chains of equally sized, tangentially joined, and rigid spheres. It is assumed that the collision dynamics in such a fluid can be approximated by instantaneous collisions. We determine the molecular size parameters from the viscosity of each pure species and show how the different effective parameters can be evaluated by extending the Vesovic-Wakeham (VW) method. We propose and implement a number of thermodynamically consistent mixing rules, taking advantage of SAFT-type analysis, in order to develop the VW method for chain molecules. The predictions of the VW-chain model have been compared in the first instance with experimental viscosity data for octane-dodecane and methane-decane mixtures, thus, illustrating that the resulting VW-chain model is capable of accurately representing the viscosity of real liquid mixtures.

  20. Viscosity of liquid mixtures: the Vesovic-Wakeham method for chain molecules.

    PubMed

    de Wijn, Astrid S; Riesco, Nicolas; Jackson, George; Trusler, J P Martin; Vesovic, Velisa

    2012-02-21

    New expressions for the viscosity of liquid mixtures, consisting of chain-like molecules, are derived by means of Enskog-type analysis. The molecules of the fluid are modelled as chains of equally sized, tangentially joined, and rigid spheres. It is assumed that the collision dynamics in such a fluid can be approximated by instantaneous collisions. We determine the molecular size parameters from the viscosity of each pure species and show how the different effective parameters can be evaluated by extending the Vesovic-Wakeham (VW) method. We propose and implement a number of thermodynamically consistent mixing rules, taking advantage of SAFT-type analysis, in order to develop the VW method for chain molecules. The predictions of the VW-chain model have been compared in the first instance with experimental viscosity data for octane-dodecane and methane-decane mixtures, thus, illustrating that the resulting VW-chain model is capable of accurately representing the viscosity of real liquid mixtures. PMID:22360255

  1. REVIEWS OF TOPICAL PROBLEMS: Supermolecular liquid-crystalline structures in solutions of amphiphilic molecules

    NASA Astrophysics Data System (ADS)

    Vedenov, A. A.; Levchenko, E. B.

    1983-09-01

    This paper reviews the physical properties of liquid-crystalline phases arising in solutions containing molecules of amphiphilic substances. The basic characteristics of micelle formation in dilute solutions, models of sphere-disk or sphere-cylinder structural transformations, as well as phase transitions related to the appearance of lyotropic mesophases in the system, including nematic, lamellar, hexagonal, and others, are examined. The results of experimental and theoretical investigation of "solvation" forces acting between micelles in the solvent, as well as recently studied models of swelling of lamellar phases are presented. The phenomena occurring near the inversion point of microemulsions in amphiphile-oil-water systems are examined briefly. The role of liquid-crystalline ordering in some biological systems is discussed.

  2. Anchoring transitions of transversely polar liquid-crystal molecules on perfluoropolymer surfaces.

    PubMed

    Dhara, Surajit; Kim, Jin Ki; Jeong, Soon Moon; Kogo, Reiri; Araoka, Fumito; Ishikawa, Ken; Takezoe, Hideo

    2009-06-01

    We report a strong discontinuous orientational transition (anchoring transition) of liquid-crystal molecules with a large transverse dipole moment. A perfluoropolymer was used as an alignment layer and the transition was observed from planar to homeotropic with decreasing temperature in the nematic phase. Conversely a gradual variation in tilt angle from homeotropic to conical was observed in a liquid crystal with a comparatively smaller transverse dipole moment on the same alignment layer. The experimental results clearly demonstrate the competition between a short-range dipolar force and long-range van der Waals force at the interfacial region. Using discontinuous anchoring transition in the sample, we demonstrate a possible bistable device for memory and light-driven display. PMID:19658464

  3. Lyotropic liquid crystal engineering-ordered nanostructured small molecule amphiphile self-assembly materials by design.

    PubMed

    Fong, Celesta; Le, Tu; Drummond, Calum J

    2012-02-01

    Future nanoscale soft matter design will be guided to a large extent by the teachings of amphiphile (lipid or surfactant) self-assembly. Ordered nanostructured lyotropic liquid crystalline mesophases may form in select mixtures of amphiphile and solvent. To reproducibly engineer the low energy amphiphile self-assembly of materials for the future, we must first learn the design principles. In this critical review we discuss the evolution of these design rules and in particular discuss recent key findings regarding (i) what drives amphiphile self-assembly, (ii) what governs the self-assembly structures that are formed, and (iii) how can amphiphile self-assembly materials be used to enhance product formulations, including drug delivery vehicles, medical imaging contrast agents, and integral membrane protein crystallisation media. We focus upon the generation of 'dilutable' lyotropic liquid crystal phases with two- and three-dimensional geometries from amphiphilic small molecules (225 references). PMID:21975366

  4. Transient self-interaction of light in a liquid-crystal polymer film containing azodye molecules

    SciTech Connect

    Simonov, A N

    1999-07-31

    Transient self-interaction of low-power He - Ne laser radiation (1 < 50 mW cm{sup -2} ) in a liquid-crystal polymer film containing chemically bound azodye molecules was observed experimentally. The self-interaction occurred in the region of a temperature-induced phase transition in the polymer film and was accompanied by the formation of quasi-periodic ring-shaped structures in the distribution of the transmitted light intensity. (this issue is dedicated to the memory of s a akhmanov)

  5. Ultralong Ordered Nanowires from the Concerted Self-Assembly of Discotic Liquid Crystal and Solvent Molecules.

    PubMed

    Park, Ji Hyun; Kim, Kyung Ho; Park, Yung Woo; Lagerwall, Jan P F; Scalia, Giusy

    2015-09-01

    The realization of long, aligned molecular wires is a great challenge, and a variety of approaches have been proposed. Interestingly, hexapentyloxytriphenylene (HAT5) discotic liquid crystal molecules, a model system of molecules with flat and aromatic cores, can spontaneously form well-aligned, micrometer long, yet only tens of nanometers thick, nanowires on solid surfaces. We have investigated the formation mechanism of these wires using different solvents with selected characteristics, including chemical structure, boiling point, vapor pressure, and surface tension. When casting from toluene and benzene solutions, atomic force microscopy reveals that the discotics spontaneously form very long and thin wires, self-aligning along a common orientation. If instead dodecane or heptane are used, different and in general thicker structures are obtained. The chemical structure of the solvent appears to have a key role, coupling to the liquid crystal self-assembly by allowing solvent molecules to enter the ordered structure if their design matches the core of HAT5 molecules, thereby guiding the assembly. However, other aspects are also relevant in the assembly, including the nature of the substrate and the rate of solvent evaporation, and these can favor or interfere with the self-assembly into long structures. The use of solvents with aromatic structure is advantageous not only because it affects the geometry of the assembly, promoting long wire formation, but it is also compatible with good quality of the intermolecular order, as suggested by a high anisotropy of the Raman spectra of the nanowires formed from these solvents. Finally, the electrical properties of ordered systems show a clearly higher electrical conductivity compared to the disorganized aggregates. PMID:26079283

  6. A new crystal form of human diamine oxidase.

    PubMed

    McGrath, Aaron P; Hilmer, Kimberly M; Collyer, Charles A; Dooley, David M; Guss, J Mitchell

    2010-02-01

    Copper amine oxidases (CAOs) are ubiquitous in nature and catalyse the oxidative deamination of primary amines to the corresponding aldehydes. Humans have three viable CAO genes (AOC1-3). AOC1 encodes human diamine oxidase (hDAO), which is the frontline enzyme for histamine metabolism. hDAO is unique among CAOs in that it has a distinct substrate preference for diamines. The structure of hDAO in space group P2(1)2(1)2(1) with two molecules in the asymmetric unit has recently been reported. Here, the structure of hDAO refined to 2.1 A resolution in space group C222(1) with one molecule in the asymmetric unit is reported. PMID:20124708

  7. a System which Uses a Continuous Optimization Approach for the Design of AN Optimum Extractant Molecule for Use in Liquid-Liquid Extraction.

    NASA Astrophysics Data System (ADS)

    Naser, Samer Fahim

    The design of an extractant molecule for use in liquid-liquid extraction, traditionally a combinatorial optimization problem, has been solved using continuous optimization. UNIFAC, a thermodynamic group contribution method which allows the calculation of an activity coefficient of a component from its chemical structure, was used as the basis for all calculations. A computer system was developed which employs a three step procedure. First, the error in the liquid-liquid equilibrium relations resulting from the specification of a target separation criteria is minimized by continuously varying the functional groups in the design group pool. Second, the theoretical molecule obtained from the first step is used as a starting point to optimize up to seven separation criteria by variation of functional groups and mole fractions to obtain the optimum theoretical extractant molecule which satisfies the equilibrium relations. Third, the theoretical molecule is used to generate alternative extractant molecules which contain integer functional group values only. Numeric molecular structure constraints were developed which help maintain the feasibility of molecules in the first two steps, and allow the rejection of infeasible molecules in the third step. These constraints include limits on boiling point and molecular weight. The system developed was successfully tested on several separation problems and has suggested extractants as good or better than ones currently in use. This is the first reported use of continuous optimization in molecular design. For large design pools, this approach, as opposed to combinatorial optimization, is several orders of magnitude faster.

  8. Effect of confinement on ionic liquid molecules in porous polymeric network

    NASA Astrophysics Data System (ADS)

    Raut, Prasad; Yuan, Shichen; Miyoshi, Toshikazu, , Dr.; Jana, Sadhan, , Dr.

    Ionic liquids (ILs) have attractive physicochemical properties but their room temperature liquid state necessitates pairing of IL with other solid, porous materials for fabrication of devices. Such materials are called ionogels. Loading of bulky IL molecules in the pores can dramatically affect the physical properties as function of the pore surface chemistry, pore size, and IL polarity. In this study porous syndiotactic polystyrene (sPS) network was made via thermos-reversible gelation. 1-Butyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide (PYR14TFSI) is incorporated into the pores of sPS. DSC study and the temperature dependence of 13C-CPMAS NMR show that on confinement; the melting point of PYR14TFSI contained in the ionogel increased in comparison to the bulk PYR14TFSI. At room temperature, WAXD study of the ionogels showed diffraction pattern for PYR14TFSI in nanopores, correspondingly 1H NOESY experiments show strong non-bonded cation-cation correlation in ionogels. The results for the bulk IL does not show non-bonded correlation at room temperature, this increment of local order in ionogel might be the results of crystallization of IL molecules in confined geometry.

  9. Room temperature ionic liquids interacting with bio-molecules: an overview of experimental and computational studies

    NASA Astrophysics Data System (ADS)

    Benedetto, Antonio; Ballone, Pietro

    2016-03-01

    We briefly review experimental and computational studies of room temperature ionic liquids (RTILs) interacting with important classes of biomolecules, including phospholipids, peptides and proteins, nucleic acids and carbohydrates. Most of these studies have been driven by the interest for RTILs applications as solvents. Thus, available experimental data cover primarily thermodynamic properties such as the reciprocal solubility of RTILs and bio-molecules, as well as phase boundaries. Less extensive data are also available on transport properties such as diffusion and viscosity of homogeneous binary (RTILs/biomolecules) and ternary (RTIL/biomolecules/water) solutions. Most of the structural information at the atomistic level, of interest especially for biochemical, pharmaceutical and nanotechnology applications, has been made available by molecular dynamics simulations. Major exceptions to this statement are represented by the results from NMR and circular dichroism spectroscopy, by selected neutron and X-ray scattering data, and by recent neutron reflectometry measurements on lipid bilayers on surfaces, hydrated by water-RTIL solutions. A final section of our paper summarizes new developments in the field of RTILs based on amino acids, that combine in themselves the two main aspects of our discussion, i.e. ionic liquids and bio-molecules.

  10. Crystallization and preliminary characterization of three different crystal forms of human saposin C heterologously expressed in Pichia pastoris

    SciTech Connect

    Schultz-Heienbrok, Robert; Rossocha, Maksim; Saenger, Wolfram

    2006-02-01

    Three different crystal forms were obtained of human saposin C. The structures could not be determined by molecular replacement using known solution structures of the protein as search models, supporting the notion of a highly flexible protein. The amphiphilic saposin proteins (A, B, C and D) act at the lipid–water interface in lysosomes, mediating the hydrolysis of membrane building blocks by water-soluble exohydrolases. Human saposin C activates glucocerebrosidase and β-galactosylceramidase. The protein has been expressed in Pichia pastoris, purified and crystallized in three different crystal forms, diffracting to a maximum resolution of 2.5 Å. Hexagonal crystals grew from 2-propanol-containing solution and contain a single molecule in the asymmetric unit according to the Matthews coefficient. Orthorhombic and tetragonal crystals were both obtained with pentaerythritol ethoxylate and are predicted to contain two molecules in the asymmetric unit. Attempts to determine the respective crystal structures by molecular replacement using either the known NMR structure of human saposin C or a related crystal structure as search models have so far failed. The failure of the molecular-replacement method is attributed to conformational changes of the protein, which are known to be required for its biological activity. Crystal structures of human saposin C therefore might be the key to mapping out the conformational trajectory of saposin-like proteins.

  11. Multiple crystal forms of N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus.

    PubMed

    Nakamura, Tsutomu; Niiyama, Mayumi; Hashimoto, Wakana; Ida, Kurumi; Abe, Manabu; Morita, Junji; Uegaki, Koichi

    2015-06-01

    Native N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus (Pf-Dac) and its selenomethionine derivative (Se-Pf-Dac) were crystallized and analyzed in the presence and absence of cadmium ion. The four crystal structures fell into three different crystal-packing groups, with the cadmium-free Pf-Dac and Se-Pf-Dac belonging to the same space group, with homologous unit-cell parameters. The crystal structures in the presence of cadmium contained distorted octahedral cadmium complexes coordinated by three chlorides, two O atoms and an S or Se atom from the N-terminal methionine or selenomethionine, respectively. The N-terminal cadmium complex was involved in crystal contacts between symmetry-related molecules through hydrogen bonding to the N-termini. While all six N-termini of Se-Pf-Dac were involved in cadmium-complex formation, only two of the Pf-Dac N-termini participated in complex formation in the Cd-containing crystal, resulting in different crystal forms. These differences are discussed in light of the higher stability of the Cd-Se bond than the Cd-S bond. This work provides an example of the contribution of cadmium towards determining protein crystal quality and packing depending on the use of the native protein or the selenomethionine derivative. PMID:26057790

  12. Conformations of banana-shaped molecules studied by 2H NMR spectroscopy in liquid crystalline solvents.

    PubMed

    Calucci, Lucia; Forte, Claudia; Csorba, Katalin Fodor; Mennucci, Benedetta; Pizzanelli, Silvia

    2007-01-11

    ClPbis11BB and Pbis11BB, two banana-shaped mesogens differing by a chlorine substituent on the central phenyl ring, show a nematic and a B2 phase, respectively. To obtain information on the structural features responsible for their different mesomorphic behavior, a study of the preferred conformations of these mesogens has been performed by NMR spectroscopy in two nematic media (Phase IV and ZLI1167), which should mimic the environment of the molecules in their own mesophases, avoiding problems of sample alignment by a magnetic field. To this aim, 2H NMR experiments have been performed on selectively deuterated isotopomers of ClPbis11BB and Pbis11BB and of two parent molecules, ClPbisB and PbisB, assumed as models in previous theoretical and experimental conformational studies. We found that only a limited number of conformations is compatible with experimental data, often very different from those inferred from theoretical calculations in vacuo, indicating a strong influence of the liquid crystalline environment on molecular conformation. No significant differences between chlorinated and non-chlorinated molecules were found, this suggesting that chlorine does not change the molecular conformational equilibrium, as previously proposed. PMID:17201428

  13. Solid-state stability studies of crystal form of tebipenem.

    PubMed

    Talaczyńska, Alicja; Lewandowska, Kornelia; Garbacki, Piotr; Zalewski, Przemysław; Skibiński, Robert; Miklaszewski, Andrzej; Mizera, Mikołaj; Cielecka-Piontek, Judyta

    2016-01-01

    The aim of this study was to determine the kinetic and thermodynamic parameters of tebipenem degradation in the solid state. The process was analyzed based on the results obtained by a high performance liquid chromatography (HPLC) method using ultraviolet diode-array detector (DAD)/electrospray ionization tandem mass spectrometry (Q-TOF-MS/MS), Fourier transform infrared spectroscopy (FT-IR) and Raman spectroscopic (RS) studies. In dry air, the degradation of tebipenem was a first-order reaction depending on the substrate concentration while at an increased relative air humidity tebipenem was degraded according to the kinetic model of autocatalysis. The thermodynamic parameters: energy of activation (Ea), enthalpy (ΔH(≠a)) and entropy (ΔS(≠a)) of tebipenem degradation were calculated. Following a spectroscopic analysis of degraded samples of tebipenem, a cleavage of the β-lactam bond was proposed as the main degradation pathway, next confirmation using HPLC-Q-TOF-MS/MS method. PMID:26043654

  14. Ultrafast molecular dynamics of liquid aromatic molecules and the mixtures with CCl4

    NASA Astrophysics Data System (ADS)

    Shirota, Hideaki

    2005-01-01

    The ultrafast molecular dynamics of liquid aromatic molecules, benzene, toluene, ethylbenzene, cumene, and 1,3-diphenylpropane, and the mixtures with CCl4 have been investigated by means of femtosecond optical heterodyne-detected Raman-induced Kerr effect spectroscopy. The picosecond Kerr transients of benzene, toluene, ethylbenzene, and cumene and the mixtures with CCl4 show a biexponential feature. 1,3-Diphenylpropane and the mixtures with CCl4 show triexponential picosecond Kerr transients. The slow relaxation time constants of the aromatic molecules and the mixtures with CCl4 are qualitatively described by the Stoke-Einstein-Debye hydrodynamic model. The ultrafast dynamics have been discussed based on the Kerr spectra in the frequency range of 0-800 cm-1 obtained by the Fourier transform analysis of the Kerr transients. The line shapes of the low-frequency intermolecular spectra located at 0-180 cm-1 frequency range have been analyzed by two Brownian oscillators (˜11 cm-1 and ˜45 cm-1 peaks) and an antisymmetric Gaussian function (˜65 cm-1 peak). The spectrum shape of 1,3-diphenylpropane is quite different from the spectrum shapes of the other aromatic molecules for the low magnitude of the low-frequency mode of 1,3-diphenylpropane and/or an intramolecular vibration. Although the concentration dependences of the low- and intermediate-frequency intermolecular modes (Brownian oscillators) do not show a significant trend, the width of high-frequency intermolecular mode (antisymmetric Gaussian) becomes narrower with the higher CCl4 concentration for all the aromatics mixtures with CCl4. The result indicates that the inhomogeneity of the intermolecular vibrational mode in aromatics/CCl4 mixtures is decreasing with the lower concentration of aromatics. The intramolecular vibrational modes of the aromatic molecules observed in the Kerr spectra are also shown with the calculation results based on the density functional theory.

  15. Extensive database of liquid phase diffusion coefficients of some frequently used test molecules in reversed-phase liquid chromatography and hydrophilic interaction liquid chromatography.

    PubMed

    Song, Huiying; Vanderheyden, Yoachim; Adams, Erwin; Desmet, Gert; Cabooter, Deirdre

    2016-07-15

    Diffusion plays an important role in all aspects of band broadening in chromatography. An accurate knowledge of molecular diffusion coefficients in different mobile phases is therefore crucial in fundamental column performance studies. Correlations available in literature, such as the Wilke-Chang equation, can provide good approximations of molecular diffusion under reversed-phase conditions. However, these correlations have been demonstrated to be less accurate for mobile phases containing a large percentage of acetonitrile, as is the case in hydrophilic interaction liquid chromatography. A database of experimentally measured molecular diffusion coefficients of some 45 polar and apolar compounds that are frequently used as test molecules under hydrophilic interaction liquid chromatography and reversed-phase conditions is therefore presented. Special attention is given to diffusion coefficients of polar compounds obtained in large percentages of acetonitrile (>90%). The effect of the buffer concentration (5-10mM ammonium acetate) on the obtained diffusion coefficients is investigated and is demonstrated to mainly influence the molecular diffusion of charged molecules. Diffusion coefficients are measured using the Taylor-Aris method and hence deduced from the peak broadening of a solute when flowing through a long open tube. The validity of the set-up employed for the measurement of the diffusion coefficients is demonstrated by ruling out the occurrence of longitudinal diffusion, secondary flow interactions and extra-column effects, while it is also shown that radial equilibration in the 15m long capillary is effective. PMID:27240944

  16. Ideal probe single-molecule experiments reveal the intrinsic dynamic heterogeneity of a supercooled liquid

    PubMed Central

    Paeng, Keewook; Park, Heungman; Hoang, Dat Tien; Kaufman, Laura J.

    2015-01-01

    The concept of dynamic heterogeneity and the picture of the supercooled liquid as a mosaic of environments with distinct dynamics that interchange in time have been invoked to explain the nonexponential relaxations measured in these systems. The spatial extent and temporal persistence of these regions of distinct dynamics have remained challenging to identify. Here, single-molecule fluorescence measurements using a probe similar in size and mobility to the host o-terphenyl unambiguously reveal exponential relaxations distributed in time and space and directly demonstrate ergodicity of the system down to the glass transition temperature. In the temperature range probed, at least 200 times the structural relaxation time of the host is required to recover ensemble-averaged relaxation at every spatial region in the system. PMID:25825739

  17. Crystallization and preliminary analysis of active nitroalkane oxidase in three crystal forms.

    PubMed

    Nagpal, Akanksha; Valley, Michael P; Fitzpatrick, Paul F; Orville, Allen M

    2004-08-01

    Nitroalkane oxidase (NAO), a flavoprotein cloned and purified from Fusarium oxysporum, catalyzes the oxidation of neutral nitroalkanes to the corresponding aldehydes or ketones, with the production of H2O2 and nitrite. In this paper, the crystallization and preliminary X-ray data analysis of three crystal forms of active nitroalkane oxidase are described. The first crystal form belongs to a trigonal space group (either P3(1)21 or P3(2)21, with unit-cell parameters a = b = 103.8, c = 487.0 A) and diffracts to at least 1.6 A resolution. Several data sets were collected using 2theta and kappa geometry in order to obtain a complete data set to 2.07 A resolution. Solvent-content and Matthews coefficient analysis suggests that crystal form 1 contains two homotetramers per asymmetric unit. Crystal form 2 (P2(1)2(1)2(1); a = 147.3, b = 153.5, c = 169.5 A) and crystal form 3 (P3(1) or P3(2); a = b = 108.9, c = 342.5 A) are obtained from slightly different conditions and also contain two homotetramers per asymmetric unit, but have different solvent contents. A three-wavelength MAD data set was collected from selenomethionine-enriched NAO (SeMet-NAO) in crystal form 3 and will be used for phasing. PMID:15272176

  18. Single molecule spectroscopy of conjugated polymer chains in an electric field-aligned liquid crystal.

    PubMed

    Chang, Wei-Shun; Link, Stephan; Yethiraj, Arun; Barbara, Paul F

    2008-01-17

    Using single molecule polarization spectroscopy, we investigated the alignment of a polymer solute with respect to the liquid crystal (LC) director in an LC device while applying an external electric field. The polymer solute is poly[2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] (or MEH-PPV), and the LC solvent is 5CB. The electric field induces a change in the LC director orientation from a planar alignment (no electric field) to a perpendicular (homeotropic) alignment with an applied field of 5.5 x 103 V/cm. We find that the polymer chains align with the LC director in both planar and homeotropic alignment when measured in the bulk of the LC solution away from the device interface. Single molecule polarization distributions measured as a function of distance from the LC device interface reveal a continuous change of the MEH-PPV alignment from planar to homeotropic. The observed polarization distributions are modeled using a conventional elastic model that predicts the depth profile of the LC director orientation for the applied electric field. The excellent agreement between experiment and simulations shows that the alignment of MEH-PPV follows the LC director throughout the LC sample. Furthermore, our results suggest that conjugated polymers such as MEH-PPV can be used as sensitive local probes to explore complex (and unknown) structures in anisotropic media. PMID:17975912

  19. Supramolecular Approaches to Graphene: From Self-Assembly to Molecule-Assisted Liquid-Phase Exfoliation.

    PubMed

    Ciesielski, Artur; Samorì, Paolo

    2016-08-01

    Graphene, a one-atom thick two-dimensional (2D) material, is at the core of an ever-growing research effort due to its combination of unique mechanical, thermal, optical and electrical properties. Two strategies are being pursued for the graphene production: the bottom-up and the top-down. The former relies on the use of covalent chemistry approaches on properly designed molecular building blocks undergoing chemical reaction to form 2D covalent networks. The latter occurs via exfoliation of bulk graphite into individual graphene sheets. Amongst the various types of exfoliations exploited so far, ultrasound-induced liquid-phase exfoliation (UILPE) is an attractive strategy, being extremely versatile, up-scalable and applicable to a variety of environments. In this review, we highlight the recent developments that have led to successful non-covalent functionalization of graphene and how the latter can be exploited to promote the process of molecule-assisted UILPE of graphite. The functionalization of graphene with non-covalently interacting molecules, both in dispersions as well as in dry films, represents a promising and modular approach to tune various physical and chemical properties of graphene, eventually conferring to such a 2D system a multifunctional nature. PMID:26928750

  20. Sent packing: protein engineering generates a new crystal form of Pseudomonas aeruginosa DsbA1 with increased catalytic surface accessibility

    PubMed Central

    McMahon, Roisin M.; Coinçon, Mathieu; Tay, Stephanie; Heras, Begoña; Morton, Craig J.; Scanlon, Martin J.; Martin, Jennifer L.

    2015-01-01

    Pseudomonas aeruginosa is an opportunistic human pathogen for which new antimicrobial drug options are urgently sought. P. aeruginosa disulfide-bond protein A1 (PaDsbA1) plays a pivotal role in catalyzing the oxidative folding of multiple virulence proteins and as such holds great promise as a drug target. As part of a fragment-based lead discovery approach to PaDsbA1 inhibitor development, the identification of a crystal form of PaDsbA1 that was more suitable for fragment-soaking experiments was sought. A previously identified crystallization condition for this protein was unsuitable, as in this crystal form of PaDsbA1 the active-site surface loops are engaged in the crystal packing, occluding access to the target site. A single residue involved in crystal-packing interactions was substituted with an amino acid commonly found at this position in closely related enzymes, and this variant was successfully used to generate a new crystal form of PaDsbA1 in which the active-site surface is more accessible for soaking experiments. The PaDsbA1 variant displays identical redox character and in vitro activity to wild-type PaDsbA1 and is structurally highly similar. Two crystal structures of the PaDsbA1 variant were determined in complex with small molecules bound to the protein active site. These small molecules (MES, glycerol and ethylene glycol) were derived from the crystallization or cryoprotectant solutions and provide a proof of principle that the reported crystal form will be amenable to co-crystallization and soaking with small molecules designed to target the protein active-site surface. PMID:26627647

  1. Real-time single-molecule observations of proteins at the solid-liquid interface

    NASA Astrophysics Data System (ADS)

    Langdon, Blake Brianna

    Non-specific protein adsorption to solid surfaces is pervasive and observed across a broad spectrum of applications including biomaterials, separations, pharmaceuticals, and biosensing. Despite great interest in and considerable literature dedicated to the phenomena, a mechanistic understanding of this complex phenomena is lacking and remains controversial, partially due to the limits of ensemble-averaging techniques used to study it. Single-molecule tracking (SMT) methods allow us to study distinct protein dynamics (e.g. adsorption, desorption, diffusion, and intermolecular associations) on a molecule-by-molecule basis revealing the protein population and spatial heterogeneity inherent in protein interfacial behavior. By employing single-molecule total internal reflection fluorescence microscopy (SM-TIRFM), we have developed SMT methods to directly observe protein interfacial dynamics at the solid-liquid interface to build a better mechanistic understanding of protein adsorption. First, we examined the effects of surface chemistry (e.g. hydrophobicity, hydrogen-bonding capacity), temperature, and electrostatics on isolated protein desorption and interfacial diffusion for fibrinogen (Fg) and bovine serum albumin (BSA). Next, we directly and indirectly probed the effects of protein-protein interactions on interfacial desorption, diffusion, aggregation, and surface spatial heterogeneity on model and polymeric thin films. These studies provided many useful insights into interfacial protein dynamics including the following observations. First, protein adsorption was reversible, with the majority of proteins desorbing from all surface chemistries within seconds. Isolated protein-surface interactions were relatively weak on both hydrophobic and hydrophilic surfaces (apparent desorption activation energies of only a few kBT). However, proteins could dynamically and reversibly associate at the interface, and these interfacial associations led to proteins remaining on the

  2. Liquid-helium temperature long-path infrared spectroscopy of molecular clusters and supercooled molecules

    NASA Astrophysics Data System (ADS)

    Bauerecker, Sigurd; Taraschewski, Michael; Weitkamp, Claus; Cammenga, Heiko K.

    2001-10-01

    Collisional cooling and supersonic jet expansion both allow us to perform infrared spectroscopy of supercooled molecules and atomic and molecular clusters. Collisional cooling has the advantage of higher sensitivity per molecule and enables working in thermal equilibrium. A new powerful method of collisional cooling is presented in this article. It is based on a cooling cell with integrated temperature-invariant White optics and pulsed or continuous sample-gas inlet. The system can be cooled with liquid nitrogen or liquid helium and operated at gas pressures between <10-5 and 13 bar. Temperatures range from 4.2 to 400 K and can be adjusted to an accuracy of ±0.2 K over most of the useable range. A three-zone heating design allows homogeneous or inhomogeneous temperature distributions. Optical path lengths can be selected up to values of 20 m for Fourier transform infrared (FTIR) and 40 m for laser operation. The cell axis is vertical, so optical windows are at room temperature. Diffusive trapping shields and low-power electric heating keep the mirrors free from perturbing deposits. The cell can be operated in a dynamic buffer-gas flow-cooling mode. A comprehensive review of existing collisional cooling cells is given. The formation of CO clusters from the gas phase was investigated using FTIR spectroscopy. For the isotope mixture consisting of 13C16O,13C18O, and 12C16O, a conspicuous change in the main spectroscopic structure of the clusters was observed between 20 and 5 K. The cluster bandwidth of the main isotope 13C16O triples. This behavior could be interpreted as a change from the crystalline to the amorphous state or as a decrease in size to smaller clusters with relatively larger surfaces. To our knowledge, this is the first IR investigation of molecular clusters obtained by collisional cooling in this temperature range. For CO2 the change from the monomer to crystalline clusters was investigated. The observed spectra vary considerably with temperature

  3. Review of Crystalline Structures of Some Selected Homologous Series of Rod-Like Molecules Capable of Forming Liquid Crystalline Phases

    PubMed Central

    Zugenmaier, Peter

    2011-01-01

    The crystal structures of four homologous series of rod-like molecules are reviewed, two of which form hydrogen bonds and two with a symmetric chemical constitution. Many of the compounds investigated turn into liquid crystalline phases upon temperature increase. It is of valuable interest to know possible conformations and possible packing arrangements as prerequisites to model liquid crystalline structures. The hydrogen bonds of homologous series of pure 4-(ω-hydroxyalkyloxy)-4′-hydroxybiphenyl (HnHBP, n the alkyloxy tail length) are realized through head to tail arrangements of the hydroxyl groups and crystallize except one compound in chiral space groups without the molecules containing any asymmetric carbon. The hydrogen bonds of the homologous series of 4-substituted benzoic acids with various lengths of the tail provide dimers through strong polar bonding of adjacent carboxyl groups and thus provide the stiff part of a mesogenic unit prerequisite for liquid crystalline phases. The homologous series of dialkanoyloxybiphenyls (BP-n, n = 1, 19), of which nine compounds could be crystallized, show liquid crystalline behavior for longer alkane chain lengths, despite the high mobility of the alkane chain ends already detectable in the crystal phase. A single molecule, half a molecule or two half molecules form the asymmetric unit in a centrosymmetric space group. The homologous series of 1,4-terephthalidene-bis-N-(4′-n-alkylaniline) (TBAA-n) exhibit a large variety of packing arrangements in the crystalline state, with or without relying on the symmetry center within the molecules. PMID:22174604

  4. Monoclinic crystal form of Aspergillus niger alpha-amylase in complex with maltose at 1.8 angstroms resolution.

    PubMed

    Vujicić-Zagar, A; Dijkstra, B W

    2006-08-01

    Aspergillus niger alpha-amylase catalyses the hydrolysis of alpha-1,4-glucosidic bonds in starch. It shows 100% sequence identity to the A. oryzae homologue (also called TAKA-amylase), three crystal structures of which have been published to date. Two of them belong to the orthorhombic space group P2(1)2(1)2(1) with one molecule per asymmetric unit and one belongs to the monoclinic space group P2(1) with three molecules per asymmetric unit. Here, the purification, crystallization and structure determination of A. niger alpha-amylase crystallized in the monoclinic space group P2(1) with two molecules per asymmetric unit in complex with maltose at 1.8 angstroms resolution is reported. Furthermore, a novel 1.6 angstroms resolution orthorhombic crystal form (space group P2(1)2(1)2) of the native enzyme is presented. Four maltose molecules are observed in the maltose-alpha-amylase complex. Three of these occupy active-site subsites -2 and -1, +1 and +2 and the hitherto unobserved subsites +4 (Asp233, Gly234) and +5 (Asp235). The fourth maltose molecule binds at the distant binding sites d1 (Tyr382) and d2 (Trp385), also previously unobserved. Furthermore, it is shown that the active-site groove permits different binding modes of sugar units at subsites +1 and +2. This flexibility of the active-site cleft close to the catalytic centre might be needed for a productive binding of substrate chains and/or release of products. PMID:16880540

  5. Molecular model of biaxial ordering in nematic liquid crystals composed of flat molecules with four mesogenic groups

    NASA Astrophysics Data System (ADS)

    Gorkunov, M. V.; Osipov, M. A.; Kocot, A.; Vij, J. K.

    2010-06-01

    Relative stability of uniaxial and biaxial nematic phases is analyzed in a model nematic liquid crystal composed of flat molecules of C2h symmetry with four mesogenic groups rigidly linked to the same center. The generalized effective quadrupole mean-field potential is proposed and its constants are evaluated numerically for the pair intermolecular potential based on Gay-Berne interaction between mesogenic groups. The dependencies of the constants on molecular shape parameters are systematically analyzed. Order parameters of the uniaxial and biaxial nematic phases are evaluated by direct minimization of the free energy at different temperatures. The corresponding phase diagrams are obtained enabling one to study the effects of molecular model parameters on the stability regions of uniaxial and biaxial phases. The results are used to clarify the nature of experimentally observed biaxial ordering in nematic liquid crystals composed of tetrapode molecules with the same symmetry.

  6. Molecular model of biaxial ordering in nematic liquid crystals composed of flat molecules with four mesogenic groups.

    PubMed

    Gorkunov, M V; Osipov, M A; Kocot, A; Vij, J K

    2010-06-01

    Relative stability of uniaxial and biaxial nematic phases is analyzed in a model nematic liquid crystal composed of flat molecules of C2h symmetry with four mesogenic groups rigidly linked to the same center. The generalized effective quadrupole mean-field potential is proposed and its constants are evaluated numerically for the pair intermolecular potential based on Gay-Berne interaction between mesogenic groups. The dependencies of the constants on molecular shape parameters are systematically analyzed. Order parameters of the uniaxial and biaxial nematic phases are evaluated by direct minimization of the free energy at different temperatures. The corresponding phase diagrams are obtained enabling one to study the effects of molecular model parameters on the stability regions of uniaxial and biaxial phases. The results are used to clarify the nature of experimentally observed biaxial ordering in nematic liquid crystals composed of tetrapode molecules with the same symmetry. PMID:20866427

  7. Influence of the layer thickness and concentration of dye molecules on the emission amplification in cholesteric liquid crystals

    SciTech Connect

    Alaverdyan, R B; Gevorgyan, A A; Chilingaryan, A D; Chilingaryan, Yu S

    2008-05-31

    The propagation of light through a planar layer of a cholesteric liquid crystal doped with dye molecules is considered. The features of the emission spectra of the crystal are studied both in the absence and presence of dielectric boundaries. The increase in the emission intensity is investigated for different layer thicknesses and different concentrations of dye molecules. It is shown that an anomalously strong increase in the emission intensity with the diffraction intrinsic polarisation takes place in the case of a comparatively small crystal thickness and a relatively low concentration of dye molecules. The obtained results can be used for the development of miniature lasers with the circular polarisation of the fundamental radiation mode. (laser applications and other topics in quantum electronics)

  8. Prospects for single-molecule detection in liquids by laser-induced fluorescence

    SciTech Connect

    Trkula, M.; Keller, R.A.; Martin, J.C.; Jett, J.H.; Dovichi, N.J.

    1983-01-01

    A laser-induced fluoresence determination of aqueous solutions of rhodamine 6G resulted in a detection limit of 18 attograms, or 22,000 molecules, of rhodamine 6G. These results allow the projection to single-molecule detection with reasonable improvements in the experimental apparatus.

  9. New crystal forms of NTPDase1 from the bacterium Legionella pneumophila

    PubMed Central

    Zebisch, Matthias; Schäfer, Petra; Lauble, Peter; Sträter, Norbert

    2013-01-01

    Nucleoside triphosphate diphosphohydrolases (NTPDases) are a large class of nucleotidases that hydrolyze the (γ/β)- and (β/α)-anhydride bonds of nucleoside triphosphates and diphosphates, respectively. NTPDases are found throughout the eukaryotic domain. In addition, a very small number of members can be found in bacteria, most of which live as parasites of eukaryotic hosts. NTPDases of intracellular and extracellular parasites are emerging as important regulators for the survival of the parasite. To deepen the knowledge of the structure and function of this enzyme class, recombinant production of the NTPDase1 from the bacterium Legionella pneumophila has been established. The protein could be crystallized in six crystal forms, of which one has been described previously. The crystals diffracted to resolutions of between 1.4 and 2.5 Å. Experimental phases determined by a sulfur SAD experiment using an orthorhombic crystal form produced an interpretable electron-density map. PMID:23519799

  10. Preliminary characterization of two different crystal forms of acylphosphatase from the hyperthermophile archaeon Sulfolobus solfataricus

    SciTech Connect

    Zuccotti, Simone; Rosano, Camillo; Bemporad, Francesco; Stefani, Massimo; Bolognesi, Martino

    2005-01-01

    S. solfataricus acylphosphatase has been expressed, purified and crystallized in two different crystal forms. Preliminary characterization of a triclinic and a monoclinic crystal form is reported and data were collected to 1.27 and 1.90 Å, respectively. Acylphosphatase is a ubiquitous small enzyme that was first characterized in mammals. It is involved in the hydrolysis of carboxyl-phosphate bonds in several acylphosphate substrates, such as carbamoylphosphate and 1,3-biphosphoglycerate; however, a consensus on acylphosphatase action in vivo has not yet been reached. Recent investigations have focused on acylphosphatases from lower phyla, such as Drosophila melanogaster and Escherichia coli, in view of the application of these small proteins as models in the study of folding, misfolding and aggregation processes. An acylphosphatase from the hyperthermophilic archaeon Sulfolobus solfataricus has been cloned, expressed and purified. Here, the growth and characterization of a triclinic and a monoclinic crystal form of the hyperthermophilic enzyme are reported; X-ray diffraction data have been collected to 1.27 and 1.90 Å resolution, respectively.

  11. Sent packing: protein engineering generates a new crystal form of Pseudomonas aeruginosa DsbA1 with increased catalytic surface accessibility

    SciTech Connect

    McMahon, Roisin M. Coinçon, Mathieu; Tay, Stephanie; Heras, Begoña; Morton, Craig J.; Scanlon, Martin J.; Martin, Jennifer L.

    2015-11-26

    The crystal structure of a P. aeruginosa DsbA1 variant is more suitable for fragment-based lead discovery efforts to identify inhibitors of this antimicrobial drug target. In the reported structures the active site of the protein can simultaneously bind multiple ligands introduced in the crystallization solution or via soaking. Pseudomonas aeruginosa is an opportunistic human pathogen for which new antimicrobial drug options are urgently sought. P. aeruginosa disulfide-bond protein A1 (PaDsbA1) plays a pivotal role in catalyzing the oxidative folding of multiple virulence proteins and as such holds great promise as a drug target. As part of a fragment-based lead discovery approach to PaDsbA1 inhibitor development, the identification of a crystal form of PaDsbA1 that was more suitable for fragment-soaking experiments was sought. A previously identified crystallization condition for this protein was unsuitable, as in this crystal form of PaDsbA1 the active-site surface loops are engaged in the crystal packing, occluding access to the target site. A single residue involved in crystal-packing interactions was substituted with an amino acid commonly found at this position in closely related enzymes, and this variant was successfully used to generate a new crystal form of PaDsbA1 in which the active-site surface is more accessible for soaking experiments. The PaDsbA1 variant displays identical redox character and in vitro activity to wild-type PaDsbA1 and is structurally highly similar. Two crystal structures of the PaDsbA1 variant were determined in complex with small molecules bound to the protein active site. These small molecules (MES, glycerol and ethylene glycol) were derived from the crystallization or cryoprotectant solutions and provide a proof of principle that the reported crystal form will be amenable to co-crystallization and soaking with small molecules designed to target the protein active-site surface.

  12. Integration and characterization of SiN nanopores for single-molecule detection in liquid-core ARROW waveguides

    NASA Astrophysics Data System (ADS)

    Rudenko, M. I.; Yin, D.; Holmes, M.; Hawkins, A. R.; Schmidt, H.

    2007-02-01

    We demonstrate a method for integrating silicon nitride nanopores in liquid core Anti Resonant Reflecting Optical Waveguides (ARROW) for single molecule electrical detection and control. We use a two-step integration process when a micropore is fabricated first, paving the way for subsequent nanopore integration in the first silicon nitride layer of the ARROW structure. Nanopores with dimensions as small as 11 nm were fabricated using a Focused Ion Beam shrinking process commensurate with single particle gating of viruses, proteins, ribosomes and other biomolecules.

  13. The Amphiphilic Character of Cellulose Molecules in True Solution in Solvent Mixtures Containing Ionic Liquid and its Utilization in Emulsification

    NASA Astrophysics Data System (ADS)

    Napso, Sofia; Cohen, Yachin; Rein, Dmitry; Khalfin, Rafail; Szekely, Noemi

    2015-03-01

    Cellulose is the most abundant renewable material in nature that is utilized as a raw material for fabrication of synthetic products. Although it is not soluble in common solvents, there is significant interest in the use of solvent mixtures containing ionic liquids (IL) and polar organic solvents for cellulose dissolution. We present evidence for true molecular dissolution of cellulose in binary mixtures of common polar organic solvents with an ionic liquid, using cryogenic transmission electron microscopy, small-angle neutron-, x-ray- and static light scattering. In particular, the measured low values of the molecular, gyration radius and persistence length indicate the absence of significant aggregation of the dissolved chains. We conjecture that the dissolved cellulose chains are amphiphilic. This can be inferred from the facile fabrication of cellulose-encapsulated colloidal oil-in-water or water-in-oil dispersions. This may be done by mixing water, oil and cellulose solution in an ionic liquid. A more practical alternative is to form first a hydrogel from the cellulose/ionic liquid solution by coagulation with water and applying it to sonicated water/oil or oil/water mixtures. Apparently the dissolution/ regeneration process affords higher mobility to the cellulose molecules so an encapsulation coating can be formed at the water-oil interface.

  14. DNA aptamer functionalized zinc oxide field effect transistors for liquid state selective sensing of small molecules

    NASA Astrophysics Data System (ADS)

    Hagen, Joshua A.; Kim, Sang N.; Bayraktaroglu, Burhan; Kelley-Loughnane, Nancy; Naik, Rajesh R.; Stone, Morley O.

    2010-08-01

    In this work, we show the use of single stranded DNA aptamers as selective biorecognition elements in a sensor based on a field effect transistor (FET) platform. Aptamers are chemically attached to the semiconducting material in the FET through the use of linker molecules and confirmed through atomic force microscopy and positive target detection. Highly selective sensing of a small molecule, riboflavin is shown down to the nano-molar level in zinc oxide FET and micro-molar level in a carbon nanotube FET. High selectivity is determined through the use of negative control target molecules with similar molecular structures as the positive control targets with little to no sensor response. The goal of this work is to develop a sensor platform where biorecognition elements can be used to functionalize an array of transistors for simultaneous sensing of multiple targets in biological fluids.

  15. The problem of internal motion of molecules in the liquid as seen from NMR relaxation studies

    NASA Astrophysics Data System (ADS)

    Hertz, H. G.

    As a brief introduction the most important formulas are given and the crucial physical aspects will be worked out. It is essentially the Woessner theory which gives the framework of the facts to be treated. A number of experimental results are presented for the following molecules: Methanol, acetic acid, DMSO, ethanol, i-propanol, toluene and propylene carbonate. It will be shown that the proton-proton distances in the molecule which result from the proton relaxation data obtained in the dispersion range together with the "classical" theory do not agree with the generally accepted molecular geometry. Moreover, the general nature of the resulting motion in its qualitative and basic features does not correspond to the pattern generally accepted. A very general description of the molecule is given which is free of the difficulties which have appeared.

  16. Intense pumping and time- and frequency-resolved CARS for driving and tracking structural deformation and recovery of liquid nitromethane molecules

    NASA Astrophysics Data System (ADS)

    Wang, Chang; Wu, Hong-lin; Song, Yun-fei; He, Xing; Yang, Yan-qiang; Tan, Duo-wang

    2015-11-01

    A modified CARS technique with an intense nonresonant femtosecond laser is presented to drive the structural deformation of liquid nitromethane molecules and track their structural relaxation process. The CARS spectra reveal that the internal rotation of the molecule can couple with the CN symmetric stretching vibration and the molecules undergo ultrafast structural deformation of the CH3 groups from 'opened umbrella' to 'closed umbrella' shape, and then experience a structural recovery process within 720 fs.

  17. Crystal form III of beta-cyclodextrin-ethanol inclusion complex: layer-type structure with dimeric motif.

    PubMed

    Aree, Thammarat; Chaichit, Narongsak

    2008-09-01

    The crystal form III of the beta-cyclodextrin (beta-CD)-ethanol inclusion complex [2(C(6)H(10)O(5))(7).1.5C(2)H(5)OH.19H(2)O] belongs to the triclinic space group P1 with unit cell constants: a=15.430(1), b=15.455(1), c=17.996(1)A, alpha=99.30(1) degrees , beta=113.18(1) degrees , gamma=103.04(1) degrees . beta-CD forms dimers comprising two identical monomers that adopt a 'round' conformation stabilized by intramolecular, interglucose O-3(n)cdots, three dots, centeredO-2(n+1) hydrogen bonds. The two beta-CD monomers of form III are isostructural to that of form I in the monoclinic space group P2(1) [Steiner, T.; Mason, S. A.; Saenger, W. J. Am. Chem. Soc.1991, 113, 5676-5687], but exhibit a striking difference from that of form II in the monoclinic space group C2 [Aree, T.; Chaichit, N. Carbohydr. Res.2003, 338, 1581-1589]. The small guest EtOH molecule orients differently in the large beta-CD cavity. In form III, two disordered EtOH molecules are embedded in the beta-CD-dimer cavity. A half occupied EtOH molecule (#1) is located above the O-4 plane of beta-CD #1, whereas another doubly disordered EtOH molecule (#2, #3) is situated at about the middle of the beta-CD-dimer cavity. The three EtOH sites are maintained in positions by making van der Waals contacts to each other and to the surrounding water sites and beta-CD O-3-H group. The EtOH molecules disordered (occupancy 0.3) above the beta-CD O-4 plane in form I and fully occupied beneath the O-4 plane in form II are strongly held in positions by hydrogen bonding with the surrounding water site and beta-CD O-6-H, O-3-H groups. Occurrence of the beta-CD dimer as a structural motif of channel-type packing (form II) and layer-type packing (form III) is attributed to the higher tendency for self aggregation under the moderate acidic conditions. At weak acidic conditions, beta-CD prefers a herringbone mode (form I). PMID:18490008

  18. Inhibitors of pendrin anion exchange identified in a small molecule screen increase airway surface liquid volume in cystic fibrosis.

    PubMed

    Haggie, Peter M; Phuan, Puay-Wah; Tan, Joseph-Anthony; Zlock, Lorna; Finkbeiner, Walter E; Verkman, A S

    2016-06-01

    Pendrin (SLC26A4) is a Cl(-)/anion exchanger expressed in the epithelium of inflamed airways where it is thought to facilitate Cl(-) absorption and HCO3 (-) secretion. Studies using pendrin knockout mice and airway epithelial cells from hearing-impaired subjects with pendrin loss of function suggest involvement of pendrin in inflammatory lung diseases, including cystic fibrosis (CF), perhaps by regulation of airway surface liquid (ASL) volume. Here we identified small-molecule pendrin inhibitors and demonstrated their efficacy in increasing ASL volume. A cell-based, functional high-throughput screen of ∼36,000 synthetic small molecules produced 3 chemical classes of inhibitors of human pendrin. After structure-activity studies, tetrahydropyrazolopyridine and pyrazolothiophenesulfonamide compounds reversibly inhibited pendrin-facilitated Cl(-) exchange with SCN(-), I(-), NO3 (-), and HCO3 (-) with drug concentration causing 50% inhibition down to ∼2.5 μM. In well-differentiated primary cultures of human airway epithelial cells from non-CF and CF subjects, treatment with IL-13, which causes inflammation with strong pendrin up-regulation, strongly increased Cl(-)/HCO3 (-) exchange and the increase was blocked by pendrin inhibition. Pendrin inhibition significantly increased ASL depth (by ∼8 μm) in IL-13-treated non-CF and CF cells but not in untreated cells. These studies implicate the involvement of pendrin-facilitated Cl(-)/HCO3 (-) in the regulation of ASL volume and suggest the utility of pendrin inhibitors in inflammatory lung diseases, including CF.-Haggie, P. M., Phuan, P.-W., Tan, J.-A., Zlock, L., Finkbeiner, W. E., Verkman, A. S. Inhibitors of pendrin anion exchange identified in a small molecule screen increase airway surface liquid volume in cystic fibrosis. PMID:26932931

  19. Polar Switching in a Lyotropic Columnar Nematic Liquid Crystal Made of Bowl-Shaped Molecules.

    PubMed

    Guilleme, Julia; Cavero, Emma; Sierra, Teresa; Ortega, Josu; Folcia, César L; Etxebarria, Jesus; Torres, Tomás; González-Rodríguez, David

    2015-08-01

    A polar response in a lyotropic columnar nematic material is reported. The material accommodates bowl-shaped molecules with strong axial dipole moments in column segments without head-to-tail invariance. Optical second-harmonic-generation methods confirm that the nematic columns align unidirectionally under an applied electric field and the material develops remnant macroscopic polarization observable for hours. The switching takes place by a flip of the columns. PMID:26078047

  20. Electrical reorientation of liquid crystal molecules inside cylindrical pores for photonic device applications

    NASA Astrophysics Data System (ADS)

    Tkachenko, V.; Dyomin, A. A.; Tkachenko, G. V.; Abbate, G.; Sukhoivanov, I. A.

    2008-05-01

    We present the simulated distribution of the local director of a nematic liquid crystal inside cylindrical macropores under the influence of an electric field. The Frank free energy approach is used to describe the nematic behavior. The influence of both molecular anchoring strength and pore radius is investigated. The results of this analysis are applied for simulation of an electrically tunable microcavity based on porous silicon infiltrated with a liquid crystal. The Bruggeman approximation is used while calculating the effective refractive index of each layer in the porous silicon multilayer structure. The reflectivity spectrum of the latter is simulated using the transfer matrix approach. The electrical tuning range of a microcavity designed for near-infrared waves is found to vary from 10.5 up to 23 nm for weak and strong surface anchoring conditions, respectively.

  1. Selective liquid crystal molecule orientation on ion beam irradiated tantalum oxide ultrathin films

    SciTech Connect

    Lim, Ji-Hun; Oh, Byeong-Yun; Lee, Won-Kyu; Lee, Kang-Min; Na, Hyun-Jae; Kim, Byoung-Yong; Seo, Dae-Shik; Han, Jeong-Min; Hwang, Jeong-Yeon

    2009-09-21

    We recently achieved the homogeneous alignment of liquid crystal (LC) on amorphous Ta{sub 2}O{sub 5} layers. This study demonstrates that LC layers could be aligned either homogeneously or vertically by increasing the growth temperature of rf magnetron sputtering device and the irradiation time of the DuoPIGatron type Ar ion beam device causing uniform and dense plasma. We attained two LC orientations by observing Ta 4f and O 1s peak shifts with x-ray photoelectron spectroscopy. Moreover, the decreased thickness of layers with high-k dielectric constants helped to decrease driving LC voltages and in turn to achieve low power consumption.

  2. Homogeneously aligned liquid crystal molecules on reformed poly(methyl methacrylate) via ion-beam irradiation

    NASA Astrophysics Data System (ADS)

    Jeong, Hae-Chang; Park, Hong-Gyu; Lee, Ju Hwan; Jang, Sang Bok; Oh, Byeong-Yun; Han, Jeong-Min; Seo, Dae-Shik

    2016-04-01

    We demonstrated uniform LC alignment using IB-irradiated poly(methyl methacrylate) (PMMA) as an alignment layer. We confirmed the topographical changes on PMMA caused by IB irradiation. Moreover, the wettability and chemical modification of the PMMA surface were investigated as functions of incidence angle. The results show that PMMA irradiated with IB at an incidence angle of 30° had a higher molecular polarity than PMMA irradiated with IB at other incidence angles, resulting in strong van der Waals interactions between the surface and LC molecules. The LC cells containing PMMA irradiated with IB at an incidence angle of 30° exhibited good thermal stability (180°) compared with LC cells containing conventional rubbing PI (150°). In addition, LC molecules on PMMA irradiated with IB at an incidence angle of 30° were observed to switch faster than those on conventional rubbing PI. Therefore, PMMA irradiated with IB under the optimal conditions may allow for PMMA to be applied in advanced LC devices as an alternative alignment layer.

  3. Nanostructures of liquid crystal phases in mixtures of bent-core and rod-shaped molecules

    SciTech Connect

    Hong, S. H.; Gleeson, J. T.; Sprunt, S.; Verduzco, R.; Jakli, A.

    2011-06-15

    We report small angle x-ray scattering (SAXS) studies of isotropic, nematic, and smectic mesophases formed by binary mixtures of bent-core (BC) and rod-shaped (RS) molecules. While optical studies indicate that the components are fully miscible, SAXS reveals fascinating structures that are consistent with segregation on a nanoscopic scale. We find that tilted smectic clusters, which have been previously reported in both the nematic and isotropic states of the pure BC materials, are also present in mixtures with up to 50 wt% of the RS compound; this is consistent with previous dielectric and flexoelectric studies on such mixtures. Unexpectedly in this concentration range the clusters are present in the isotropic and in the induced smectic phase range, as well as throughout the nematic phase. The results in the smectic phase also reveal complex layering phenomena, providing important insight into the interaction between bent and rod-shaped molecules. These studies will be crucial in the design of promising new functional nanomaterials.

  4. Nanostructures of Liquid Crystal Phases in Mixtures of Bent-core and Rod-shaped Molecules

    SciTech Connect

    S Hong; R Verduzco; J Gleeson; S Sprunt; A Jakli

    2011-12-31

    We report small angle x-ray scattering (SAXS) studies of isotropic, nematic, and smectic mesophases formed by binary mixtures of bent-core (BC) and rod-shaped (RS) molecules. While optical studies indicate that the components are fully miscible, SAXS reveals fascinating structures that are consistent with segregation on a nanoscopic scale. We find that tilted smectic clusters, which have been previously reported in both the nematic and isotropic states of the pure BC materials, are also present in mixtures with up to 50 wt% of the RS compound; this is consistent with previous dielectric and flexoelectric studies on such mixtures. Unexpectedly in this concentration range the clusters are present in the isotropic and in the induced smectic phase range, as well as throughout the nematic phase. The results in the smectic phase also reveal complex layering phenomena, providing important insight into the interaction between bent and rod-shaped molecules. These studies will be crucial in the design of promising new functional nanomaterials.

  5. Effect of co-solutes and process variables on crystallinity and the crystal form of freeze-dried myo-inositol.

    PubMed

    Izutsu, Ken-Ichi; Kusano, Riho; Arai, Ryoko; Yoshida, Hiroyuki; Ito, Masataka; Shibata, Hiroko; Sugano, Kiyohiko; Goda, Yukihiro; Terada, Katsuhide

    2016-07-25

    The purpose of this study was to elucidate how co-solutes affect the crystallization of small solute molecules during freeze-drying and subsequent storage. Crystallization profiles of myo-inositol and its mixture with dextran 40k in frozen solutions and dried solids were assessed by thermal analysis (DSC), powder-X-ray diffraction, and simultaneous DSC and PXRD analysis. Higher mass ratios of dextran maintained myo-inositol in the non-crystalline mixture state, in frozen solutions, during freeze-drying process, and exposure of dried solids to higher temperatures. Co-lyophilization with a lower mass ratio of dextran resulted in solids containing a variety of myo-inositol crystal forms and crystallinity depending on the composition and thermal history of the process. Heating of some inositol-rich amorphous solids showed crystallization of myo-inositol in the metastable form and its transition to stable form before melting. Heat-treatment of inositol-rich frozen solutions resulted in high crystallinity stable-form inositol solids, leaving dextran in the amorphous state. Sufficient direct molecular interactions (e.g., hydrogen bonding) should explain the stability of dextran-rich amorphous solids. Optimizing solute composition and processes should be a potent way to control crystal form and crystallinity of components in freeze-dried formulations. PMID:27282535

  6. Structure of struthiocalcin-1, an intramineral protein from Struthio camelus eggshell, in two crystal forms.

    PubMed

    Ruiz-Arellano, Rayana R; Medrano, Francisco J; Moreno, Abel; Romero, Antonio

    2015-04-01

    Biomineralization is the process by which living organisms produce minerals. One remarkable example is the formation of eggshells in birds. Struthiocalcins present in the ostrich (Struthio camellus) eggshell matrix act as biosensors of calcite growth during eggshell formation. Here, the crystal structure of struthiocalcin-1 (SCA-1) is reported in two different crystal forms. The structure is a compact single domain with an α/β fold characteristic of the C-type lectin family. In contrast to the related avian ovocleidin OC17, the electrostatic potential on the molecular surface is dominated by an acidic patch. Scanning electron microscopy combined with Raman spectroscopy indicates that these intramineral proteins (SCA-1 and SCA-2) induce calcium carbonate precipitation, leading to the formation of a stable form of calcite in the mature eggshell. Finally, the implications of these two intramineral proteins SCA-1 and SCA-2 in the nucleation of calcite during the formation of eggshells in ratite birds are discussed. PMID:25849392

  7. Liquid-crystalline octopus dendrimers: block molecules with unusual mesophase morphologies.

    PubMed

    Gehringer, Lionel; Bourgogne, Cyril; Guillon, Daniel; Donnio, Bertrand

    2004-03-31

    The synthesis and the mesomorphic properties of several new main-chain liquid-crystalline dendrimers, thereafter designated as octopus dendrimers in accordance with their eight sidearms, are reported. In these dendritic systems, the arborescence is ensured by anisotropic segments, acting as branching cells with a double multiplicity, which are incorporated at every node of the dendritic architecture. In such a way, these compounds radically differ from the classical end-functionalized liquid-crystalline dendrimers, the most commonly reported systems. Following our previous report on purely homolithic systems, that is, the building blocks constituting the dendritic matrix are all identical, several heterolithic systems made of different anisotropic blocks have been prepared. The dendritic branches and corresponding dendrimers were synthesized using a modular construction. Polarized optical microscopy and X-ray diffraction studies showed that all of these new octopus dendrimers exhibit either smectic-like or columnar phases with novel morphologies, the nature of the mesophases depending on the number of terminal chains attached to the peripheral groups. The mesomorphism of these heterolithic dendrimers is discussed in terms of their intrinsic architecture and compared to the analogous homolithic octopus systems. Models for the molecular organizations within both the smectic and the columnar phases are proposed on the basis of small Bragg angle X-ray diffraction studies and are supported by molecular modelizations. Moreover, this study showed that the mesophase stability is very sensitive to the nature and to the mutual arrangement (the spatial location) of the mesogenic segments within the dendritic matrix, illustrating the intimate relationships existing between the mesomorphic properties and the molecular architecture of these dendrimers. PMID:15038740

  8. Fast and General Method To Predict the Physicochemical Properties of Druglike Molecules Using the Integral Equation Theory of Molecular Liquids.

    PubMed

    Palmer, David S; Mišin, Maksim; Fedorov, Maxim V; Llinas, Antonio

    2015-09-01

    We report a method to predict physicochemical properties of druglike molecules using a classical statistical mechanics based solvent model combined with machine learning. The RISM-MOL-INF method introduced here provides an accurate technique to characterize solvation and desolvation processes based on solute-solvent correlation functions computed by the 1D reference interaction site model of the integral equation theory of molecular liquids. These functions can be obtained in a matter of minutes for most small organic and druglike molecules using existing software (RISM-MOL) (Sergiievskyi, V. P.; Hackbusch, W.; Fedorov, M. V. J. Comput. Chem. 2011, 32, 1982-1992). Predictions of caco-2 cell permeability and hydration free energy obtained using the RISM-MOL-INF method are shown to be more accurate than the state-of-the-art tools for benchmark data sets. Due to the importance of solvation and desolvation effects in biological systems, it is anticipated that the RISM-MOL-INF approach will find many applications in biophysical and biomedical property prediction. PMID:26212723

  9. Effects of layer order on the mobility of mesogenic molecules in SmA liquid-crystalline emulsions

    NASA Astrophysics Data System (ADS)

    Bono, Shinji; Takanishi, Yoichi; Yamamoto, Jun

    2016-03-01

    We fabricate smectic-A liquid-crystalline emulsions (SmA-LCEs) in which monodisperse 8CB-swollen micelles are dispersed in water. Synchrotron X-ray measurements reveal that the correlation length of the layer order in LCEs cannot diverge at the nematic (N)-SmA transition, and the saturated length linearly increases with the increase in the diameter of LC-swollen micelles. Moreover, we investigate the permeation of 7CB N molecules into 8CB SmA-LCEs by measuring the enhancement of the depolarized light scattering intensity due to the shift of the SmA-N phase transition, and confirm that the layer order suppresses the mobility of LC molecules in LCEs similar to the bulk state of SmA LCs. The mobility drastically accelerates near the SmA-N transition temperature due to the continuous extinction of the smectic layer order. The slow permeation process of 7CB is also confirmed via synchrotron X-ray diffraction examining the shrinkage of the smectic layer repeat distance, caused by intercalation of 7CB.

  10. Dual-Responsive Viscoelastic Lyotropic Liquid Crystal Fluids to Control the Diffusion of Hydrophilic and Hydrophobic Molecules.

    PubMed

    Wang, Dong; Cao, Yueying; Cao, Meiwen; Sun, Yawei; Wang, Jiqian; Hao, Jingcheng

    2016-07-01

    A smart lyotropic liquid crystal (LLC) system was prepared to control the diffusion rate of hydrophilic and hydrophobic molecules. The LLC system is composed of a nonionic surfactant (tetraethylene glycol monododecylether; C12 EO4 ) and an anionic azobenzene surfactant (Azo-surfactant). C12 EO4 was the main component of the LLC system. The Azo-surfactant, which can undergo photo-isomerization, played the role of trigger in this system. LLC gels formed in a solution comprised of Azo-surfactant (10 mm) and C12 EO4 (300 mm). The LLC gels became broken when more Azo-surfactant was added (e.g., up to 15 mm) and the viscoelasticity was lost. Surprisingly, when we used UV light to irradiate the 300 mm C12 EO4 /15 mm Azo-surfactant sample, the gel was recovered and high viscoelasticity was observed. However, under visible-light irradiation, the gel became broken again. The gel formation could also be triggered by heating the sample. On heating the 300 mm C12 EO4 /15 mm Azo-surfactant sample, the system thickened to a point at which typical gel behavior was registered. When the sample was cooled, the gel broke again. The LLC could be used for controlled release of hydrophilic and hydrophobic molecules, and could be considered as a versatile vehicle for the delivery of actives in systems of practical importance. PMID:27028313

  11. Determination of relative positions and localizations of paramagnetic probe molecules in liquid crystal by analysis of concentration broadening of EPR spectra

    NASA Astrophysics Data System (ADS)

    Pomogailo, Daria A.; Paramonov, Nikita A.; Chumakova, Natalia A.; Vorobiev, Andrey Kh.

    2016-07-01

    The angular dependences of concentration broadening of EPR spectra for nitroxide spin probes in liquid crystals were experimentally measured. The obvious angular dependence of the broadening found for oriented smectic liquid crystal HOPDOB proves the paired localization of the probe molecules. The numerical calculation of the angular dependence taking into account the magnetic dipolar and spin exchange interactions have been used for quantitative determination of position of probes in the pairs. The probable localization of the probes in the smectic layer is discussed.

  12. Computer assisted optimization of liquid chromatographic separations of small molecules using mixed-mode stationary phases.

    PubMed

    Ordoñez, Edgar Y; Benito Quintana, José; Rodil, Rosario; Cela, Rafael

    2012-05-18

    Mixed-mode stationary phases are gaining adepts in liquid chromatography (LC) as more and more applications are published and new commercial columns appear in the market ought to their ability to retain and separate analytes with multiple functionalities. The increased number of adjustable variables gives these columns an enhanced value for the chromatographer, but, on the other hand, it complicates the process of developing satisfactory separations when complex samples must be analyzed. Thus, the availability of computer assisted methods development (CAMD) tools is highly desirable in this field. Therefore, the first specific tool for the CAMD of LC separations in mixed-mode columns is presented. The tool consists in two processes. The first one develops a retention model for peaks in a predefined experimental domain of pH and buffer concentration. In this domain, the retention as a function of the proportion of organic modifier is modeled using a two-stage re-calibration process departing from isocratic retention data and then, from gradient elutions. With this two-stage approach, reliability is gained. In the second process, the model is finally interpolated and used for the unattended optimization of the different possible elution modes available in these columns. This optimization process is driven by an evolutionary algorithm. The development and application of this new chemometrics tool is demonstrated by the optimization of a mixture of neutral and ionizable compounds. Hence, several different types of gradients were generated, showing a good agreement between simulated and experimental data, with retention time errors lower than 5% in most cases. On the other hand, classical CAMD tools, such as design of experiments, were unable to efficiently deal with mixed-mode optimizations, rendering errors above 30% for several compounds. PMID:22494641

  13. New crystal forms of Diocleinae lectins in the presence of different dimannosides

    SciTech Connect

    Moreno, Frederico Bruno Mendes Batista; Bezerra, Gustavo Arruda; Oliveira, Taianá Maia de; Souza, Emmanuel Prata de; Rocha, Bruno Anderson Matias da; Benevides, Raquel Guimarães; Delatorre, Plínio; Cavada, Benildo Sousa; Azevedo, Walter Filgueira Jr de

    2006-11-01

    The crystallization and preliminary X-ray data of Canavalia gladiata lectin (CGL) and C. maritima lectin (CML) complexed with Man(α1-2)Man(α1)OMe, Man(α1-3)Man(α1)OMe and Man(α1-4)Man(α1)OMe in two crystal forms [the complexes with Man(α1-3)Man(α1)OMe and Man(α1-4)Man(α1)OMe crystallized in space group P3{sub 2} and those with Man(α1-2)Man(α1)OMe crystallized in space group I222], which differed from those of the native proteins (P2{sub 1}2{sub 1}2 for CML and C222 for CGL), are reported. Studying the interactions between lectins and sugars is important in order to explain the differences observed in the biological activities presented by the highly similar proteins of the Diocleinae subtribe. Here, the crystallization and preliminary X-ray data of Canavalia gladiata lectin (CGL) and C. maritima lectin (CML) complexed with Man(α1-2)Man(α1)OMe, Man(α1-3)Man(α1)OMe and Man(α1-4)Man(α1)OMe in two crystal forms [the complexes with Man(α1-3)Man(α1)OMe and Man(α1-4)Man(α1)OMe crystallized in space group P3{sub 2} and those with Man(α1-2)Man(α1)OMe crystallized in space group I222], which differed from those of the native proteins (P2{sub 1}2{sub 1}2 for CML and C222 for CGL), are reported. The crystal complexes of ConA-like lectins with Man(α1-4)Man(α1)OMe are reported here for the first time.

  14. CIS-ZnS quantum dots for self-aligned liquid crystal molecules with superior electro-optic properties

    NASA Astrophysics Data System (ADS)

    Lee, Won-Kyu; Hwang, Seung Jun; Cho, Min-Jae; Park, Hong-Gyu; Han, Jin-Woo; Song, Seogjeong; Jang, Jong Hyun; Seo, Dae-Shik

    2012-12-01

    We demonstrate self-aligned and high-performance liquid crystal (LC) systems doped with 1-dimensional (1D) chain-like clusters of CuInS2 (CIS)-ZnS core-shell quantum dots (QDs). By changing the cell fabrication method of the LC-QD composites, we can selectively control the orientation of the LC molecules between the homogeneous and homeotropic states without conventional LC alignment layers. The homeotropic alignment of LCs was achieved by random dropcasting and the homogeneous alignment was performed using a capillary injection of LC-QDs due to the random or linear diffusion of QD clusters into ITO defects. The electrically compensated bend (ECB)- and vertically aligned (VA) mode LC displays (LCDs) containing our LC-QD composite both showed superior electro-optic (EO) properties. A 37.1% reduction in the threshold voltage (Vth) and a 36.6% decrease in the response time were observed for ECB mode LCDs, and a 47.0% reduction in the Vth and a 38.3% decrease in the response time were observed for VA mode LCDs, meaning that the proposed LC-QD composites have a great potential for the production of advanced flexible LCDs.We demonstrate self-aligned and high-performance liquid crystal (LC) systems doped with 1-dimensional (1D) chain-like clusters of CuInS2 (CIS)-ZnS core-shell quantum dots (QDs). By changing the cell fabrication method of the LC-QD composites, we can selectively control the orientation of the LC molecules between the homogeneous and homeotropic states without conventional LC alignment layers. The homeotropic alignment of LCs was achieved by random dropcasting and the homogeneous alignment was performed using a capillary injection of LC-QDs due to the random or linear diffusion of QD clusters into ITO defects. The electrically compensated bend (ECB)- and vertically aligned (VA) mode LC displays (LCDs) containing our LC-QD composite both showed superior electro-optic (EO) properties. A 37.1% reduction in the threshold voltage (Vth) and a 36.6% decrease in

  15. Isotope ratio monitoring of small molecules and macromolecules by liquid chromatography coupled to isotope ratio mass spectrometry.

    PubMed

    Godin, Jean-Philippe; Hau, Jörg; Fay, Laurent-Bernard; Hopfgartner, Gérard

    2005-01-01

    In the field of isotope ratio mass spectrometry, the introduction of an interface allowing the connection of liquid chromatography (LC) and isotope ratio mass spectrometry (IRMS) has opened a range of new perspectives. The LC interface is based on a chemical oxidation, producing CO2 from organic molecules. While first results were obtained from the analysis of low molecular weight compounds, the application of compound-specific isotope analysis by irm-LC/MS to other molecules, in particular biomolecules, is presented here. The influence of the LC flow rate on the CO2 signal and on the observed delta13C values is demonstrated. The limits of quantification for angiotensin III and for leucine were 100 and 38 pmol, respectively, with a standard deviation of the delta13C values better than 0.4 per thousand. Also, accuracy and precision of delta13C values for elemental analyser-IRMS and flow injection analysis-IRMS (FIA-LC/MS) were compared. For compounds with molecular weights ranging from 131 to 66,390 Da, precision was better than 0.3 per thousand, and accuracy varied from 0.1 to 0.7 per thousand. In a second part of the work, a two-dimensional (2D)-LC method for the separation of 15 underivatised amino acids is demonstrated; the precision of delta13C values for several amino acids by irm-LC/MS was better than 0.3 per thousand at natural abundance. For labelled mixtures, the coefficient of variation was between 1% at 0.07 atom % excess (APE) for threonine and alanine, and around 10% at 0.03 APE for valine and phenylalanine. The application of irm-LC/MS to the determination of the isotopic enrichment of 13C-threonine in an extract of rat colon mucosa demonstrated a precision of 0.5 per thousand, or 0.001 atom %. PMID:16124031

  16. Polymorphism of diflunisal: isolation and solid-state characteristics of a new crystal form.

    PubMed

    Martínez-Ohárriz, M C; Martín, C; Goñi, M M; Rodríguez-Espinosa, C; Tros de Ilarduya-Apaolaza, M C; Sánchez, M

    1994-02-01

    Three polymorphs (I, II, and III forms) and a new crystal form (form IV) of diflunisal were prepared and characterized by powder X-ray diffractometry, differential scanning calorimetry (DSC), hot-stage microscopy, IR spectroscopy, and dissolution studies. According to the different X-ray diffraction profiles, an identification system for the polymorphs can be developed based on the different peak positions of the diffraction patterns. The mutual transition behavior of the polymorphs was investigated and the melting points and melting enthalpies were determined from DSC and thermomicroscopy data. All forms first recrystallize to the more stable form (form I) and then melt at 210 degrees C; only one weak transition peak was detected corresponding to transformation of form III to form I. Differences observed in IR spectra indicate that intramolecular hydrogen bonding occurs between hydroxyl and carbonyl groups and/or between fluorine atoms. The intrinsic dissolution rates were determined from compressed disks in an aqueous medium. Unexpectedly the dissolution rate of form IV was lower than that of the most stable modification form I. PMID:8169784

  17. Effects of polymer concentration on the morphology of calcium phosphate crystals formed in polyacrylamide hydrogels

    NASA Astrophysics Data System (ADS)

    Yokoi, Taishi; Kawashita, Masakazu; Ohtsuki, Chikara

    2013-11-01

    Growing crystals in hydrogels is an attractive method to form inorganic solids with designed morphology under ambient conditions. Precipitation of the inorganic solids in a hydrogel matrix can be regarded as mimicking the process of biomineralization. In the construction of biominerals, an organic template composed of insoluble macromolecules is used to control the crystal growth of the inorganic compounds. The morphological control in biomineralization can be applied to artificial reaction systems. In this study, the morphology of calcium phosphate crystals formed in polymeric hydrogels of various polymer concentrations was investigated. Spherical octacalcium phosphate (OCP) precipitated in the polyacrylamide (PAAm) hydrogels. Fibrous crystals gradually covered the surface of the spherical crystals as the polymer concentration of the gel increased. The morphology of the OCP crystals changed from sea urchin shapes to wool-ball shapes with increasing PAAm concentration. The morphological change is generated by the template effect of the polymer wall, which is made up of stacked PAAm sheets, surrounding the spherical OCP crystals.

  18. [About the Spatial Organization of Double-stranded DNA Molecules in the Cholesteric Liquid-crystalline Phase and Dispersion Particles of this Phase].

    PubMed

    Yevdokimov, Yu M; Skuridin, S G; Salyanov, V I; Volkov, V V; Dadinova, L A; Kompanets, O N; Kats, E I

    2015-01-01

    The answer to a question on the organization of molecules in a cholesteric phase is well enough proved in case of low molecular mass compounds. However, in case of double-stranded nucleic acids molecules the unequivocal answer to such question is a subject of discussions. In this work an attempt to generalize the well known literary data on the structure of the cholesteric phase formed by double-stranded DNA molecules was undertaken. Besides the experimental results of authors describing the packing of these molecules in the cholesteric liquid-crystalline dispersion particles are added to these data. Comparison of the results obtained offers the possibility to come out with an assumption of high probability of the existence of both the short-range positional and long-range orientational order in arrangement of double-stranded DNA molecules in a liquid-crystalline phase, and in the particles of dispersions of this phase generated under certain conditions. The occurrence of the orientational order, i.e. rotation of 'quasinematic' layers of double-stranded DNA molecules by a small angle, defines the formation of spatially twisted (cholesteric) structure with characteristic for it physical and chemical properties. PMID:26591596

  19. Adsorption of apolar molecules at the water liquid-vapor interface: A Monte Carlo simulations study of the water-n-octane system

    NASA Astrophysics Data System (ADS)

    Jedlovszky, Pál; Varga, Imre; Gilányi, Tibor

    2003-07-01

    The adsorption of n-octane at the water liquid-vapor interface has been investigated by Monte Carlo computer simulation. For this purpose, simulation of five different water-apolar interfacial systems have been performed, in which the number of n-octane molecules has been varied. The results clearly show that the apolar n-octane molecules are adsorbed from the vapor phase at the interface. The adsorption is driven by the weak attraction due to the dispersion forces acting between the water molecules and the methyl and methylene groups of the octanes. This weak attraction is, however, amplified by the fact that it is added up for the CH2 and CH3 groups belonging to the same molecule. Consistently, the n-octane molecules located closest to the aqueous phase are found to prefer all-trans conformation and parallel alignment with the plane of the interface. On the other hand, entropic effects become more important among the molecules of the outer part of the adsorption layer. Hence, the preferred orientation of these molecules is perpendicular to the interface, as they can be extended toward the less dense region of the apolar phase; and gauche dihedrals appear more frequently here than among the molecules located next to the aqueous phase.

  20. CIS-ZnS quantum dots for self-aligned liquid crystal molecules with superior electro-optic properties.

    PubMed

    Lee, Won-Kyu; Hwang, Seung Jun; Cho, Min-Jae; Park, Hong-Gyu; Han, Jin-Woo; Song, Seogjeong; Jang, Jong Hyun; Seo, Dae-Shik

    2013-01-01

    We demonstrate self-aligned and high-performance liquid crystal (LC) systems doped with 1-dimensional (1D) chain-like clusters of CuInS(2) (CIS)-ZnS core-shell quantum dots (QDs). By changing the cell fabrication method of the LC-QD composites, we can selectively control the orientation of the LC molecules between the homogeneous and homeotropic states without conventional LC alignment layers. The homeotropic alignment of LCs was achieved by random dropcasting and the homogeneous alignment was performed using a capillary injection of LC-QDs due to the random or linear diffusion of QD clusters into ITO defects. The electrically compensated bend (ECB)- and vertically aligned (VA) mode LC displays (LCDs) containing our LC-QD composite both showed superior electro-optic (EO) properties. A 37.1% reduction in the threshold voltage (V(th)) and a 36.6% decrease in the response time were observed for ECB mode LCDs, and a 47.0% reduction in the V(th) and a 38.3% decrease in the response time were observed for VA mode LCDs, meaning that the proposed LC-QD composites have a great potential for the production of advanced flexible LCDs. PMID:23142966

  1. Highly sensitive silicon nanowire biosensor with novel liquid gate control for detection of specific single-stranded DNA molecules.

    PubMed

    Adam, Tijjani; Hashim, U

    2015-05-15

    The study demonstrates the development of a liquid-based gate-control silicon nanowire biosensor for detection of specific single-stranded DNA (ssDNA) molecules. The sensor was fabricated using conventional photolithography coupled with an inductively coupled plasma dry etching process. Prior to the application of DNA to the device, its linear response to pH was confirmed by serial dilution from pH 2 to pH 14. Then, the sensor surface was silanized and directly aminated with (3-aminopropyl) triethoxysilane to create a molecular binding chemistry for biofunctionalization. The resulting Si‒O‒Si‒ components were functionalized with receptor ssDNA, which interacted with the targeted ssDNA to create a field across the silicon nanowire and increase the current. The sensor shows selectivity for the target ssDNA in a linear range from target ssDNA concentrations of 100 pM to 25 nM. With its excellent detection capabilities, this sensor platform is promising for detection of specific biomarkers and other targeted proteins. PMID:25453738

  2. Structural and atoms-in-molecules analysis of hydrogen-bond network around nitroxides in liquid water.

    PubMed

    Houriez, Céline; Masella, Michel; Ferré, Nicolas

    2010-09-28

    In this study, we investigated the hydrogen-bond network patterns involving the NO moieties of five small nitroxides in liquid water by analyzing nanosecond scale molecular dynamics trajectories. To this end, we implemented two types of hydrogen-bond definitions, based on electronic structure, using Bader's atoms-in-molecules analysis and based on geometric criteria. In each definition framework, the nitroxide/water hydrogen-bond networks appear very variable from a nitroxide to another. Moreover, each definition clearly leads to a different picture of nitroxide hydration. For instance, the electronic structure-based definition predicts a number of hydrogen bonds around the nitroxide NO moiety usually larger than geometric structure-based ones. One particularly interesting result is that the strength of a nitroxide/water hydrogen bond does not depend on its linearity, leading us to question the relevance of geometric definition based on angular cutoffs to study this type of hydrogen bond. Moreover, none of the hydrogen-bond definitions we consider in the present study is able to quantitatively correlate the strength of nitroxide/water hydrogen-bond networks with the aqueous nitroxide spin properties. This clearly exhibits that the hydrogen-bonding concept is not reliable enough to draw quantitative conclusions concerning such properties. PMID:20886951

  3. Structural and atoms-in-molecules analysis of hydrogen-bond network around nitroxides in liquid water

    NASA Astrophysics Data System (ADS)

    Houriez, Céline; Masella, Michel; Ferré, Nicolas

    2010-09-01

    In this study, we investigated the hydrogen-bond network patterns involving the NO moieties of five small nitroxides in liquid water by analyzing nanosecond scale molecular dynamics trajectories. To this end, we implemented two types of hydrogen-bond definitions, based on electronic structure, using Bader's atoms-in-molecules analysis and based on geometric criteria. In each definition framework, the nitroxide/water hydrogen-bond networks appear very variable from a nitroxide to another. Moreover, each definition clearly leads to a different picture of nitroxide hydration. For instance, the electronic structure-based definition predicts a number of hydrogen bonds around the nitroxide NO moiety usually larger than geometric structure-based ones. One particularly interesting result is that the strength of a nitroxide/water hydrogen bond does not depend on its linearity, leading us to question the relevance of geometric definition based on angular cutoffs to study this type of hydrogen bond. Moreover, none of the hydrogen-bond definitions we consider in the present study is able to quantitatively correlate the strength of nitroxide/water hydrogen-bond networks with the aqueous nitroxide spin properties. This clearly exhibits that the hydrogen-bonding concept is not reliable enough to draw quantitative conclusions concerning such properties.

  4. Structure and energetics of model amphiphilic molecules at the water liquid-vapor interface - A molecular dynamics study

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Benjamin, Ilan

    1993-01-01

    A molecular dynamics study of adsorption of p-n-pentylphenol at infinite dilution at the water liquid-vapor interface is reported. The calculated free energy of adsorption is -8.8 +/- 0.7 kcal/mol, in good agreement with the experimental value of -7.3 kcal/mol. The transition between the interfacial region and the bulk solution is sharp and well-defined by energetic, conformational, and orientational criteria. At the water surface, the phenol head group is mostly immersed in aqueous solvent. The most frequent orientation of the hydrocarbon tail is parallel to the interface, due to dispersion interactions with the water surface. This arrangement of the phenol ring and the alkyl chain requires that the chain exhibits a kink. As the polar head group is being moved into the solvent, the chain length increases and the tail becomes increasingly aligned toward the surface normal, such that the nonpolar part of the molecule exposed to water is minimized. The same effect was achieved when phenol was replaced by a more polar head group, phenolate.

  5. Polymorphism of cis-1,4-cyclohexanediol, a new plastic crystal former. Considerations on isomeric cyclohexanediols plastic crystal forming abilities

    NASA Astrophysics Data System (ADS)

    Bebiano, Suse V. S.; Rosado, Mário T. S.; Castro, Ricardo A. E.; Ramos Silva, M.; Canotilho, João; Maria, Teresa M. R.; Eusébio, M. Ermelinda S.

    2014-12-01

    In this work an investigation on the polymorphism of cis-1,4-cyclohexanediol has been undertaken with emphasis on solid forms obtained in heating/cooling cycles, performed between 0 °C and 115 °C. A multidisciplinary investigation using differential scanning calorimetry, polarized light thermal microscopy and X-ray diffraction analysis was performed. A crystalline structure of the title compound was solved for the first time: an anisotropic solid phase, polymorph II, which gives rise on heating to a plastic crystalline phase, polymorph I, at T = (101.1 ± 0.2) °C, which melts at T = (108.5 ± 0.2) °C. A complex thermal behavior is observed in cooling/heating cycles performed on the molten compound, with evidence of the existence of other polymorphic forms (another ordered one, form III and form IV, tentatively assigned as plastic crystal). A comparative analysis of the crystalline structures of cis-1,4-cyclohexanediol, cis-1,2-cyclohexanediol, both plastic crystal formers, and of trans-1,4-cyclohexanediol, trans-(1S,2S)-cyclohexanediol, which do not present this mesophase, is performed by Hirshfeld surface analysis. Some similarities could be found between the plastic crystal formers which contrast with the results for the trans-isomers, namely in what concerns fingerprint plots (with much higher anisotropy for the latter), asphericity values (quite similar for the plastic crystalline formers with higher values found for the trans-isomers). It is also worth noting that in cis-1,2- and cis-1,4-cyclohexanediol, the H-bond contacts are confined in one side of the Hirshfeld surface, with the apolar segments of the molecule in the opposite side of the surface. This is also observed for trans-(1S,2S)-cyclohexanediol, but for this non-plastic crystal former, close C-H⋯H-C contacts are identified. For this class of compounds Hirshfeld surface analysis gives significant clues for their different plastic crystal forming abilities.

  6. Packing Interface Energetics in Different Crystal Forms of the λ Cro Dimer

    PubMed Central

    Ahlstrom, Logan S.; Miyashita, Osamu

    2014-01-01

    Variation among crystal structures of the λ Cro dimer highlights conformational flexibility. The structures range from a wild type closed to a mutant fully open conformation, but it is unclear if each represents a stable solution state or if one may be the result of crystal packing. Here we use molecular dynamics (MD) simulation to investigate the energetics of crystal packing interfaces and the influence of site-directed mutagenesis on them, in order to examine the effect of crystal packing on wild type and mutant Cro dimer conformation. Replica exchange MD of mutant Cro in solution shows that the observed conformational differences between the wild type and mutant protein are not the direct consequence of mutation. Instead, simulation of Cro in different crystal environments reveals that mutation affects the stability of crystal forms. Molecular Mechanics Poisson-Boltzmann Surface Area binding energy calculations reveal the detailed energetics of packing interfaces. Packing interfaces can have diverse properties in strength, energetic components, and some are stronger than the biological dimer interface. Further analysis shows that mutation can strengthen packing interfaces by as much as ~5 kcal/mol in either crystal environment. Thus, in the case of Cro, mutation provides an additional energetic contribution during crystal formation that may stabilize a fully open higher energy state. Moreover, the effect of mutation in the lattice can extend to packing interfaces not involving mutation sites. Our results provide insight into possible models for the effect of crystallization on Cro conformational dynamics and emphasize careful consideration of protein crystal structures. PMID:24218107

  7. Electro-optic response of the anticlinic, antiferroelectric liquid-crystal phase of a biaxial bent-core molecule with tilt angle near 45∘.

    PubMed

    Nakata, Michi; Chen, Dong; Shao, Renfan; Korblova, Eva; Maclennan, Joseph E; Walba, David M; Clark, Noel A

    2012-03-01

    We describe the unusual electro-optic response of a biaxial bent-core liquid crystal molecule that exhibits an anticlinic, antiferroelectric smectic phase (Sm-C(A)P(A)) with a molecular tilt angle close to 45°. In the ground state, the sample shows very low birefringence. A weak applied electric field distorts the antiferroelectric ground state, inducing a small azimuthal reorientation of the molecules on the tilt cone. This results in only a modest increase in the birefringence but an anomalously large (∼40°) analog rotation of the extinction direction. This unusual electro-optic response is shown to be a consequence of the molecular biaxiality. PMID:22587111

  8. Distance fluctuation of a single molecule in Lennard-Jones liquid based on generalized Langevin equation and mode coupling theory

    NASA Astrophysics Data System (ADS)

    Li, Ping; Dong, Yunhong; Zhao, Nanrong; Hou, Zhonghuai

    2014-04-01

    Distance fluctuation of a single molecule, modeled as an idealized bead-spring chain, dissolved in a Lennard-Jones liquid is studied by using a multidimensional generalized Langevin equation, where the friction kernel ζ(t) is calculated from the kinetic mode coupling theory (MCT). Temporal behavior of the distance autocorrelation function shows three typical regimes of time dependence, starting with a constant, followed by a power law of t-α, and finally an exponential decay. Particular attentions are paid to the time span of the power law regime, which corresponds to anomalous subdiffusion behavior, and the MCT framework enables us to investigate thoroughly how this regime depends on microscopic details such as the bead-to-solvent mass ratio MR, chain spring frequency ω, and the chain length N. Interestingly, the exponent α is robust to be 1/2 against the change of these parameters, although the friction kernel ζ(t) shows nontrivial dependence on time. In addition, we find that the starting time of the power-law region t1 scales with Γ-1, with Γ = 4ω2/ζ0 where ζ0 is the zero-frequency friction which decreases rapidly with increasing bead mass. On the other hand, the ending time t2 is not sensitive to varying ω or ζ0, but it increases with N rapidly before it reaches a constant for N larger than some threshold value. Our work may provide a unified strategy starting from the microscopic level to understand the anomalous subdiffusive behavior regarding large scale conformational change of polymers or proteins.

  9. Calculation of the Standard Molal Thermodynamic Properties of Crystalline, Liquid, and Gas Organic Molecules at High Temperatures and Pressures

    NASA Astrophysics Data System (ADS)

    Helgeson, Harold C.; Owens, Christine E.; Knox, Annette M.; Richard, Laurent

    1998-03-01

    Calculation of the thermodynamic properties of organic solids, liquids, and gases at high temperatures and pressures is a requisite for characterizing hydrothermal metastable equilibrium states involving these species and quantifying the chemical affinities of irreversible reactions of organic molecules in natural gas, crude oil, kerogen, and coal with minerals and organic, inorganic, and biomolecular aqueous species in interstitial waters in sedimentary basins. To facilitate calculations of this kind, coefficients for the Parameters From Group Contributions (PFGC) equation of state have been compiled for a variety of groups in organic liquids and gases. In addition, molecular weights, critical temperatures and pressures, densities at 25°C and 1 bar, transition, melting, and boiling temperatures ( Tt,Pr, Tm,Pr, and Tv,Pr, respectively) and standard molal enthalpies of transition (Δ H° t,Pr), melting (Δ H° m,Pr), and vaporization (Δ H° v,Pr) of organic species at 1 bar ( Pr) have been tabulated, together with an internally consistent and comprehensive set of standard molal Gibbs free energies and enthalpies of formation from the elements in their stable state at 298.15 K ( Tr) and Pr (Δ G° f and Δ H° f, respectively). The critical compilation also includes standard molal entropies ( S°) and volumes ( V°) at Tr and Pr, and standard molal heat capacity power function coefficients to compute the standard molal thermodynamic properties of organic solids, liquids, and gases as a function of temperature at 1 bar. These properties and coefficients have been tabulated for more than 500 crystalline solids, liquids, and gases, and those for many more can be computed from the equations of state group additivity algorithms. The crystalline species correspond to normal alkanes (C nH 2( n+1) ) with carbon numbers ( n, which is equal to the number of moles of carbon atoms in one mole of the species) ranging from 5 to 100, and 23 amino acids including glycine (C 2H 5NO

  10. Liquid crystal catalytic surfactant films for decomposing and sensing pollutants by electrolysis

    SciTech Connect

    Rusling, J.F.; Howe, D.J.; Nassar, A.E.

    1993-12-31

    Living organisms utilize protein biocatalysts incorporated in lipid bilayer membranes. Some synthetic lipid-like surfactant molecules can be self assembled into bilayer structures resembling biomembranes. Films composed of stacks of bilayers were prepared by casting solutions of insoluble surfactants onto solid electrodes. Catalysts were incorporated either after or before casting. In their liquid crystal forms, films containing metal phthalocyanine tetrasulfonates or the redox protein myoglobin were excellent, stable electrochemical catalysts for dehalogenation of pollutants such as trichloracetic acid and ethylene dibromide. Electrons are transported to reactions sites via the incorporated catalysts, and the films also preconcentrate the organohalides to enhance reaction rates. Characterization and applications of these films will be discussed.

  11. Two-State or Non-Two-State? An Excess Spectroscopy-based Approach to Differentiate the Existing Forms of Molecules in Liquids Mixtures

    PubMed Central

    Zhou, Yu; Zheng, Yan-Zhen; Sun, Hai-Yuan; Deng, Geng; Yu, Zhi-Wu

    2015-01-01

    Characterization/identification of the clusters/associates in liquids has long been a challenging topic. In this paper, we report a method to identify molecules with two different existing forms in a binary liquid solution. In this so-called two-state situation, the excess infrared spectra of a vibration mode of the respective molecule will show identical band shape if the other component is transparent in the region. More conveniently, the positions of the positive peak, negative peak, and zero-value will be seen to be fixed with varying compositions of the binary system. In the case of non-two-state mixtures, for example the mere solvation of solute by solvent, those positions will be variable. The conclusions are supported/demonstrated by computational simulation and experiments on two binary systems, D2O−H2O and C6F5I−cyclo-C6H12. PMID:26542641

  12. Crystal form control and particle size control of RG3487, a nicotinic α7 receptor partial agonist.

    PubMed

    Kuang, Shanming; Zhang, Pingsheng; Dong, Eric Z; Jennings, Geremia; Zhao, Baoshu; Pierce, Michael

    2016-07-11

    This paper describes solid form control and particle size control of RG3487, a nicotinic receptor partial agonist. Four crystal forms were identified by polymorph screen under ∼100 varying conditions. Form A and Form B are anhydrates, while Forms C and D are solvates. Forms A, which is enantiotropically related to Form B, is the more thermodynamically stable form under ambient conditions and the desired form selected for clinical development. The crystal form control of Form A was achieved by crystallization solvent selection which consistently produced the desired form. Several process parameters impacting particle size of Form A in the final crystallization step were identified and investigated through both online and offline particle size measurement. The investigation results were utilized to control crystallization processes which successfully produced Form A with different particle size in 500g scale. PMID:27167333

  13. Stabilization of He2(A(sup 3)Sigma(sub u)(+)) molecules in liquid helium by optical pumping for vacuum UV laser

    NASA Technical Reports Server (NTRS)

    Zmuidzinas, J. S. (Inventor)

    1978-01-01

    A technique is disclosed for achieving large populations of metastable spin-aligned He2(a 3 Sigma u +) molecules in superfluid helium to obtain lasing in the vacuum ultraviolet wavelength regime around 0.0800 micron m by electronically exciting liquid (superfluid) helium with a comparatively low-current electron beam and spin aligning the metastable molecules by means of optical pumping with a modestly-powered (100mW) circularly-polarized continuous wave laser operating at, for example, 0.9096 or 0.4650 micron m. Once a high concentration of spin-aligned He2 (a 3 Sigma u +) is achieved with lifetimes of a few milliseconds, a strong microwave signal destroys the spin alignment and induces a quick collisional transition of He2 (a 3 Sigma u +) molecules to the a 1 Sigma u + state and thereby a lasing transition to the X 1 Sigma g + state.

  14. Optimization of the GAFF force field to describe liquid crystal molecules: the path to a dramatic improvement in transition temperature predictions.

    PubMed

    Boyd, Nicola Jane; Wilson, Mark R

    2015-10-14

    The physical properties and phase transitions of thermotropic liquid crystals are highly sensitive to small changes in chemical structure. However, these changes are challenging to model, as both the phase diagram and mesophase properties obtained from fully atomistic simulations are strongly dependent on the force field model employed, and the current generation of chemical force fields has not proved accurate enough to provide reliable predictions of transition temperatures for many liquid crystals. This paper presents a strategy for improving the nematic clearing point, TNI, in atomistic simulations, by systematic optimization of the General Amber Force Field (GAFF) for key mesogenic fragments. We show that with careful optimization of the parameters describing a series of liquid crystal fragment molecules, it is possible to transfer these parameters to larger liquid crystal molecules and make accurate predictions for nematic mesophase formation. This new force field, GAFF-LCFF, is used to predict the nematic-isotropic clearing point to within 5 °C for the nematogen 1,3-benzenedicarboxylic acid,1,3-bis(4-butylphenyl)ester, an improvement of 60 °C over the standard GAFF force field. PMID:26343382

  15. Crystallization and preliminary X-ray diffraction analysis of Hypocrea jecorina Cel7A in two new crystal forms

    PubMed Central

    Bodenheimer, Annette M.; Cuneo, Matthew J.; Swartz, Paul D.; He, Junhong; O’Neill, Hugh M.; Myles, Dean A. A.; Evans, Barbara R.; Meilleur, Flora

    2014-01-01

    Cel7A (previously known as cellobiohydrolase I) from Hypocrea jecorina was crystallized in two crystalline forms, neither of which have been previously reported. Both forms co-crystallize under the same crystallization conditions. The first crystal form belonged to space group C2, with unit-cell parameters a = 152.5, b = 44.9, c = 57.6 Å, β = 101.2°, and diffracted X-rays to 1.5 Å resolution. The second crystal form belonged to space group P6322, with unit-cell parameters a = b ≃ 155, c ≃ 138 Å, and diffracted X-rays to 2.5 Å resolution. The crystals were obtained using full-length Cel7A, which consists of a large 434-residue N-terminal catalytic domain capable of cleaving cellulose, a 27-residue flexible linker and a small 36-residue C-terminal carbohydrate-binding module (CBM). However, a preliminary analysis of the electron-density maps suggests that the linker and CBM are disordered in both crystal forms. Complete refinement and structure analysis are currently in progress. PMID:24915091

  16. Compared organization of the molecules of NaDEHP and AOT: Determination of the microscopic organization of the sodium bis(2-ethylhexyl)phosphate molecule in the solid state in the reversed hexagonal liquid crystal state

    NASA Astrophysics Data System (ADS)

    Lovera, J.; Lovera, P.; Gregoire, P.

    1988-11-01

    A method to determine the average shape of some molecules is described and applied to sodium bis(2-ethylhexyl)phosphate (NaDEHP) and sodium bis(2-ethylhexyl)sulfosuccinate (AOT). The volumes and lengths of the polar and apolar parts of these molecules are obtained from specific gravity measurements and from the lattice parameters of the hexagonal and lamellar liquid crystal structures. The shape of both molecules is described as a prism. The cross section of the elementary rod in the hexagonal structure intercepts respectively 2.5 and 6 molecules. The noninteger value obtained for NaDEHP is explained by a disorder inside the rod, and the mean value of 6 obtained for AOT is related neither to the symmetry of the lattice nor to the hexagonal average shape of the rod. The parameter limiting the height of the prism is the size of the phosphate coordinance tetrahedron, in the case of NaDEHP, and the length of the succinate chain, in the case of AOT.

  17. Cloning, purification, crystallization and preliminary X-ray analysis of the catalytic domain of human receptor-like protein tyrosine phosphatase [gamma] in three different crystal forms

    SciTech Connect

    Kish, Kevin; McDonnell, Patricia A.; Goldfarb, Valentina; Gao, Mian; Metzler, William J.; Langley, David R.; Bryson, James W.; Kiefer, Susan E.; Carpenter, Brian; Kostich, Walter A.; Westphal, Ryan S.; Sheriff, Steven

    2013-03-07

    Protein tyrosine phosphatase {gamma} is a membrane-bound receptor and is designated RPTP{gamma}. RPTP{gamma} and two mutants, RPTP{gamma}(V948I, S970T) and RPTP{gamma}(C858S, S970T), were recombinantly expressed and purified for X-ray crystallographic studies. The purified enzymes were crystallized using the hanging-drop vapor-diffusion method. Crystallographic data were obtained from several different crystal forms in the absence and the presence of inhibitor. In this paper, a description is given of how three different crystal forms were obtained that were used with various ligands. An orthorhombic crystal form and a trigonal crystal form were obtained both with and without ligand, and a monoclinic crystal form was only obtained in the presence of a particularly elaborated inhibitor.

  18. Influence of Ionic Liquids on Thermodynamics of Small Molecule-DNA Interaction: The Binding of Ethidium Bromide to Calf Thymus DNA.

    PubMed

    Mishra, Arpit; Ekka, Mary Krishna; Maiti, Souvik

    2016-03-17

    Ionic liquids (ILs) are salts with poor ionic coordination, resultantly remaining in liquid state below 100 °C and some may retain liquid state even at room temperature. ILs are known to provide a conducive environment for many biological enzymatic reactions, but their interaction with biomacromolecules are poorly understood. In the present study, we investigate the effect of various ionic liquids on DNA-small molecule interaction using calf thymus DNA (ctDNA)-ethidium bromide (EB) as a model system. The effect of various ionic liquids on these interactions is studied by an array of techniques such as circular dichroism (CD), UV melting, fluorescence exclusion and isothermal titration calorimetry. Interestingly, we observed that presence of IL increased the stability of ctDNA without altering its structure. The binding affinities Kbs for EB binding to ctDNA in the presence of 300 mM ILs are about half order of magnitude smaller than the Kbs in absence of ILs and correspond to a less favorable free energy. We noted that, when adjusted to corresponding buffer condition, the unfavorable shift in ΔG of ctDNA-EB interaction is attributed to decreased entropy in the case of ILs, whereas the same effect by NaCl was due to increased enthalpy. PMID:26907668

  19. Self-organization processes and topological defects in nanolayers in a nematic liquid crystal

    SciTech Connect

    Chuvyrov, A. N.; Girfanova, F. M. Mal'tsev, I. S.

    2008-05-15

    Atomic force microscopy is used to study the self-organization processes that occur during the formation of topological defects in nanomolecular layers in a nematic liquid crystal with the homeotropic orientation of its molecules with respect to the substrate. In this case, a smectic monolayer with a thickness of one molecule length (about 2.2 nm) forms on the substrate, and a nanomolecular layer of a nematic liquid crystal forms above this monolayer. In such virtually two-dimensional layers, numerous different nanoclusters, namely, hut structures, pyramids, raft structures with symmetry C{sub nm} (where n = 2, 4, 5, 6, 7, ?, {infinity}), cones, and nanopools, form [1]. They have a regular shape close to the geometry of solid crystals. Modulated linear structures and topological point defects appear spontaneously in the nanopools and raft structures.

  20. Continuous Flow Liquid Microjunction Surface Sampling Probe Connected On-line with HPLC/MS for Spatially Resolved Analysis of Small Molecules and Proteins

    SciTech Connect

    Van Berkel, Gary J; Kertesz, Vilmos

    2013-01-01

    RATIONALE: A continuous flow liquid microjunction surface sampling probe extracts soluble material from surfaces for direct ionization and detection by MS. Demonstrated here is the on-line coupling of such a probe with HPLC/MS enabling extraction, separation and detection of small molecules and proteins from surfaces in a spatially resolved (~0.5 mm diameter spots) manner. Methods: A continuous flow liquid microjunction surface sampling probe was connected to a 6-port, 2-position valve for extract collection and injection to an HPLC column. A QTRAP 5500 hybrid triple quadrupole linear ion trap equipped with a Turbo V ion source operated in positive ESI mode was used for all experiments. System operation was tested with extraction, separation and detection of propranolol and associated metabolites from drug dosed tissues and proteins from dried sheep blood spots on paper. Results: Confirmed in the tissue were the parent drug and two different hydroxypropranolol glucuronides. The mass spectrometric response for these compounds from different locations in the liver showed an increase with increasing extraction time (5, 20 and 40 s extractions). For on-line separation and detection/identification of extracted proteins from dried sheep blood spots, two major protein peaks dominated the chromatogram and could be correlated with the expected masses for the hemoglobin and chains. Conclusions: Spatially resolved sampling, separation, and detection of small molecules and proteins from surfaces can be accomplished using a continuous flow liquid microjunction surface sampling probe coupled on-line with HPLC/MS detection.

  1. Purification, crystallization and preliminary crystallographic studies of haemoglobin from mongoose (Helogale parvula) in two different crystal forms induced by pH variation.

    PubMed

    Mohamed Abubakkar, M; Saraboji, K; Ponnuswamy, M N

    2013-02-01

    Haemoglobin (Hb) is a respiratory pigment; it is a tetrameric protein that ferries oxygen from the lungs to tissues and transports carbon dioxide on the return journey. The oxygen affinity of haemoglobin is regulated by the concentration of oxygen surrounding it and several efforts have revealed the shapes of Hb in different states and with different functions. However, study of the molecular basis of Hbs from low-oxygen-affinity species is critically needed in order to increase the understanding of the mechanism behind oxygen adaptation. The present study reports the preliminary crystallographic study of low-oxygen-affinity haemoglobin from mongoose, a burrowing mammal. Haemoglobin from mongoose was purified by anion-exchange chromatography, crystallized using the hanging-drop vapour-diffusion method and diffraction data sets were collected from monoclinic (2.3 Å resolution) and orthorhombic (2.9 Å resolution) crystal forms obtained by pH variation. The monoclinic and orthorhombic asymmetric units contained half and a whole biological molecule, respectively. PMID:23385751

  2. A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity

    PubMed Central

    Breustedt, Daniel A.; Chatwell, Lorenz; Skerra, Arne

    2009-01-01

    Tear lipocalin (TLC) with the bound artificial ligand 1,4-butanediol has been crystallized in space group P21 with four protein molecules in the asymmetric unit and its X-ray structure has been solved at 2.6 Å resolution. TLC is a member of the lipocalin family that binds ligands with diverse chemical structures, such as fatty acids, phospholipids and cholesterol as well as microbial siderophores and the antibiotic rifampin. Previous X-ray structural analysis of apo TLC crystallized in space group C2 revealed a rather large bifurcated ligand pocket and a partially disordered loop region at the entrace to the cavity. Analysis of the P21 crystal form uncovered major conformational changes (i) in β-strands B, C and D, (ii) in loops 1, 2 and 4 at the open end of the β-­barrel and (iii) in the extended C-terminal segment, which is attached to the β-­barrel via a disulfide bridge. The structural comparison indicates high conformational plasticity of the loop region as well as of deeper parts of the ligand pocket, thus allowing adaptation to ligands that differ vastly in size and shape. This illustrates a mechanism for promiscuity in ligand recognition which may also be relevant for some other physiologically important members of the lipocalin protein family. PMID:19770509

  3. How to make big molecules fly out of liquid water: applications, features and physics of laser assisted liquid phase dispersion mass spectrometry.

    PubMed

    Charvat, Ales; Abel, Bernd

    2007-07-14

    Applications, features, and mechanistic details of laser assisted liquid phase dispersion mass spectrometry are highlighted and discussed. It has been used in the past to directly isolate charged molecular aggregates from the liquid phase and to determine their molecular weight employing sensitive time-of-flight mass spectrometry. The liquid matrix in this MALDI (matrix assisted laser desorption and ionization) type approach consists of a 10 microm diameter free liquid filament in vacuum (or a free droplet) which is excited with a focused infrared laser pulse tuned to match the absorption frequency of the OH-stretch vibration of bulk water near 2.8 microm. Due to these features we will refer to the approach as free liquid matrix assisted laser dispersion of ions or ionic aggregates (IR-FL-MALDI), although also LILBID ("laser induced liquid beam (bead) desorption and ionization") has been proposed early as a descriptive acronym for the technique and may be used alternatively. Low-charge-state macromolecular adducts are isolated in the gas phase from solution via a yet poorly characterized mechanism which sensitively depends upon the laser intensity and wavelength, and after the gentle liquid-to-vacuum transfer the aggregates are analyzed via time-of-flight (TOF) mass spectrometry (MS). Possible mechanisms for the isolation and charging of biomolecules directly from liquid solution are discussed in the present contribution. Recent technical advances such as minimizing the sample consumption, strategies for high throughput mass spectrometry, and coupling of liquid beam MS with HPLC will be highlighted as well. An interesting feature of IR-FL-MALDI is what we call the linear response, i.e., a surprising linearity of the gas phase mass signal on the solution concentration over many orders of magnitude for a large number of biomolecular systems as well as ions. Due to these features the approach may be regarded as a true solution probing spectroscopy, which enables

  4. Rapid Discrimination of Polymorphic Crystal Forms by Nonlinear Optical Stokes Ellipsometric Microscopy.

    PubMed

    Schmitt, Paul D; DeWalt, Emma L; Dow, Ximeng Y; Simpson, Garth J

    2016-06-01

    The use of nonlinear optical Stokes ellipsometric (NOSE) microscopy for rapid discrimination of two polymorphic forms of the small molecule d-mannitol is presented. Fast (8 MHz) polarization modulated beam-scanning microscopy and a recently developed iterative, nonlinear least-squares fitting algorithm were combined to allow discrimination of orthorhombic and monoclinic crystal structures of d-mannitol with data acquisition times of <7 s per field of view with a signal-to-noise ratio (SNR) of ∼300. Discrimination between polymorphic forms within the 99.99% confidence interval was achieved by standard statistical tests of the recovered probability density functions for the measured observables following two class linear discriminant analysis. These measurements target bottlenecks in small-volume, high-throughput solid form screening experiments for polymorph discovery in the development of emerging active pharmaceutical ingredients. PMID:27092390

  5. Liquid self-diffusion of H2O and DMF molecules in Co-MOF-74: molecular dynamics simulations and dielectric spectroscopy studies.

    PubMed

    Bermúdez-García, J M; Vicent-Luna, J M; Yáñez-Vilar, S; Hamad, S; Sánchez-Andújar, M; Castro-García, S; Calero, S; Señarís-Rodríguez, M A

    2016-07-20

    In this work we use molecular dynamics simulations to study the diffusion of N,N-dimethylformamide (DMF) and H2O as a function of temperature within the well-known metal-organic framework Co2(dobdc)·[G] (G = 2DMF·1H2O), also known as Co-MOF-74. The molecular dynamics simulations show that the diffusivity of guest molecules, which is almost negligible at low temperatures (T < 200 K), increases in the range of 200 < T (K) < 400 up to 3 and 4 orders of magnitude for DMF and H2O, respectively. This molecular diffusion can be easily detected by dielectric spectroscopy as it gives rise to extrinsic interfacial polarization effects that result in an apparent "colossal" dielectric constant at room temperature, εr' ∼ 42 000 (T = 300 K, ν = 10 Hz). Furthermore, the measured dielectric constant exhibits a thermal dependence similar to that of the diffusion coefficient, revealing the parallelism of the dielectric response and the molecular diffusion as a function of temperature. These results highlight: (a) the great utility of the fast and non-destructive dielectric and impedance spectroscopy techniques for the study and detection of the molecular transport of small polar molecules within porous metal-organic frameworks and related materials; (b) the peculiarity and uniqueness of MOF materials with "medium" size nanopores containing guest molecules as they are solid materials in which the guest molecules display a liquid state-like behaviour close to room temperature; and PMID:27353249

  6. Study of the translational diffusion of the benzophenone ketyl radical in comparison with stable molecules in room temperature ionic liquids by transient grating spectroscopy

    SciTech Connect

    Nishiyama, Y.; Fukuda, M.; Terazima, M.; Kimura, Y.

    2008-04-28

    Transient grating (TG) spectroscopy has been applied to the photoinduced hydrogen-abstraction reaction of benzophenone (BP) in various kinds of room temperature ionic liquids (RTILs). After the photoexcitation of BP in RTILs, the formation of a benzophenone ketyl radical (BPK) was confirmed by the transient absorption method, and the TG signal was analyzed to determine the diffusion coefficients of BPK and BP. For comparison, diffusion coefficients of carbon monoxide (CO), diphenylacetylene (DPA), and diphenylcyclopropenone (DPCP) in various RTILs were determined by the TG method using the photodissociation reaction of DPCP. While the diffusion coefficients of the stable molecules BP, DPA, and DPCP were always larger than those predicted by the Stokes-Einstein (SE) relation in RTILs, that of BPK was much smaller than those of the stable molecules and relatively close to that predicted by the SE relation in all solvents. For the smallest molecule CO, the deviation from the SE relation was evident. The diffusion coefficients of stable molecules are better represented by a power law of the inverse of the viscosity when the exponent was less than unity. The ratios of the diffusion coefficient of BP to that of BPK were larger in RTILs (2.7-4.0) than those (1.4-2.3) in conventional organic solvents. The slow diffusion of BPK in RTILs was discussed in terms of the fluctuation of the local electric field produced by the surrounding solvent ions.

  7. Structural Properties, Order-Disorder Phenomena, and Phase Stability of Orotic Acid Crystal Forms.

    PubMed

    Braun, Doris E; Nartowski, Karol P; Khimyak, Yaroslav Z; Morris, Kenneth R; Byrn, Stephen R; Griesser, Ulrich J

    2016-03-01

    Orotic acid (OTA) is reported to exist in the anhydrous (AH), monohydrate (Hy1), and dimethyl sulfoxide monosolvate (SDMSO) forms. In this study we investigate the (de)hydration/desolvation behavior, aiming at an understanding of the elusive structural features of anhydrous OTA by a combination of experimental and computational techniques, namely, thermal analytical methods, gravimetric moisture (de)sorption studies, water activity measurements, X-ray powder diffraction, spectroscopy (vibrational, solid-state NMR), crystal energy landscape, and chemical shift calculations. The Hy1 is a highly stable hydrate, which dissociates above 135 °C and loses only a small part of the water when stored over desiccants (25 °C) for more than one year. In Hy1, orotic acid and water molecules are linked by strong hydrogen bonds in nearly perfectly planar arranged stacked layers. The layers are spaced by 3.1 Å and not linked via hydrogen bonds. Upon dehydration the X-ray powder diffraction and solid-state NMR peaks become broader, indicating some disorder in the anhydrous form. The Hy1 stacking reflection (122) is maintained, suggesting that the OTA molecules are still arranged in stacked layers in the dehydration product. Desolvation of SDMSO, a nonlayer structure, results in the same AH phase as observed upon dehydrating Hy1. Depending on the desolvation conditions, different levels of order-disorder of layers present in anhydrous OTA are observed, which is also suggested by the computed low energy crystal structures. These structures provide models for stacking faults as intergrowth of different layers is possible. The variability in anhydrate crystals is of practical concern as it affects the moisture dependent stability of AH with respect to hydration. PMID:26741914

  8. Structural Properties, Order–Disorder Phenomena, and Phase Stability of Orotic Acid Crystal Forms

    PubMed Central

    2016-01-01

    Orotic acid (OTA) is reported to exist in the anhydrous (AH), monohydrate (Hy1), and dimethyl sulfoxide monosolvate (SDMSO) forms. In this study we investigate the (de)hydration/desolvation behavior, aiming at an understanding of the elusive structural features of anhydrous OTA by a combination of experimental and computational techniques, namely, thermal analytical methods, gravimetric moisture (de)sorption studies, water activity measurements, X-ray powder diffraction, spectroscopy (vibrational, solid-state NMR), crystal energy landscape, and chemical shift calculations. The Hy1 is a highly stable hydrate, which dissociates above 135 °C and loses only a small part of the water when stored over desiccants (25 °C) for more than one year. In Hy1, orotic acid and water molecules are linked by strong hydrogen bonds in nearly perfectly planar arranged stacked layers. The layers are spaced by 3.1 Å and not linked via hydrogen bonds. Upon dehydration the X-ray powder diffraction and solid-state NMR peaks become broader, indicating some disorder in the anhydrous form. The Hy1 stacking reflection (122) is maintained, suggesting that the OTA molecules are still arranged in stacked layers in the dehydration product. Desolvation of SDMSO, a nonlayer structure, results in the same AH phase as observed upon dehydrating Hy1. Depending on the desolvation conditions, different levels of order–disorder of layers present in anhydrous OTA are observed, which is also suggested by the computed low energy crystal structures. These structures provide models for stacking faults as intergrowth of different layers is possible. The variability in anhydrate crystals is of practical concern as it affects the moisture dependent stability of AH with respect to hydration. PMID:26741914

  9. Orientational order in liquids upon condensation in nanochannels: An optical birefringence study on rodlike and disclike molecules in monolithic mesoporous silica

    NASA Astrophysics Data System (ADS)

    Wolff, Matthias; Knorr, Klaus; Huber, Patrick; Kityk, Andriy V.

    2010-12-01

    We present high-resolution optical birefringence measurements upon sequential filling of an array of parallel-aligned nanochannels (14 nm mean diameter) with rodlike (acetonitrile) and disclike (hexafluorobenzene) molecules. We will demonstrate that such birefringence isotherms, when performed simultaneously with optically isotropic and index-matched counterparts (neopentane and hexafluoromethane), allow one to characterize the orientational state of the confined liquids with a high accuracy as a function of pore filling. The pore condensates are almost bulklike, optically isotropic liquids. For both anisotropic species we find, however, a weak orientational order (of a few percent at maximum) upon film condensation in the monolithic mesoporous membrane. It occurs upon formation of the second and third adsorbed layer, only, and vanishes gradually upon onset of capillary condensation. Presumably, it originates in the breaking of the full rotational symmetry of the interaction potential at the cylindrical, free liquid-vapor interface in the film-condensed state rather than at the silica-liquid interface. This conclusion is corroborated by comparisons of our experimental results with molecular-dynamics simulations reported in the literature.

  10. Laser-induced fluorescence of flowing samples as an approach to single-molecule detection in liquids

    SciTech Connect

    Dovichi, N.J.; Martin, J.C.; Jett, J.H.; Trkula, M.; Keller, R.A.

    1984-03-01

    A flow cytometer system was used to detect aqueous rhodamine 6G by laser-induced fluorescence. Best results were obtained with careful spectral and spatial filtering. At the detection limit, the probability of a rhodamine 6G molecule being present in the detector's probed volume of 11 pL is about 0.6 . With a flow rate of 0.42 ..mu..L/s, a detection limit of 8.9 x 10/sup -14/ M was obtained for a 1-s time constant. At the detection limit, 18 ag or 22,000 molecules of rhodamine 6G flowed through the probed volume during the signal integration period. Signal linearity extends over greater than 5 orders of magnitude limited only by saturation of the detection electronics at high concentration. The results presented here allow a projection to single-molecule detection with reasonable improvements to the apparatus. 25 references, 5 figures, 7 tables.

  11. The Formation of Oxygen-Containing Molecules in Liquid Water Environments on the Surface of Titan (Invited)

    NASA Astrophysics Data System (ADS)

    Neish, C.

    2010-12-01

    Saturn’s moon Titan represents a unique locale for studying prebiotic chemistry. Reactions occurring in its thick nitrogen - methane atmosphere produce a wide variety of organic molecules. Observations by the Voyager spacecraft found evidence for six gas-phase hydrocarbons and three nitriles, along with an enveloping haze layer shrouding the surface of the moon (Hanel et al., 1981; Kunde et al., 1981; Maguire et al., 1981). More recently, the INMS instrument on the Cassini spacecraft has found evidence for organic molecules up to its mass limit of 100 Da at altitudes as high as 1200 km (Waite et al., 2005; Vuitton et al. 2007). Laboratory experiments that simulate the reactions occurring in Titan’s atmosphere produce many of the same organic molecules observed by Voyager and Cassini, along with organic precipitates known as tholins. Tholins have the general formula CxHyNz and are spectrally similar to Titan’s haze (Khare et al., 1984). Though interesting from the point of view of organic chemistry, the molecules found in Titan’s atmosphere stop short of addressing questions related to the origins of life. Oxygen - a key element for most known biological molecules - is generally lacking in Titan’s atmosphere. The most abundant oxygenated molecule, CO, is present at only ~50 ppm (de Kok et al., 2007). However, if Titan’s atmospheric organic molecules mix with water found in cryovolcanic lavas or impact melts, they may react to produce oxygen-containing, prebiotic species. In this paper, I will show that reactions between Titan tholins and low temperature aqueous solutions produce a wide variety of oxygen-containing species. These reactions display first-order kinetic behaviour with half-lives between 0.4 to 7 days at 273 K (in water) and between 0.3 and 14 days at 253 K (in 13 wt. % ammonia-water). Tholin hydrolysis is thus very fast compared to the freezing timescales of impact melts and volcanic sites on Titan, which take hundreds to thousands of years

  12. Thermodynamic stability and structural properties of cluster crystals formed by amphiphilic dendrimers

    NASA Astrophysics Data System (ADS)

    Lenz, Dominic A.; Mladek, Bianca M.; Likos, Christos N.; Blaak, Ronald

    2016-05-01

    We pursue the goal of finding real-world examples of macromolecular aggregates that form cluster crystals, which have been predicted on the basis of coarse-grained, ultrasoft pair potentials belonging to a particular mathematical class [B. M. Mladek et al., Phys. Rev. Lett. 46, 045701 (2006)]. For this purpose, we examine in detail the phase behavior and structural properties of model amphiphilic dendrimers of the second generation by means of monomer-resolved computer simulations. On augmenting the density of these systems, a fluid comprised of clusters that contain several overlapping and penetrating macromolecules is spontaneously formed. Upon further compression of the system, a transition to multi-occupancy crystals takes place, the thermodynamic stability of which is demonstrated by means of free-energy calculations, and where the FCC is preferred over the BCC-phase. Contrary to predictions for coarse-grained theoretical models in which the particles interact exclusively by effective pair potentials, the internal degrees of freedom of these molecules cause the lattice constant to be density-dependent. Furthermore, the mechanical stability of monodisperse BCC and FCC cluster crystals is restricted to a bounded region in the plane of cluster occupation number versus density. The structural properties of the dendrimers in the dense crystals, including their overall sizes and the distribution of monomers are also thoroughly analyzed.

  13. Structure, Solubility and Stability of Orbifloxacin Crystal Forms: Hemihydrate versus Anhydrate.

    PubMed

    Santos, Olimpia Maria Martins; Freitas, Jennifer Tavares Jacon; Cazedey, Edith Cristina Laignier; de Araújo, Magali Benjamim; Doriguetto, Antonio Carlos

    2016-01-01

    Orbifloxacin (ORBI) is a widely used antimicrobial drug of the fluoroquinolone class. In the official pharmaceutical compendia the existence of polymorphism in this active pharmaceutical ingredient (API) is reported. No crystal structure has been reported for this API and as described in the literature, its solubility is very controversial. Considering that different solid forms of the same API may have different physicochemical properties, these different solubilities may have resulted from analyses inadvertently carried out on different polymorphs. The solubility is the most critical property because it can affect the bioavailability and may compromise the quality of a drug product. The crystalline structure of ORBI determined by SCXRD is reported here for the first time. The structural analysis reveals that the ORBI molecule is zwitterionic and hemihydrated. ORBI hemihydrated form was characterized by the following techniques: TG/DTA, FTIR-ATR, and PXRD. A second crystalline ORBI form is also reported: the ORBI anhydrous form was obtained by heating the hemihydrate. These ORBI solid forms were isomorphous, since no significant change in unit cell and space group symmetry were observed. The solid-state phase transformation between these forms is discussed and the equilibrium solubility data were examined in order to check the impact of the differences observed in their crystalline structures. PMID:27005603

  14. Thermodynamic stability and structural properties of cluster crystals formed by amphiphilic dendrimers.

    PubMed

    Lenz, Dominic A; Mladek, Bianca M; Likos, Christos N; Blaak, Ronald

    2016-05-28

    We pursue the goal of finding real-world examples of macromolecular aggregates that form cluster crystals, which have been predicted on the basis of coarse-grained, ultrasoft pair potentials belonging to a particular mathematical class [B. M. Mladek et al., Phys. Rev. Lett. 46, 045701 (2006)]. For this purpose, we examine in detail the phase behavior and structural properties of model amphiphilic dendrimers of the second generation by means of monomer-resolved computer simulations. On augmenting the density of these systems, a fluid comprised of clusters that contain several overlapping and penetrating macromolecules is spontaneously formed. Upon further compression of the system, a transition to multi-occupancy crystals takes place, the thermodynamic stability of which is demonstrated by means of free-energy calculations, and where the FCC is preferred over the BCC-phase. Contrary to predictions for coarse-grained theoretical models in which the particles interact exclusively by effective pair potentials, the internal degrees of freedom of these molecules cause the lattice constant to be density-dependent. Furthermore, the mechanical stability of monodisperse BCC and FCC cluster crystals is restricted to a bounded region in the plane of cluster occupation number versus density. The structural properties of the dendrimers in the dense crystals, including their overall sizes and the distribution of monomers are also thoroughly analyzed. PMID:27250325

  15. THERMALLY STABLE NANOCRYSTALLINE TIO2 PHOTOCATALYSTS SYNTHESIZED VIA SOL-GEL METHODS MODIFIED WITH IONIC LIQUID AND SURFACTANT MOLECULES

    EPA Science Inventory

    Recently, sol-gel methods employing ionic liquids (ILs) have shown significant implications for the synthesis of well-defined nanostructured inorganic materials. Herein, we synthesized nanocrystalline TiO2 particles via an alkoxide sol-gel method employing a water-immi...

  16. Structure of a high-resolution crystal form of human triosephosphate isomerase: improvement of crystals using the gel-tube method

    SciTech Connect

    Kinoshita, Takayoshi Maruki, Riyo; Warizaya, Masaichi; Nakajima, Hidenori; Nishimura, Shintaro

    2005-04-01

    A high-resolution structure of human triosephosphate isomerase was obtained from crystals improved by means of the gel-tube method. Crystals of human triosephosphate isomerase with two crystal morphologies were obtained using the normal vapour-diffusion technique with identical crystallization conditions. One had a disordered plate shape and the crystals were hollow (crystal form 1). As a result, this form was very fragile, diffracted to 2.8 Å resolution and had similar crystallographic parameters to those of the structure 1hti in the Protein Data Bank. The other had a fine needle shape (crystal form 2) and was formed more abundantly than crystal form 1, but was unsuitable for structure analysis. Since the normal vapour-diffusion method could not control the crystal morphology, gel-tube methods, both on earth and under microgravity, were applied for crystallization in order to control and improve the crystal quality. Whereas crystal form 1 was only slightly improved using this method, crystal form 2 was greatly improved and diffracted to 2.2 Å resolution. Crystal form 2 contained a homodimer in the asymmetric unit, which was biologically essential. Its overall structure was similar to that of 1hti except for the flexible loop, which was located at the active centre Lys13.

  17. Review of recent advances in the preparation of organic polymer monoliths for liquid chromatography of large molecules.

    PubMed

    Arrua, R Dario; Talebi, Mohammad; Causon, Tim J; Hilder, Emily F

    2012-08-13

    In recent years the use of monolithic polymers in separation science has greatly increased due to the advantages these materials present over particle-based stationary phases, such as their relative ease of preparation and good permeability. For these reasons, these materials present high potential as stationary phases for the separation and purification of large molecules such as proteins, peptides, nucleic acids and cells. An example of this is the wide range of commercial available polymer-based monolithic columns now present in the market. This review summarizes recent developments in the synthesis of monolithic polymers for separation science, such as the incorporation of nanostructures in the polymeric scaffold as well as the preparation of hybrid structures. The different methods used in the surface functionalization of monolithic columns are also reviewed. Finally, we critically discuss the recent applications of this column technology in the separation of large molecules under different chromatographic mode. PMID:22790694

  18. A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity

    SciTech Connect

    Breustedt, Daniel A.; Chatwell, Lorenz; Skerra, Arne

    2009-10-01

    The crystal structure of tear lipocalin determined in space group P2{sub 1} revealed large structural deviations from the previously solved X-ray structure in space group C2, especially in the loop region and adjoining parts of the β-barrel which give rise to the ligand-binding site. These findings illustrate a novel mechanism for promiscuity in ligand recognition by the lipocalin protein family. Tear lipocalin (TLC) with the bound artificial ligand 1,4-butanediol has been crystallized in space group P2{sub 1} with four protein molecules in the asymmetric unit and its X-ray structure has been solved at 2.6 Å resolution. TLC is a member of the lipocalin family that binds ligands with diverse chemical structures, such as fatty acids, phospholipids and cholesterol as well as microbial siderophores and the antibiotic rifampin. Previous X-ray structural analysis of apo TLC crystallized in space group C2 revealed a rather large bifurcated ligand pocket and a partially disordered loop region at the entrace to the cavity. Analysis of the P2{sub 1} crystal form uncovered major conformational changes (i) in β-strands B, C and D, (ii) in loops 1, 2 and 4 at the open end of the β-barrel and (iii) in the extended C-terminal segment, which is attached to the β-barrel via a disulfide bridge. The structural comparison indicates high conformational plasticity of the loop region as well as of deeper parts of the ligand pocket, thus allowing adaptation to ligands that differ vastly in size and shape. This illustrates a mechanism for promiscuity in ligand recognition which may also be relevant for some other physiologically important members of the lipocalin protein family.

  19. Application of liquid chromatography-tandem mass spectrometry in quantitative bioanalyses of organic molecules in aquatic environment and organisms.

    PubMed

    Bussy, Ugo; Li, Ke; Li, Weiming

    2016-05-01

    Analytical methods using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) for the simultaneous determination of metabolites or contaminants (or both) in various tissues of aquatic organisms and in the aquatic environment have received increasing attention in the last few years. This review discusses the findings relevant to such procedures published between 2005 and 2015. The aim is to evaluate the advantages, restrictions, and performances of the procedures from sample preparation to mass spectrometry measurement. To support these discussions, a general knowledge on LC-MS/MS is also provided. PMID:26996906

  20. A new extended diffusion model for rotational motion of symmetric-top molecules in the liquid phase

    NASA Astrophysics Data System (ADS)

    Lascombe, J.; Besnard, M.; Maraval, P.

    1982-11-01

    In this paper, we present first a model called partially relaxed rotation model (PRR), to treat the reorientation motion of a symmetric top which rotates freely around its molecular axis with a tumbling motion relaxed according to a characteristic time τ 1. We show that this model can easily be extended to develop a 2τ model where both tumbling and spinning motion around the molecular axis are relaxed with a second characteristic time τ 2. As limiting cases one can obtain from the 2τ model, the Gordon-McClung and PRR models. Next, we illustrate the PPR and 2τ models by calculating Raman and infrared rotational spectral densities of liquid cyclopropane at room temperature. We also discuss in the PRR model the influence of the characteristic relaxation time τ 1, on the Raman rotational profile Î21( overlineν) Finally, we emphasize on the example of room-temperature liquid cyclopropane, the advantage of the PRR model to treat a E″ degenerated Raman profile with negligible Coriolis vibrational-rotational interaction. bl

  1. Fabrication of an ionic liquid-based macroporous polymer monolithic column via atom transfer radical polymerization for the separation of small molecules.

    PubMed

    Zhang, Hang; Bai, Ligai; Wei, Zhen; Liu, Sha; Liu, Haiyan; Yan, Hongyuan

    2016-03-01

    A polymer monolithic column was prepared in a stainless steel column (50×4.6mm i.d.) via atom transfer radical polymerization technique using triallyl isocyanurate and ionic liquid (1-allyl-3-methylimidazolium chloride) as co-monomers, ethylene dimethacrylate as cross linking agent, polyethylene glycol 200, 1,4-butanediol, and N, N- dimethylformamide as porogen system, CCl4 as initiator, and FeCl2 as catalyst. The optimized polymer columns were characterized by scanning electron microscope, nitrogen adsorption-desorption instrument, mercury intrusion porosimetry, infrared spectrometer, and thermogravimetric analysis technique. Respectively, all of these factors above could illustrate that the optimized columns had relative uniform macroporous structure and high thermal stability. A series of basic and acidic small molecules, isomers, and homologues were used to evaluate the performance of these monoliths and enhanced column efficiency was obtained. PMID:26717814

  2. Two-Dimensional Skyrmion Lattice Formation in a Nematic Liquid Crystal Consisting of Highly Bent Banana Molecules.

    PubMed

    Kang, Sungmin; Lee, Eun-Woo; Li, Tianqi; Liang, Xiaobin; Tokita, Masatoshi; Nakajima, Ken; Watanabe, Junji

    2016-09-12

    We synthesized a novel banana-shaped molecule based on a 1,7-naphthalene central core that exhibits a distinct mesomorphism of the nematic-to-nematic phase transition. Both the X-ray profile and direct imaging of atomic force microscopy (AFM) investigations clearly indicates the formation of an anomalous nematic phase possessing a two-dimensional (2D) tetragonal lattice with a large edge (ca. 59 Å) directed perpendicular to the director in the low-temperature nematic phase. One plausible model is proposed by an analogy of skyrmion lattice in which two types of cylinders formed from left- and right-handed twist-bend helices stack into a 2D tetragonal lattice, diminishing the inversion domain wall. PMID:27511324

  3. Adsorption of R-OH molecules on TiO2 surfaces at the solid-liquid interface.

    PubMed

    Sánchez, Verónica M; de la Llave, Ezequiel; Scherlis, Damian A

    2011-03-15

    The exploration of TiO2 surface reactivity from first-principles calculations has been almost always limited to the gas phase, even though most of the chemically relevant applications of this interface involve the solid-liquid boundary. The reason for this limitation is the complexity of the solid-liquid interface, which poses a serious challenge to standard ab initio methodologies as density functional theory (DFT). In this work we study the interaction of H2O, CH3OH, H2O2, and HCO2H with anatase (101) and rutile (110) surfaces in aqueous solution, employing a continuum solvation model in a DFT framework in periodic boundary conditions [ J. Chem. Phys. 2009 , 131 , 174108 ]. Different adsorption configurations were analyzed, examining the effect of the first water monolayer explicitly included in the simulation. For water and methanol, molecular adsorption was found to be the most stable in the presence of the solvent, while for hydrogen peroxide the preferred configuration depended on the surface. The explicit inclusion of the first water monolayer turns out to be important since it may play a role in the stabilization of the adsorbates at the interface. In general, the slightly positive adsorption energy values obtained (with respect to water) suggest that CH3OH and H2O2 will poorly adsorb from an aqueous solution at the titania surface. Among the three species investigated other than water, the formic acid was the only one to exhibit a higher affinity for the surface than H2O. PMID:21314168

  4. Three-dimensional colloidal crystals in liquid crystalline blue phases

    PubMed Central

    Ravnik, Miha; Alexander, Gareth P.; Yeomans, Julia M.; Žumer, Slobodan

    2011-01-01

    Applications for photonic crystals and metamaterials put stringent requirements on the characteristics of advanced optical materials, demanding tunability, high Q factors, applicability in visible range, and large-scale self-assembly. Exploiting the interplay between structural and optical properties, colloidal lattices embedded in liquid crystals (LCs) are promising candidates for such materials. Recently, stable two-dimensional colloidal configurations were demonstrated in nematic LCs. However, the question as to whether stable 3D colloidal structures can exist in an LC had remained unanswered. We show, by means of computer modeling, that colloidal particles can self-assemble into stable, 3D, periodic structures in blue phase LCs. The assembly is based on blue phases providing a 3D template of trapping sites for colloidal particles. The particle configuration is determined by the orientational order of the LC molecules: Specifically, face-centered cubic colloidal crystals form in type-I blue phases, whereas body-centered crystals form in type-II blue phases. For typical particle diameters (approximately 100 nm) the effective binding energy can reach up to a few 100 kBT, implying robustness against mechanical stress and temperature fluctuations. Moreover, the colloidal particles substantially increase the thermal stability range of the blue phases, for a factor of two and more. The LC-supported colloidal structure is one or two orders of magnitude stronger bound than, e.g., water-based colloidal crystals. PMID:21368186

  5. Preparation of porous polymer monolithic column using functionalized graphene oxide as a functional crosslinker for high performance liquid chromatography separation of small molecules.

    PubMed

    Li, Yaping; Qi, Li; Ma, Huimin

    2013-09-21

    A newly developed porous polymer monolith was prepared through copolymerization of 3-(trimethoxysilyl)propylmethacrylate modified graphene oxide with glycidyl methacrylate and ethylene dimethacrylate as a functional crosslinker, which was synthesized through silanization reaction of graphene oxide prepared by Hummers method with 3-(trimethoxysilyl)propylmethacrylate. The monolith was characterized by Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, transmission electron microscopy, scanning electron microscopy, mercury intrusion porosimetry and nitrogen adsorption measurement. The monolith column was applied as the stationary phase of high performance liquid chromatography and its chromatographic performance was evaluated by separation of small molecules in the isocratic reversed-phase mode. The chromatograms of hydrophobic steroids and polar aromatic amines on the prepared monolith displayed the enhanced separation performance over those on the parent monolith. The reproducibility of the column was less than 3.5% in terms of relative standard deviation of retention time. The results demonstrate that copolymerization of functionalized graphene oxide into porous polymer monolith was an effective tool for chromatography separation enhancement of small molecules in an isocratic mode. PMID:23884304

  6. DFT Study of the Reaction Mechanisms of Carbon Dioxide and its Isoelectronic Molecules CS2 and OCS Dissolved in Pyrrolidinium and Imidazolium Acetate Ionic Liquids.

    PubMed

    Danten, Y; Cabaço, M I; Coutinho, J A P; Pinaud, Noël; Besnard, M

    2016-06-16

    The reaction mechanisms of CO2 and its isoelectronic molecules OCS and CS2 dissolved in N-butyl-N-methylpyrrolidinium acetate and in 1-butyl-3-methylimidazolium acetate were investigated by DFT calculations in "gas phase". The analysis of predicted multistep pathways allowed calculating energies of reaction and energy barriers of the processes. The major role played by the acetate anion in the degradation of the solutes CS2 and OCS as well as in the capture of OCS and CO2 by the imidazolium ring is highlighted. In both ionic liquids, this anion governs the conversion of CS2 into OCS and of OCS into CO2 through interatomic S-O exchanges between the anion and the solutes with formation of thioacetate anions. In imidazolium acetate, the selective capture of CS2 and OCS by the imidazolium ring competes with the S-O exchanges. From the calculated values of the energy barriers a basicity scale of the anions is proposed. The (13)C NMR chemical shifts of the predicted adducts were calculated and agree well with the experimental observations. It is argued that the scenario issued from the calculated pathways is shown qualitatively to be independent from the functionals and basis set used, constitute a valuable tool in the understanding of chemical reactions taking place in liquid phase. PMID:27186961

  7. Automated screening of reversed-phase stationary phases for small-molecule separations using liquid chromatography with mass spectrometry.

    PubMed

    Appulage, Dananjaya K; Wang, Evelyn H; Carroll, Frances; Schug, Kevin A

    2016-05-01

    There are various reversed-phase stationary phases that offer significant differences in selectivity and retention. To investigate different reversed-phase stationary phases (aqueous stable C18 , biphenyl, pentafluorophenyl propyl, and polar-embedded alkyl) in an automated fashion, commercial software and associated hardware for mobile phase and column selection were used in conjunction with liquid chromatography and a triple quadrupole mass spectrometer detector. A model analyte mixture was prepared using a combination of standards from varying classes of analytes (including drugs, drugs of abuse, amino acids, nicotine, and nicotine-like compounds). Chromatographic results revealed diverse variations in selectivity and peak shape. Differences in the elution order of analytes on the polar-embedded alkyl phase for several analytes showed distinct selectivity differences compared to the aqueous C18 phase. The electron-rich pentafluorophenyl propyl phase showed unique selectivity toward protonated amines. The biphenyl phase provided further changes in selectivity relative to C18 with a methanolic phase, but it behaved very similarly to a C18 when an acetonitrile-based mobile phase was evaluated. This study shows the value of rapid column screening as an alternative to excessive mobile phase variation to obtain suitable chromatographic settings for analyte separation. PMID:26959840

  8. Vibrational and thermal analyses of multicomponent crystal forms of the anti-HIV drugs lamivudine and zalcitabine.

    PubMed

    Martins, Felipe T; Guimarães, Freddy Fernandes; Honorato, Sara B; Ayala, Alejandro P; Ellena, Javier

    2015-06-10

    The vibrational and thermal characterizations of four multicomponent molecular crystals of lamivudine, namely, lamivudine hydrochloride anhydrate (1), lamivudine hydrochloride monohydrate (2), lamivudine duplex I (3), with a 8:2:2:1:4 lamivudine:maleic acid:HCl:(CH3)2CHOH:H2O stoichiometry, being all three more soluble in water than the commercial solid form of lamivudine, and lamivudine maleate (4), have been performed here by infrared (IR) and Raman spectroscopy, differential scanning calorimetry (DSC), and thermogravimetry (TG). Furthermore, the vibrational spectra of zalcitabine hydrochloride (5), isostructural to 1 but with a methylene moiety in the 3'-position of the five-membered ring instead of sulfur in lamivudine, have also been measured in order to point out the role of this molecular substitution and conformation in the vibrational modes of the salts. In fact, scattering bands at the high frequency range relative to CH stretching modes are not superimposable in the Raman spectra of 1 and 5, even though these crystal forms are assembled with the same molecular conformation and intermolecular packing. At the same time, the structural similarity between 1 and 5 can be reflected in their IR spectra, as in the carbonyl and iminium stretching bands shifted to lower frequencies as consequence of their hydrogen bonding engagement. Furthermore, a scattering band at 3057 cm(-1) is observed only in the Raman spectra of crystal forms present with their 5'-CH2OH moiety in-gauche conformation, namely, 2-4. It is absent in the Raman spectra of 1 and 5 whose 5'-CH2OH moiety adopts (+)gauche conformation. In-gauche conformation, the 5'-OH oxygen is pointed toward one of the two aromatic CH hydrogens. Consequently, there is formation of an intramolecular hydrogen bond between them, shifting the aromatic CH stretching band to a lower frequency. The DFT calculations have also revealed in-phase and out-of-phase couplings of the two aromatic CH stretchings in the Raman

  9. Crystal forms and surface textures of alluvial diamonds from the Western Region of the Central African Republic

    NASA Astrophysics Data System (ADS)

    Censier, C.; Tourenq, J.

    1995-06-01

    The most common crystal forms of the diamonds from the alluvial deposits in the Western Region of the Central African Republic were examined by scanning electron microscope (SEM) in an attempt to determine their geological history. The marks observed are related to two distinct periods in the geological history of the diamonds: the magmatic episode and their hydraulic transport. The effects of significant magmatic corrosion undergone by the diamonds during their ascent from the upper mantle are shown by the predominance of rhombododecahedral forms over octahedral forms and the frequent occurrence on the crystal faces of pyramidal depressions with triangular (111) or square (100) bases, as well as of V-shaped figures (111) or stepped figures (on the faces around the ternary axes). Some impact marks probably occurred during the explosive episode of kimberlite extrusion. Other impact marks, the marks of general wear, and the high proportion of gemstone-quality diamonds indicate the lengthy transport. They thus also indicate that the diamonds have undergone a prolonged geological history after the erosion of the kimberlite. This suggests that the kimberlite are separated from the Carnot Sandstone Formation by a considerable distance. The diamonds were stored in Albian-Maastrichtian rocks before they become concentrated in the Recent alluvium.

  10. In situ 3D topographic and shape analysis by synchrotron radiation X-ray microtomography for crystal form identification in polymorphic mixtures.

    PubMed

    Yin, Xian-Zhen; Xiao, Ti-Qiao; Nangia, Ashwini; Yang, Shuo; Lu, Xiao-Long; Li, Hai-Yan; Shao, Qun; He, You; York, Peter; Zhang, Ji-Wen

    2016-01-01

    Polymorphism denotes the existence of more than one crystal structure of a substance, and great practical and theoretical interest for the chemical and pharmaceutical industries. In many cases, it is challenging to produce a pure crystal form and establish a sensitive detection method for the identification of crystal form in a mixture of polymorphs. In this study, an accurate and sensitive method based on synchrotron radiation X-ray computed microtomography (SR-μCT) was devised to identify the polymorphs of clopidogrel bisulphate (CLP). After 3D reconstruction, crystal particles were extracted and dozens of structural parameters were calculated. Whilst, the particle shapes of the two crystal forms were all irregular, the surface of CLP II was found to be rougher than CLP I. In order to classify the crystal form based on the quantitative morphological property of particles, Volume Bias Percentage based on Surface Smoothing (VBP) was defined and a new method based on VBP was successfully developed, with a total matching rate of 99.91% for 4544 particles and a lowest detectable limit of 1%. More important for the mixtures in solid pharmaceutical formulations, the interference of excipients can be avoided, a feature cannot achieved by other available analytical methods. PMID:27097672

  11. Preliminary X-ray investigations of several crystal forms of the ferripyoverdine FpvA outer membrane receptor from Pseudomonas aeruginosa bound to ferripyoverdine

    SciTech Connect

    Wirth, Christophe; Hoegy, Françoise; Pattus, Franc; Cobessi, David

    2006-05-01

    The crystallization and X-ray data analysis of three crystal forms of the outer membrane pyoverdine transducer FpvA from P. aeruginosa bound to ferripyoverdine are described. The resolution of the crystals ranges from 3.15 to 2.7 Å depending on the crystal form; all were obtained in the presence of C{sub 8}E{sub 4} detergent. Ferripyoverdine transport across the outer membrane of Pseudomonas aeruginosa by the pyoverdine receptor FpvA and the transcriptional regulation of FpvA involve interactions of the FpvA N-terminal TonB box and signalling domain with proteins from the inner membrane. Several crystallization conditions of FpvA–Pvd-Fe solubilized in C{sub 8}E{sub 4} detergent were obtained and X-ray data were collected from three crystal forms. The resolution limits range from 3.15 to 2.7 Å depending on the crystal form. From preliminary analysis of the electron-density maps, the first full-length structure of an outer membrane receptor including a signalling domain should be determined.

  12. In situ 3D topographic and shape analysis by synchrotron radiation X-ray microtomography for crystal form identification in polymorphic mixtures

    PubMed Central

    Yin, Xian-Zhen; Xiao, Ti-Qiao; Nangia, Ashwini; Yang, Shuo; Lu, Xiao-Long; Li, Hai-Yan; Shao, Qun; He, You; York, Peter; Zhang, Ji-Wen

    2016-01-01

    Polymorphism denotes the existence of more than one crystal structure of a substance, and great practical and theoretical interest for the chemical and pharmaceutical industries. In many cases, it is challenging to produce a pure crystal form and establish a sensitive detection method for the identification of crystal form in a mixture of polymorphs. In this study, an accurate and sensitive method based on synchrotron radiation X-ray computed microtomography (SR-μCT) was devised to identify the polymorphs of clopidogrel bisulphate (CLP). After 3D reconstruction, crystal particles were extracted and dozens of structural parameters were calculated. Whilst, the particle shapes of the two crystal forms were all irregular, the surface of CLP II was found to be rougher than CLP I. In order to classify the crystal form based on the quantitative morphological property of particles, Volume Bias Percentage based on Surface Smoothing (VBP) was defined and a new method based on VBP was successfully developed, with a total matching rate of 99.91% for 4544 particles and a lowest detectable limit of 1%. More important for the mixtures in solid pharmaceutical formulations, the interference of excipients can be avoided, a feature cannot achieved by other available analytical methods. PMID:27097672

  13. In situ 3D topographic and shape analysis by synchrotron radiation X-ray microtomography for crystal form identification in polymorphic mixtures

    NASA Astrophysics Data System (ADS)

    Yin, Xian-Zhen; Xiao, Ti-Qiao; Nangia, Ashwini; Yang, Shuo; Lu, Xiao-Long; Li, Hai-Yan; Shao, Qun; He, You; York, Peter; Zhang, Ji-Wen

    2016-04-01

    Polymorphism denotes the existence of more than one crystal structure of a substance, and great practical and theoretical interest for the chemical and pharmaceutical industries. In many cases, it is challenging to produce a pure crystal form and establish a sensitive detection method for the identification of crystal form in a mixture of polymorphs. In this study, an accurate and sensitive method based on synchrotron radiation X-ray computed microtomography (SR-μCT) was devised to identify the polymorphs of clopidogrel bisulphate (CLP). After 3D reconstruction, crystal particles were extracted and dozens of structural parameters were calculated. Whilst, the particle shapes of the two crystal forms were all irregular, the surface of CLP II was found to be rougher than CLP I. In order to classify the crystal form based on the quantitative morphological property of particles, Volume Bias Percentage based on Surface Smoothing (VBP) was defined and a new method based on VBP was successfully developed, with a total matching rate of 99.91% for 4544 particles and a lowest detectable limit of 1%. More important for the mixtures in solid pharmaceutical formulations, the interference of excipients can be avoided, a feature cannot achieved by other available analytical methods.

  14. Photo-aligned blend films of azobenzene-containing polyimides with and without side-chains for inducing inclined alignment of liquid crystal molecules

    NASA Astrophysics Data System (ADS)

    Usami, Kiyoaki; Sakamoto, Kenji

    2011-08-01

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

  15. Mixed-mode anion-cation exchange/hydrophilic interaction liquid chromatography-electrospray mass spectrometry as an alternative to reversed phase for small molecule drug discovery

    PubMed

    Strege; Stevenson; Lawrence

    2000-10-01

    Within pharmaceutical drug discovery, significant needs currently exist for the analysis and purification of structurally diverse samples prior to or immediately following high-throughput screening. These processes are required to facilitate rapid and accurate biological profiling, structural determination, and resupply of new drug candidates. Reversed-phase high-performance liquid chromatography (RP-HPLC) coupled with electrospray ionization mass spectrometry (ESI-MS) for both analytical and preparative applications has become the small molecule separation/detection tool of choice for meeting many of these needs. However, the separation selectivity provided by RP-HPLC has been limited to the hydrophobicity-based resolution of relatively nonpolar sample components, and for high-throughput drug discovery applications, no sufficient alternative procedures have been identified. In this investigation, a mixed-mode anion-cation exchange/hydrophilic interaction chromatography (ACE-HILIC) method has been developed to provide both direct compatibility with ESI-MS and evaporative light-scattering detection (ELSD) and separation selectivity highly orthogonal to RP-HPLC. The technique employed silica-based small-pore weak ion exchange resins eluted with a combined aqueous and pH gradient. A diverse set of dipeptide probes was employed for the elucidation of the relative contributions of three retention mechanisms. ACE-HILIC-ESI-MS-ELSD should prove useful for the analysis and purification of compounds from both biological (e.g., natural products) and synthetic (e.g., combinatorial chemistry) sources of molecular diversity. PMID:11028621

  16. Expression, purification, crystallization and preliminary X-ray characterization of two crystal forms of stationary-phase survival E protein from Campylobacter jejuni

    SciTech Connect

    Gonçalves, A. M. D.; Rêgo, A. T.; Thomaz, M.; Enguita, F. J.; Carrondo, M. A.

    2008-03-01

    Survival E (SurE) protein from Campylobacter jejuni, a Gram-negative mesophile, has been overexpressed in Escherichia coli as a soluble protein, successfully purified and crystallized in two distinct crystal forms. Survival E (SurE) protein from Campylobacter jejuni, a Gram-negative mesophile, has been overexpressed in Escherichia coli as a soluble protein, successfully purified and crystallized in two distinct crystal forms. The first form belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with a tetramer in the asymmetric unit and unit-cell parameters a = 80.5, b = 119.0, c = 135.3 Å. The second form belongs to space group C2, with unit-cell parameters a = 121.4, b = 47.1, c = 97.8 Å, and contains a dimer in the asymmetric unit. Diffraction data have been collected from these crystal forms to 2.5 and 2.95 Å resolution, respectively.

  17. An MCBJ case study: The influence of π-conjugation on the single-molecule conductance at a solid/liquid interface

    PubMed Central

    Hong, Wenjing; Valkenier, Hennie; Mészáros, Gábor; Manrique, David Zsolt; Mishchenko, Artem; Putz, Alexander; García, Pavel Moreno; Lambert, Colin J; Hummelen, Jan C

    2011-01-01

    Summary π-Conjugation plays an important role in charge transport through single molecular junctions. We describe in this paper the construction of a mechanically controlled break-junction setup (MCBJ) equipped with a highly sensitive log I–V converter in order to measure ultralow conductances of molecular rods trapped between two gold leads. The current resolution of the setup reaches down to 10 fA. We report single-molecule conductance measurements of an anthracene-based linearly conjugated molecule (AC), of an anthraquinone-based cross-conjugated molecule (AQ), and of a dihydroanthracene-based molecule (AH) with a broken conjugation. The quantitative analysis of complementary current–distance and current–voltage measurements revealed details of the influence of π-conjugation on the single-molecule conductance. PMID:22043460

  18. Molecule nanoweaver

    DOEpatents

    Gerald, II; Rex E.; Klingler, Robert J.; Rathke, Jerome W.; Diaz, Rocio; Vukovic, Lela

    2009-03-10

    A method, apparatus, and system for constructing uniform macroscopic films with tailored geometric assemblies of molecules on the nanometer scale. The method, apparatus, and system include providing starting molecules of selected character, applying one or more force fields to the molecules to cause them to order and condense with NMR spectra and images being used to monitor progress in creating the desired geometrical assembly and functionality of molecules that comprise the films.

  19. An ab initio molecular dynamics study of the liquid-vapor interface of an aqueous NaCl solution: inhomogeneous density, polarity, hydrogen bonds, and frequency fluctuations of interfacial molecules.

    PubMed

    Choudhuri, Jyoti Roy; Chandra, Amalendu

    2014-11-21

    We have presented a first principles simulation study of the structural and dynamical properties of a liquid-vapor interfacial system of a concentrated (5.3 M) aqueous NaCl solution. We have used ab initio molecular dynamics to examine the structural and dynamical properties of the bulk and interfacial regions. The structural aspects of the system that have been considered here include the inhomogeneous density profiles of ions and water molecules, hydrogen bond distributions, orientational profiles, and also vibrational frequency distributions in the bulk and interfacial regions. It is found that the sodium ions are mostly located in the interior, while the chloride anions occupy a significant portion of the interface of the slab. The water dipoles at the interface prefer to orient parallel to the surface. The dynamical aspects of the interfaces are investigated in terms of diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational spectral diffusion. The results of the interfacial dynamics are compared with those of the corresponding bulk region. It is observed that the interfacial molecules exhibit faster diffusion and orientational relaxation with respect to the bulk. However, the interfacial molecules are found to have longer hydrogen bond lifetimes than those of the bulk. We have also investigated the correlations of hydrogen bond relaxation with the vibrational frequency fluctuations of interfacial water molecules. PMID:25416903

  20. Adding Mono- and Multivalent Ions to Lyotropic Chromonic Liquid Crystals

    NASA Astrophysics Data System (ADS)

    Tortora, Luana; Park, Heung-Shik; Antion, Kelly; Woolwerton, Chris; Finotello, Daniele; Lavrentovich, Oleg

    2006-03-01

    Lyotropic Chromonic Liquid Crystals (LCLCs) are a distinct class of liquid crystals formed in aqueous solutions by molecules with rigid polyaromatic cores and ionic groups at the periphery [1-4]. The phase diagrams of these materials should depend on entropic factors (as in the Onsager model) and electrostatic interactions. Using optical polarizing microscopy, we studied the effects of mono- and multivalent ions on the phase diagrams of Blue 27 [3] and Sunset Yellow [2]. The monovalent ions change the temperatures of phase transitions, as described in [4], while the effect of multivalent ions is more dramatic and, in addition to the changed temperatures of phase transitions by tens of degrees, it often involves condensation of LCLC aggregates into domains with birefringence much higher than that in a normal nematic phase. Work supported by OBR B-7844. [1]J. Lydon, Current Opin. Colloid & Interface Sci. 3, 458 (1998);8, 480-489 (2004); [2]V. R. Horowitz, L. A. Janowitz, A. L. Modic, P. J. Heiney, and P. J. Collings, 2005, Phys. Rew. E 72, 041710; [3]Yu. A. Nastishin, H. Liu, T. Schneider, T., V. Nazarenko, R. Vasyuta, S. V. Shiyanovskii, and O. D. Lavrentovich, 2005, Phys. Rev. E 72, 041711; [4]A.F. Kostko, B. H. Cipriano, O. A. Pinchuk, L. Ziserman, M. A. Anisimov, D. Danino, and S. R. Raghavan. J. Phys. Chem. B 109, 19126-19133 (2005)

  1. Unusual temperature dependence of the splay elastic constant of a rodlike nematic liquid crystal doped with a highly kinked bent-core molecule

    NASA Astrophysics Data System (ADS)

    Lee, Ji-Hoon; Yoon, Tae-Hoon; Choi, E.-Joon

    2013-12-01

    We report an unusual temperature dependence of the elastic constants of a rodlike nematic liquid crystal (RLC) mixed with a highly kinked bent-core liquid crystal (BLC). On cooling through the nematic phase, the splay elastic constant (K11) of the RLC-BLC mixture increased below the nematic-isotropic phase transition temperature, but started to decrease midway through the nematic phase. The decrease of K11 was more prominent with a greater concentration of BLC. On the other hand, the bend elastic constant (K33) of the RLC-BLC mixture monotonically increased through the nematic phase with decreasing temperature.

  2. Semiconductor nanorod liquid crystals

    SciTech Connect

    Li, Liang-shi; Walda, Joost; Manna, Liberato; Alivisatos, A. Paul

    2002-01-28

    Rodlike molecules form liquid crystalline phases with orientational order and positional disorder. The great majority of materials in which liquid crystalline phases have been observed are comprised of organic molecules or polymers, even though there has been continuing and growing interest in inorganic liquid crystals. Recent advances in the control of the sizes and shapes of inorganic nanocrystals allow for the formation of a broad class of new inorganic liquid crystals. Here we show the formation of liquid crystalline phases of CdSe semiconductor nanorods. These new liquid crystalline phases may have great importance for both application and fundamental study.

  3. Fabrication and evaluation of an organic monolithic column based upon the polymerisation of hexyl methacrylate with 1,6-hexanediol ethoxylate diacrylate for the separation of small molecules by capillary liquid chromatography.

    PubMed

    Alshitari, Wael; Quigley, Cristina Legido; Smith, Norman

    2015-08-15

    This paper describes the fabrication of a new porous monolith, prepared in 100μm i.d. capillaries by the co-polymerisation of hexyl methacrylate with 1,6-hexanediol ethoxylate diacrylate, poly (HMA-co-1,6 HEDA), in the presence of azobisisobutyronitrile, 1, 4-butanediol and 1-propanol were used as porogens for the monoliths; the monoliths were then used as a stationary phase for capillary liquid chromatography. Two cross linkers namely 1,6 HEDA and EDMA were utilised in order to investigate the effects of cross linker length on the separation efficiency of small molecules, and it was found that the efficiency of the separation improved tenfold when using the longer cross linker, 1,6 HEDA. This improvement is associated with the increase in number of methylene groups which resulted in an increased number of mesopores, less than 50nm. The 1,6 HEDA based monolith showed a high porosity (90%) and no evidence of swelling or shrinking with the use of organic solvents. Moreover, the 1,6 HEDA monolith demonstrated high reproducibility for the separation of the retained compounds anisole and naphthalene; these showed retention time RSDs of 1.79% and 2.74% respectively. The fabricated monolith also demonstrated high selectivity for neutral non-polar molecules, weak acids, and basic molecules. The asymmetry factors for basic molecules (nortriptyline and amitriptyline) were 1.5 and 1.3 respectively, indicating slight tailing, which is often noticeable on silica based phases due to secondary interactions between basic moieties and the hydroxyl groups of the silica. PMID:25966388

  4. Capillary and nano-liquid chromatography-tandem mass spectrometry for the quantification of small molecules in microdialysis samples: comparison with microbore dimensions.

    PubMed

    Lanckmans, Katrien; Van Eeckhaut, Ann; Sarre, Sophie; Smolders, Ilse; Michotte, Yvette

    2006-10-27

    Enhanced sensitivity is a well known benefit of miniaturised LC-electrospray (ESI)-MS/MS methods. The suitability of miniaturised LC-MS/MS for quantification of small molecules in dialysates was investigated using the anti-epileptic drug oxcarbazepine, its active metabolite, 10,11-dihydro-10-hydroxycarbamazepine, and the internal standard for microdialysis probe calibration, 2-methyl-5H-dibenz(b,f)azepine-5-carboxamide, as test compounds. ESI-MS detection is sensitive to matrix effects. Therefore, dialysate matrix effects were investigated by comparing the responses of standards made in water, Ringer's solution (salt solution used as perfusion fluid) and blank dialysate matrix. Due to the occurrence of ion suppression or enhancement, direct injection of dialysis samples onto the analytical column could not be applied for quantification of small molecules in dialysis samples. Column switching was necessary for desalting and preconcentration of the dialysates. However, this approach was not able to completely eliminate salt effects when the injection volume exceeded 1 microL. No differences in response between Ringer's solution and dialysate matrix were detected at capillary and nano-dimensions. Calibration standards should be prepared with Ringer's solution instead of water for quantitative analysis of microdialysates. A microbore, capillary and nano-LC-ESI-MS/MS method were compared in terms of method feasibility, linearity, sensitivity, accuracy and precision. Downscaling to capillary and nano-dimensions resulted in a gain in detection sensitivity of 5 and 50, respectively. Miniaturised LC-MS/MS was found to be fit for quantification of small molecules in dialysates with acceptable accuracy and method precision. PMID:16938304

  5. Preparation and characterization of poly(triallyl isocyanurate-co-trimethylolpropane triacrylate) monolith and its applications in the separation of small molecules by liquid chromatography.

    PubMed

    Zhong, Jing; Hao, Mengbei; Li, Ruo; Bai, Ligai; Yang, Gengliang

    2014-03-14

    A new polymeric monolith was prepared in stainless-steel column and fused-silica capillary, respectively, by atom transfer radical polymerization technique. In the polymerization, triallyl isocyanurate (TAIC) was used as the functional monomer; trimethylolpropane triacrylate (TMPTA) as the crosslinking agent; polyethylene glycol 200 and 1,2-propanediol as the co-porogens; carbon tetrachloride as the initiator and ferrous chloride as the catalyst. The conditions of polymerization were optimized. Morphology of the prepared poly(TAIC-co-TMPTA) monolith was investigated by scanning electron microscopy; pore properties were assayed by mercury porosimetry and nitrogen adsorption. The characterization indicated that the prepared reversed-phase monolith possessed uniform structure, good permeability and mechanical stability. The column was used as the stationary phase of reversed phase high performance liquid chromatography (RP-HPLC) and capillary liquid chromatography (CLC) to separate the mixture of aromatic compounds. The new column performed around 125,000 theoretical plates per meter. The column showed good reproducibility: the relative standard deviation values of the retention factor values for aromatic compounds were less than 1.52% (n=7, column-to-column). PMID:24556171

  6. Interstellar molecules

    NASA Astrophysics Data System (ADS)

    Smith, D.

    1987-09-01

    Some 70 different molecular species have so far been detected variously in diffuse interstellar clouds, dense interstellar clouds, and circumstellar shells. Only simple (diatomic and triatomic) species exist in diffuse clouds because of the penetration of destructive UV radiations, whereas more complex (polyatomic) molecules survive in dense clouds as a result of the shielding against this UV radiation provided by dust grains. A current list of interstellar molecules is given together with a few other molecular species that have so far been detected only in circumstellar shells. Also listed are those interstellar species that contain rare isotopes of several elements. The gas phase ion chemistry is outlined via which the observed molecules are synthesized, and the process by which enrichment of the rare isotopes occurs in some interstellar molecules is described.

  7. Interstellar Molecules

    ERIC Educational Resources Information Center

    Solomon, Philip M.

    1973-01-01

    Radioastronomy reveals that clouds between the stars, once believed to consist of simple atoms, contain molecules as complex as seven atoms and may be the most massive objects in our Galaxy. (Author/DF)

  8. Modeling Molecules

    NASA Technical Reports Server (NTRS)

    2000-01-01

    The molecule modeling method known as Multibody Order (N) Dynamics, or MBO(N)D, was developed by Moldyn, Inc. at Goddard Space Flight Center through funding provided by the SBIR program. The software can model the dynamics of molecules through technology which stimulates low-frequency molecular motions and properties, such as movements among a molecule's constituent parts. With MBO(N)D, a molecule is substructured into a set of interconnected rigid and flexible bodies. These bodies replace the computation burden of mapping individual atoms. Moldyn's technology cuts computation time while increasing accuracy. The MBO(N)D technology is available as Insight II 97.0 from Molecular Simulations, Inc. Currently the technology is used to account for forces on spacecraft parts and to perform molecular analyses for pharmaceutical purposes. It permits the solution of molecular dynamics problems on a moderate workstation, as opposed to on a supercomputer.

  9. Enumerating molecules.

    SciTech Connect

    Visco, Donald Patrick, Jr.; Faulon, Jean-Loup Michel; Roe, Diana C.

    2004-04-01

    This report is a comprehensive review of the field of molecular enumeration from early isomer counting theories to evolutionary algorithms that design molecules in silico. The core of the review is a detail account on how molecules are counted, enumerated, and sampled. The practical applications of molecular enumeration are also reviewed for chemical information, structure elucidation, molecular design, and combinatorial library design purposes. This review is to appear as a chapter in Reviews in Computational Chemistry volume 21 edited by Kenny B. Lipkowitz.

  10. Quest for organic polymer-based monolithic columns affording enhanced efficiency in high performance liquid chromatography separations of small molecules in isocratic mode

    PubMed Central

    Svec, Frantisek

    2011-01-01

    The separations of small molecules using columns containing porous polymer monoliths invented two decades ago went a long way from the very modest beginnings to the current capillary columns with efficiencies approaching those featured by their silica-based counterparts. This review article presents a variety of techniques that have been used to form capillary formats of monolithic columns with enhanced separation performance in isocratic elutions. The following text first describes the traditional approaches used for the preparation of efficient monoliths comprising variations in polymerization conditions including temperature as well as composition of monomers and porogenic solvents. Encouraging results of these experiments fueled research of completely new preparation methods such as polymerization to an incomplete conversion, use of single crosslinker, hypercrosslinking, and incorporation of carbon nanotubes that are described in the second part of the text. PMID:21816401

  11. Probing the interplay between electrostatic and dispersion interactions in the solvation of nonpolar nonaromatic solute molecules in ionic liquids: An OKE spectroscopic study of CS2/[CnC1im][NTf2] mixtures (n = 1-4)

    NASA Astrophysics Data System (ADS)

    Xue, Lianjie; Tamas, George; Gurung, Eshan; Quitevis, Edward L.

    2014-04-01

    The intermolecular dynamics of dilute solutions of CS2 in 1-alkyl-3-methylimidazolium bis[(trifluoromethane)sulfonyl]amide ([CnC1im][NTf2] for n = 1-4) were studied at 295 K using femtosecond optical Kerr effect (OKE) spectroscopy. The OKE spectra of the CS2/ionic liquid (IL) mixtures were analyzed using an additivity model to obtain the CS2 contribution to the OKE spectrum from which information about the intermolecular modes of CS2 in these mixtures was gleaned. The intermolecular spectrum of CS2 in these mixtures is lower in frequency and narrower than that of neat CS2, as found previously for CS2 in [C5C1im][NTf2]. Moreover, a dependence of the spectra on alkyl chain length is observed that is attributed to the interplay between electrostatic and dispersion interactions. The surprising result in this study is the solubility of CS2 in [C1C1im][NTf2], which involves the interaction of a nonpolar nonaromatic molecular solute and only the charged groups of the IL. We propose that the solubility of CS2 in [C1C1im][NTf2] is determined by three favorable factors - (1) large polarizability of the solute molecule; (2) small size of the solute molecule; and (3) low cohesive energy in the high-charge density regions of the IL.

  12. Self-powdering and nonlinear optical domain structures in ferroelastic β‧-Gd2(MoO4)3 crystals formed in glass

    NASA Astrophysics Data System (ADS)

    Tsukada, Y.; Honma, T.; Komatsu, T.

    2009-08-01

    Ferroelastic β'-Gd 2(MoO 4) 3, (GMO), crystals are formed through the crystallization of 21.25Gd 2O 3-63.75MoO 3-15B 2O 3 glass (mol%), and two scientific curious phenomena are observed. (1) GMO crystals formed in the crystallization break into small pieces with a triangular prism or pyramid shape having a length of 50-500 μm spontaneously during the crystallizations in the inside of an electric furnace, not during the cooling in air after the crystallization. This phenomenon is called "self-powdering phenomenon during crystallization" in this paper. (2) Each self-powdered GMO crystal grain shows a periodic domain structure with different refractive indices, and a spatially periodic second harmonic generation (SHG) depending on the domain structure is observed. It is proposed from polarized micro-Raman scattering spectra and the azimuthal dependence of second harmonic intensities that GMO crystals are oriented in each crystal grain and the orientation of (MoO 4) 2- tetrahedra in GMO crystals changes periodically due to spontaneous strains in ferroelastic GMO crystals.

  13. Effect of TiO2-Crystal Forms on the Photo-Degradation of EVA/PLA Blend Under Accelerated Weather Testing

    NASA Astrophysics Data System (ADS)

    Van Cong, Do; Trang, Nguyen Thi Thu; Giang, Nguyen Vu; Lam, Tran Dai; Hoang, Thai

    2016-05-01

    Photo-degradation of poly (ethylene-co-vinyl acetate) (EVA)/poly (lactic acid) (PLA) blend and EVA/PLA/TiO2 nanocomposites was carried out under accelerated weather testing conditions by alternating cycles of ultraviolet (UV) light and moisture at controlled and elevated temperatures. The characters, properties, and morphology of these materials before and after accelerated weather testing were determined by Fourier transform infrared spectroscopy, colour changes, viscosity, tensile test, thermogravimetric analysis, and field emission scanning electron microscopy. The increases in the content of oxygen-containing groups, colour changes; the decreases in viscosity, tensile properties, and thermal stability of these materials after accelerated weather testing are the evidence for the photo-degradation of the blend and nanocomposites. After accelerated weather testing, the appearance of many micro-holes and micro-pores on the surface of the collected samples was observed. The photo-degradation degree of the nanocomposites depended on the TiO2-crystal form. Rutile TiO2 do not enhance the degradation, but anatase and mixed crystals TiO2 nanoparticles promoted the degradation of the nanocomposites. Particularly, the mixed crystals TiO2 nanoparticles showed the highest photo-catalytic activity of the nanocomposites.

  14. Orientation Difference of Chemically Immobilized and Physically Adsorbed Biological Molecules on Polymers Detected at the Solid/Liquid Interfaces in Situ

    PubMed Central

    Ye, Shuji; Nguyen, Khoi Tan; Boughton, Andrew P.; Mello, Charlene M.; Chen, Zhan

    2009-01-01

    A surface sensitive second order nonlinear optical technique, sum frequency generation (SFG) vibrational spectroscopy, was applied to study peptide orientation on polymer surfaces, supplemented by a linear vibrational spectroscopy, attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR). Using the antimicrobial peptide Cecropin P1 as a model system, we have quantitatively demonstrated that chemically immobilized peptides on polymers adopt a more ordered orientation than less tightly bound physically adsorbed peptides. These differences were also observed in different chemical environments, e.g., air versus water. Although numerous studies have reported a direct correlation between the choice of immobilization method and the performance of an attached biological molecule, the lack of direct biomolecular structure and orientation data has made it difficult to elucidate the relationship between structure, orientation and function at a surface. In this work, we directly studied the effect of chemical immobilization method on biomolecular orientation/ordering, an important step for future studies of biomolecular activity. The methods for orientation analysis described within are also of relevance to understanding biosensors, biocompatibility, marine-antifouling, membrane protein functions, and antimicrobial peptide activities. PMID:19961170

  15. High-performance liquid chromatography separation of small molecules on a porous poly (trimethylol propane triacrylate-co-N-isopropylacrylamide-co-ethylene dimethacrylate) monolithic column.

    PubMed

    Liu, Haiyan; Bai, Xiaomei; Wei, Dan; Yang, Gengliang

    2014-01-10

    A porous monolith was prepared by in situ free-radical polymerization using N-isopropylacrylamide (NIPAAm) and trimethylol propane triacrylate (TMPTA) as functional monomers, ethylene dimethacrylate (EDMA) as crosslinking agent. The chemical group of the monolith was assayed by a Fourier transform infrared spectroscopy (FT-IR) method and the morphology of optimized monolithic column was characterized by scanning electron microscopy (SEM). The mechanical strength and permeability have been studied in detail as well. The run-to-run and column-to-column reproducibility of the retention times were less than 0.9% and 3.0%, respectively. Furthermore, the influence of temperature and mobile phase composition on the separation of aromatic compounds was investigated. The results indicated that poly (trimethylol propane triacrylate-co-N-isopropylacrylamide-co-ethylenedimethacrylate) (TMPTA-co-NIPAAm-co-EDMA) monolithic column not only had high porosity and strong rigidity, but also was a promising tool for analyzing small molecule compounds with a short analysis time by controlling the column temperature. PMID:24290767

  16. Pyrrole-Terminated Ionic Liquid Surfactant: One Molecule with Multiple Functions for Controlled Synthesis of Diverse Multispecies Co-Doped Porous Hollow Carbon Spheres.

    PubMed

    Li, Jian; Zhu, Wei; Ji, Jingwei; Wang, Peng; Lan, Yue; Gao, Ning; Yin, Xianpeng; Wang, Hui; Li, Guangtao

    2016-05-01

    Rationally and efficiently controlling chemical composition, microstructure, and morphology of carbon nanomaterials plays a crucial role in significantly enhancing their functional properties and expending their applications. In this work, a novel strategy for simultaneously controlling these structural parameters was developed on the base of a multifunctional precursor approach, in which the precursor not only serves as carbon source and structure-directing agent, but also contains two heteroatom doping sites. As exemplified by using pyrrole-terminated ionic liquid surfactant as such precursor, in conjunction with sol-gel chemistry this strategy allows for efficiently producing well-defined hollow carbon spheres with controlled microstructure and chemical compositions. Remarkably, the dual-doping sites in confined silica channels provide an exciting opportunity and flexibility to access various doped carbons through simply anion exchange or altering the used oxidative polymerization agent, especially the multispecies codoped materials by combination of the two doping modes. All the results indicate that the described strategy may open up a new avenue for efficiently synthesizing functional carbon materials with highly controllable capability. PMID:27093191

  17. Development of an automated dual-mode supercritical fluid chromatography and reversed-phase liquid chromatography mass-directed purification system for small-molecule drug discovery.

    PubMed

    Hettiarachchi, Kanaka; Kong, May; Yun, Andersen; Jacobsen, John R; Xue, Qifeng

    2014-04-01

    We report the development of a dual-mode mass-directed supercritical fluid chromatography and reversed-phase liquid chromatography purification system. The addition of a third pump allows for flexible mobile phase control between the two techniques, and enables operation of either chromatography mode within minutes by activation of a set of switching valves on a single system. Software control, fluidic pathways, interface to the mass spectrometer, and fraction collection have been modified for compatibility between both separation methods. The conditioning solvent and tuning parameters for the mass spectrometer were adjusted to achieve an ideal signal trace in either mode with good linearity (r(2) > 0.970) over a range of concentrations and minimal noise for accurate peak detection and isolation. The registration success rate is 90% and overall sample recovery for either technique is 80-90%. Combining two orthogonal separation and purification modes in one single system has improved the purification throughput of complex mixtures and has been a valuable, cost-saving tool in our laboratory. PMID:24470330

  18. Design of water molecule and its surrounding

    NASA Astrophysics Data System (ADS)

    Danylo, R. I.; Okhrimenko, B. A.; Yablochkova, K. S.

    2015-02-01

    Hydrogen bonds and their fluctuations are one of the factors that determine the unique properties of water [1]. Building models of formation and rupture of hydrogen bonds due to non-eigen vibrations of a molecule of water is to a large extent determined by the availability of accurate information on the geometric structure of the water molecule. Geometric parameters of the water molecule have been well studied for the gaseous state. This was aided by the possibility of an experimental study of the regularities in the rotational spectra of molecules. However, some questions about the geometry of the water molecule in the liquid state remain unanswered. For example, many sources state that the valence angle of the water molecule decreases during the transition into the liquid state [2]. Based on the experimental data of molecular vibration spectra in D2O and H2O molecules [3], the authors have estimated valence angle of water in the liquid state. Consequently, the value of the valence angle of water in liquid state was determined to be (89 +/-2)°. A question of determination of libration vibrations of water molecule, as well as the analysis of its consequent inversion doubling, based on the new information on the equilibrium angle of the water molecules in the liquid state, constitutes an interest and is discussed in the present paper.

  19. Water molecules orientation in surface layer

    NASA Astrophysics Data System (ADS)

    Klingo, V. V.

    2000-08-01

    The water molecules orientation has been investigated theoretically in the water surface layer. The surface molecule orientation is determined by the direction of a molecule dipole moment in relation to outward normal to the water surface. Entropy expressions of the superficial molecules in statistical meaning and from thermodynamical approach to a liquid surface tension have been found. The molecules share directed opposite to the outward normal that is hydrogen protons inside is equal 51.6%. 48.4% water molecules are directed along to surface outward normal that is by oxygen inside. A potential jump at the water surface layer amounts about 0.2 volts.

  20. Self-powdering and nonlinear optical domain structures in ferroelastic beta'-Gd{sub 2}(MoO{sub 4}){sub 3} crystals formed in glass

    SciTech Connect

    Tsukada, Y.; Honma, T.; Komatsu, T.

    2009-08-15

    Ferroelastic beta'-Gd{sub 2}(MoO{sub 4}){sub 3}, (GMO), crystals are formed through the crystallization of 21.25Gd{sub 2}O{sub 3}-63.75MoO{sub 3}-15B{sub 2}O{sub 3} glass (mol%), and two scientific curious phenomena are observed. (1) GMO crystals formed in the crystallization break into small pieces with a triangular prism or pyramid shape having a length of 50-500 {mu}m spontaneously during the crystallizations in the inside of an electric furnace, not during the cooling in air after the crystallization. This phenomenon is called 'self-powdering phenomenon during crystallization' in this paper. (2) Each self-powdered GMO crystal grain shows a periodic domain structure with different refractive indices, and a spatially periodic second harmonic generation (SHG) depending on the domain structure is observed. It is proposed from polarized micro-Raman scattering spectra and the azimuthal dependence of second harmonic intensities that GMO crystals are oriented in each crystal grain and the orientation of (MoO{sub 4}){sup 2-} tetrahedra in GMO crystals changes periodically due to spontaneous strains in ferroelastic GMO crystals. - Graphical abstract: This figure shows the polarized optical photograph at room temperature for a particle (piece) obtained by a heat treatment of the glass at 590 deg. C for 2 h in an electric furnace in air. This particle was obtained through the self-powdering behavior in the crystallization of glass. The periodic domain structure is observed. Ferroelastic beta'-Gd{sub 2}(MoO{sub 4}){sub 3} crystals are formed in the particle, and second harmonic generations are detected, depending on the domain structure.

  1. Ionic-content dependence of viscoelasticity of the lyotropic chromonic liquid crystal sunset yellow

    NASA Astrophysics Data System (ADS)

    Zhou, Shuang; Cervenka, Adam J.; Lavrentovich, Oleg D.

    2014-10-01

    A lyotropic chromonic liquid crystal (LCLC) is an orientationally ordered system made by self-assembled aggregates of charged organic molecules in water, bound by weak noncovalent attractive forces and stabilized by electrostatic repulsions. We determine how the ionic content of the LCLC, namely, the presence of mono- and divalent salts and p H enhancing agent, alter the viscoelastic properties of the LCLC. Aqueous solutions of the dye sunset yellow with a uniaxial nematic order are used as an example. By applying a magnetic field to impose orientational deformations, we measure the splay K1, twist K2, and bend K3 elastic constants and rotation viscosity γ1 as a function of concentration of additives. The data indicate that the viscoelastic parameters are influenced by ionic content in dramatic and versatile ways. For example, the monovalent salt NaCl decreases K3 and K2 and increases γ1, while an elevated p H decreases all the parameters. We attribute these features to the ion-induced changes in length and flexibility of building units of LCLC, the chromonic aggregates, a property not found in conventional thermotropic and lyotropic liquid crystals formed by covalently bound units of fixed length.

  2. Nanoconstructions Based on Spatially Ordered Nucleic Acid Molecules

    NASA Astrophysics Data System (ADS)

    Yevdokimov, Yu. M.

    Different strategies for the design of nanoconstructions whose building blocks are both linear molecules of double-stranded nucleic acids and nucleic acid molecules fixed in the spatial structure of particles of liquid-crystalline dispersions are described.

  3. The fabrication of monolithic capillary column based on poly (bisphenol A epoxy vinyl ester resin-co-ethylene glycol dimethacrylate) and its applications for the separation of small molecules in high performance liquid chromatography.

    PubMed

    Niu, Wenjing; Wang, Lijuan; Bai, Ligai; Yang, Gengliang

    2013-07-01

    A new polymeric monolith was synthesized in fused-silica capillary by in situ polymerization technique. In the polymerization, bisphenol A epoxy vinyl ester resin (VER) was used as the functional monomer, ethylene glycol dimethacrylate (EDMA) as the crosslinking monomer, 1,4-butanediol, 1-propanol and water as the co-porogens, and azobisisobutyronitrile (AIBN) as the initiator. The conditions of polymerization have been optimized. Morphology of the prepared poly (VER-co-EDMA) monolith was investigated by the scanning electron microscopy (SEM); pore properties were assayed by mercury porosimetry and nitrogen adsorption. The optimized poly (VER-co-EDMA) monolith showed a uniform structure, good permeability and mechanical stability. Then, the column was used as the stationary phase of high performance liquid chromatography (HPLC) to separate the mixture of benzene derivatives. The best column efficiency achieved for phenol was 235790 theoretical plates per meter. Baseline separations of benzene derivatives and halogenated benzene compounds under optimized isocratic mode conditions were achieved with high column efficiency. The column showed good reproducibility: the relative standard deviation (RSD) values based on the retention times (n=3) for run-to-run, column-to-column and batch-to-batch were less than 0.98, 1.68, 5.48%, respectively. Compared with poly (BMA-co-EDMA) monolithic column, the proposed monolith exhibited more efficiency in the separation of small molecules. PMID:23726080

  4. Investigation of critical lines and global phase behavior of unequal size of molecules in binary gas-liquid mixtures in the combined pressure-temperature-concentration planes around the van Laar point

    NASA Astrophysics Data System (ADS)

    Gençaslan, Mustafa; Keskin, Mustafa

    2016-09-01

    We investigate critical curves and global phase behavior of unequal size of molecules in binary gas-liquid mixtures at the van Laar point and its vicinity. The van Laar point is only point at which the mathematical double point curve is stable, and also the intersection of the tricritical point and the double critical end point. The critical line structure is displayed for various combinations of the chain length and system parameters in the reduced pressure (P∗) temperature (T∗) plane, as is usually done with experimental results and temperature-concentration (T, x) plane. The P∗,T∗ diagrams are discussed in accordance with the Scott and van Konynenburg binary phase diagram classification. We found that our P∗,T∗ plots correspond to the type II, type III, type IV phase diagram behaviors and they are in good agreement with the theoretical and experimental studies. It is also found that the critical lines and phase behavior are extremely sensitive to small modifications in the system parameters.

  5. Mind Molecules

    PubMed Central

    Snyder, Solomon H.

    2011-01-01

    Scientific styles vary tremendously. For me, research is largely about the unfettered pursuit of novel ideas and experiments that can test multiple ideas in a day, not a year, an approach that I learned from my mentor Julius “Julie” Axelrod. This focus on creative conceptualizations has been my métier since working in the summers during medical school at the National Institutes of Health, during my two years in the Axelrod laboratory, and throughout my forty-five years at Johns Hopkins University School of Medicine. Equally important has been the “high” that emerges from brainstorming with my students. Nothing can compare with the eureka moments when, together, we sense new insights and, better yet, when high-risk, high-payoff experiments succeed. Although I have studied many different questions over the years, a common theme emerges: simple biochemical approaches to understanding molecular messengers, usually small molecules. Equally important has been identifying, purifying, and cloning the messengers' relevant biosynthetic, degradative, or target proteins, at all times seeking potential therapeutic relevance in the form of drugs. In the interests of brevity, this Reflections article is highly selective, and, with a few exceptions, literature citations are only of findings of our laboratory that illustrate notable themes. PMID:21543333

  6. Spectroscopic modeling of water molecule

    NASA Astrophysics Data System (ADS)

    Danylo, R. I.; Okhrimenko, B. A.

    2013-12-01

    This research is devoted to the vibrational spectroscopy inverse problem solution that gives a possibility to design a molecule and make conclusions about its geometry. The valence angle finding based on the usage of inverse spectral vibrational spectroscopy problem is a well-known task. 3N-matrix method was chosen to solve the proposed task. The usage of this method permits to make no assumptions about the molecule force field, besides it can be applied to molecules of matter in liquid state. Anharmonicity constants assessment is an important part of the valence angle finding. The reduction to zero vibrations is necessary because used matrix analytical expression were found in the harmonic approach. In order to find the single-valued inverse spectral problem of vibrational spectroscopy solution a shape parameter characterizing "mixing" of ω1 and ω2 vibrations forms must be found. The minimum of such a function Υ called a divergence parameter was found. This function characterizes method's accuracy. The valence angle assessment was reduced to the divergence parameter minimization. The β value concerning divergence parameter minimum was interpreted as the desired valence angle. The proposed method was applied for water molecule in liquid state: β = (88,8 ±1,7)° . The found angle fits the water molecule nearest surrounding tetrahedral model including hydrogen bond curvature in the first approximation.

  7. Structural and vibrational studies of the molecular crystals formed by 2,6-diphenyl-4-(2,4,6-triphenyl-1-pyridino) phenolate with nitric and sulphuric acids

    NASA Astrophysics Data System (ADS)

    Baran, J.; Barnes, A. J.; Drozd, M.; Janczak, J.; Ratajczak, H.; limitSˈled limitzˈ, M.

    2001-12-01

    The crystal structure of 2,6-diphenyl-4-(2,4,6-triphenyl-1-pyridino) phenol-nitrate-water has been found to belong to the P2 1/ n space group of the monoclinic system, with Z=4, a=12.498(2) Å, b=19.223(4) Å, c=14.025(3) Å, and β=90.25(3)°. The 2,6-diphenyl-4-(2,4,6-triphenyl-1-pyridino) phenol-hydrogen sulphate crystal has a similar structure, with Z=4, a=13.139(3) Å, b=18.926(4) Å, c=13.406(3) Å, and β=92.68(3)°. In the nitric acid complex, two water molecules and two nitrate ions are linked by a network of hydrogen bonds, with each water molecule also accepting a hydrogen bond from the phenolic OH group and each nitrate ion additionally involved in a short C-H…O contact. Similarly in the sulphuric acid complex, two hydrogen sulphate ions form a hydrogen-bonded cyclic dimer, with each hydrogen sulphate ion also accepting a hydrogen bond from the phenolic OH group and additionally involved in a short C-H…O contact. The observed infrared and Raman spectra are in accordance with these structures.

  8. Enhancing proton conduction via doping of supramolecular liquid crystals (4-alkoxybenzoic acids) with imidazole

    NASA Astrophysics Data System (ADS)

    Liang, Ting; Wu, Yong; Tan, Shuai; Yang, Xiaohui; Wei, Bingzhuo

    2015-09-01

    Enhancing proton conduction via doping was first achieved in hydrogen-bonded liquid crystals consisting of benzoic acids. Supramolecular liquid crystals formed by pure 4-alkoxybenzoic acids (nAOBA, n = 8, 10, 12) exhibited the maximum proton conductivity of 5.0 × 10-8 S cm-1. Doping of nAOBA with 25 mol% imidazole (Im0.25) had little impact on mesomorphism but increased proton conductivities by at least 3 orders of magnitude. The liquid crystals formed by nAOBA-Im0.25 exhibited the maximum proton conductivity of 1.9 × 10-4 S cm-1. It was proposed that structure diffusion of imidazole bridged interdimer proton transfer to form continuous conducting pathways in mesomorphic nAOBA-Im0.25.

  9. Colloidal cholesteric liquid crystal in spherical confinement.

    PubMed

    Li, Yunfeng; Jun-Yan Suen, Jeffrey; Prince, Elisabeth; Larin, Egor M; Klinkova, Anna; Thérien-Aubin, Héloïse; Zhu, Shoujun; Yang, Bai; Helmy, Amr S; Lavrentovich, Oleg D; Kumacheva, Eugenia

    2016-01-01

    The organization of nanoparticles in constrained geometries is an area of fundamental and practical importance. Spherical confinement of nanocolloids leads to new modes of packing, self-assembly, phase separation and relaxation of colloidal liquids; however, it remains an unexplored area of research for colloidal liquid crystals. Here we report the organization of cholesteric liquid crystal formed by nanorods in spherical droplets. For cholesteric suspensions of cellulose nanocrystals, with progressive confinement, we observe phase separation into a micrometer-size isotropic droplet core and a cholesteric shell formed by concentric nanocrystal layers. Further confinement results in a transition to a bipolar planar cholesteric morphology. The distribution of polymer, metal, carbon or metal oxide nanoparticles in the droplets is governed by the nanoparticle size and yields cholesteric droplets exhibiting fluorescence, plasmonic properties and magnetic actuation. This work advances our understanding of how the interplay of order, confinement and topological defects affects the morphology of soft matter. PMID:27561545

  10. Colloidal cholesteric liquid crystal in spherical confinement

    PubMed Central

    Li, Yunfeng; Jun-Yan Suen, Jeffrey; Prince, Elisabeth; Larin, Egor M.; Klinkova, Anna; Thérien-Aubin, Héloïse; Zhu, Shoujun; Yang, Bai; Helmy, Amr S.; Lavrentovich, Oleg D.; Kumacheva, Eugenia

    2016-01-01

    The organization of nanoparticles in constrained geometries is an area of fundamental and practical importance. Spherical confinement of nanocolloids leads to new modes of packing, self-assembly, phase separation and relaxation of colloidal liquids; however, it remains an unexplored area of research for colloidal liquid crystals. Here we report the organization of cholesteric liquid crystal formed by nanorods in spherical droplets. For cholesteric suspensions of cellulose nanocrystals, with progressive confinement, we observe phase separation into a micrometer-size isotropic droplet core and a cholesteric shell formed by concentric nanocrystal layers. Further confinement results in a transition to a bipolar planar cholesteric morphology. The distribution of polymer, metal, carbon or metal oxide nanoparticles in the droplets is governed by the nanoparticle size and yields cholesteric droplets exhibiting fluorescence, plasmonic properties and magnetic actuation. This work advances our understanding of how the interplay of order, confinement and topological defects affects the morphology of soft matter. PMID:27561545

  11. Physics of Molecules

    NASA Astrophysics Data System (ADS)

    Williams, D.; Murdin, P.

    2000-11-01

    Many varieties of molecule have been detected in the Milky Way and in other galaxies. The processes by which these molecules are formed and destroyed are now broadly understood (see INTERSTELLAR CHEMISTRY). These molecules are important components of galaxies in two ways. Firstly, radiation emitted by molecules enables us to trace the presence of diffuse gas, to infer its physical properties and ...

  12. Lyotropic chromonic liquid crystals: From viscoelastic properties to living liquid crystals

    NASA Astrophysics Data System (ADS)

    Zhou, Shuang

    Lyotropic chromonic liquid crystal (LCLC) represents a broad range of molecules, from organic dyes and drugs to DNA, that self-assemble into linear aggregates in water through face-to-face stacking. These linear aggregates of high aspect ratio are capable of orientational order, forming, for example nematic phase. Since the microscopic properties (such as length) of the chromonic aggregates are results of subtle balance between energy and entropy, the macroscopic viscoelastic properties of the nematic media are sensitive to change of external factors. In the first part of this thesis, by using dynamic light scattering and magnetic Frederiks transition techniques, we study the Frank elastic moduli and viscosity coefficients of LCLC disodium cromoglycate (DSCG) and sunset yellow (SSY) as functions of concentration c , temperature T and ionic contents. The elastic moduli of splay (K1) and bend (K3) are in the order of 10pN, about 10 times larger than the twist modulus (K2). The splay modulus K1 and the ratio K1/K3 both increase substantially as T decreases or c increases, which we attribute to the elongation of linear aggregates at lower T or higher c . The bend viscosity is comparable to that of thermotropic liquid crystals, while the splay and twist viscosities are several orders of magnitude larger, changing exponentially with T . Additional ionic additives into the system influence the viscoelastic properties of these systems in a dramatic and versatile way. For example, monovalent salt NaCl decreases bend modulus K3 and increases twist viscosity, while an elevated pH decreases all the parameters. We attribute these features to the ion-induced changes in length and flexibility of building units of LCLC, the chromonic aggregates, a property not found in conventional thermotropic and lyotropic liquid crystals form by covalently bound units of fixed length. The second part of the thesis studies a new active bio-mechanical hybrid system called living liquid crystal

  13. Spiral and target patterns in bivalve nacre manifest a natural excitable medium from layer growth of a biological liquid crystal

    PubMed Central

    Cartwright, Julyan H. E.; Checa, Antonio G.; Escribano, Bruno; Sainz-Díaz, C. Ignacio

    2009-01-01

    Nacre is an exquisitely structured biocomposite of the calcium carbonate mineral aragonite with small amounts of proteins and the polysaccharide chitin. For many years, it has been the subject of research, not just because of its beauty, but also to discover how nature can produce such a superior product with excellent mechanical properties from such relatively weak raw materials. Four decades ago, Wada [Wada K (1966) Spiral growth of nacre. Nature 211:1427] proposed that the spiral patterns in nacre could be explained by using the theory Frank [Frank F (1949) The influence of dislocations on crystal growth. Discuss Faraday Soc 5:48–54] had put forward of the growth of crystals by means of screw dislocations. Frank's mechanism of crystal growth has been amply confirmed by experimental observations of screw dislocations in crystals, but it is a growth mechanism for a single crystal, with growth fronts of molecules. However, the growth fronts composed of many tablets of crystalline aragonite visible in micrographs of nacre are not a molecular-scale but a mesoscale phenomenon, so it has not been evident how the Frank mechanism might be of relevance. Here, we demonstrate that nacre growth is organized around a liquid-crystal core of chitin crystallites, a skeleton that the other components of nacre subsequently flesh out in a process of hierarchical self-assembly. We establish that spiral and target patterns can arise in a liquid crystal formed layer by layer through the Burton–Cabrera–Frank [Burton W, Cabrera N, Frank F (1951) The growth of crystals and the equilibrium structure of their surfaces. Philos Trans R Soc London Ser A 243:299–358] dynamics, and furthermore that this layer growth mechanism is an instance of an important class of physical systems termed excitable media. Artificial liquid crystals grown in this way may have many technological applications. PMID:19528636

  14. Spiral and target patterns in bivalve nacre manifest a natural excitable medium from layer growth of a biological liquid crystal.

    PubMed

    Cartwright, Julyan H E; Checa, Antonio G; Escribano, Bruno; Sainz-Díaz, C Ignacio

    2009-06-30

    Nacre is an exquisitely structured biocomposite of the calcium carbonate mineral aragonite with small amounts of proteins and the polysaccharide chitin. For many years, it has been the subject of research, not just because of its beauty, but also to discover how nature can produce such a superior product with excellent mechanical properties from such relatively weak raw materials. Four decades ago, Wada [Wada K (1966) Spiral growth of nacre. Nature 211:1427] proposed that the spiral patterns in nacre could be explained by using the theory Frank [Frank F (1949) The influence of dislocations on crystal growth. Discuss Faraday Soc 5:48-54] had put forward of the growth of crystals by means of screw dislocations. Frank's mechanism of crystal growth has been amply confirmed by experimental observations of screw dislocations in crystals, but it is a growth mechanism for a single crystal, with growth fronts of molecules. However, the growth fronts composed of many tablets of crystalline aragonite visible in micrographs of nacre are not a molecular-scale but a mesoscale phenomenon, so it has not been evident how the Frank mechanism might be of relevance. Here, we demonstrate that nacre growth is organized around a liquid-crystal core of chitin crystallites, a skeleton that the other components of nacre subsequently flesh out in a process of hierarchical self-assembly. We establish that spiral and target patterns can arise in a liquid crystal formed layer by layer through the Burton-Cabrera-Frank [Burton W, Cabrera N, Frank F (1951) The growth of crystals and the equilibrium structure of their surfaces. Philos Trans R Soc London Ser A 243:299-358] dynamics, and furthermore that this layer growth mechanism is an instance of an important class of physical systems termed excitable media. Artificial liquid crystals grown in this way may have many technological applications. PMID:19528636

  15. Lithium-loaded liquid scintillators

    DOEpatents

    Dai, Sheng; Kesanli, Banu; Neal, John S.

    2012-05-15

    The invention is directed to a liquid scintillating composition containing (i) one or more non-polar organic solvents; (ii) (lithium-6)-containing nanoparticles having a size of up to 10 nm and surface-capped by hydrophobic molecules; and (iii) one or more fluorophores. The invention is also directed to a liquid scintillator containing the above composition.

  16. The Fe-rich clay microsystems in basalt-komatiite lavas: importance of Fe-smectites for pre-biotic molecule catalysis during the Hadean eon.

    PubMed

    Meunier, Alain; Petit, Sabine; Cockell, Charles S; El Albani, Abderrazzak; Beaufort, Daniel

    2010-06-01

    During the Hadean to early Archean period (4.5-3.5 Ga), the surface of the Earth's crust was predominantly composed of basalt and komatiite lavas. The conditions imposed by the chemical composition of these rocks favoured the crystallization of Fe-Mg clays rather than that of Al-rich ones (montmorillonite). Fe-Mg clays were formed inside chemical microsystems through sea weathering or hydrothermal alteration, and for the most part, through post-magmatic processes. Indeed, at the end of the cooling stage, Fe-Mg clays precipitated directly from the residual liquid which concentrated in the voids remaining in the crystal framework of the mafic-ultramafic lavas. Nontronite-celadonite and chlorite-saponite covered all the solid surfaces (crystals, glass) and are associated with tiny pyroxene and apatite crystals forming the so-called "mesostasis". The mesostasis was scattered in the lava body as micro-settings tens of micrometres wide. Thus, every square metre of basalt or komatiite rocks was punctuated by myriads of clay-rich patches, each of them potentially behaving as a single chemical reactor which could concentrate the organics diluted in the ocean water. Considering the high catalytic potentiality of clays, and particularly those of the Fe-rich ones (electron exchangers), it is probable that large parts of the surface of the young Earth participated in the synthesis of prebiotic molecules during the Hadean to early Archean period through innumerable clay-rich micro-settings in the massive parts and the altered surfaces of komatiite and basaltic lavas. This leads us to suggest that Fe,Mg-clays should be preferred to Al-rich ones (montmorillonite) to conduct experiments for the synthesis and the polymerisation of prebiotic molecules. PMID:20213161

  17. Solute diffusion in liquid metals

    NASA Technical Reports Server (NTRS)

    Bhat, B. N.

    1973-01-01

    A gas model of diffusion in liquid metals is presented. In this model, ions of liquid metals are assumed to behave like the molecules in a dense gas. Diffusion coefficient of solute is discussed with reference to its mass, ionic size, and pair potential. The model is applied to the case of solute diffusion in liquid silver. An attempt was made to predict diffusion coefficients of solutes with reasonable accuracy.

  18. The Molecules of the Cell Membrane.

    ERIC Educational Resources Information Center

    Bretscher, Mark S.

    1985-01-01

    Cell membrane molecules form a simple, two-dimensional liquid controlling what enters and leaves the cell. Discusses cell membrane molecular architecture, plasma membranes, epithelial cells, cycles of endocytosis and exocytosis, and other topics. Indicates that some cells internalize, then recycle, membrane area equivalent to their entire surface…

  19. Liquid crystal orientation control in photonic liquid crystal fibers

    NASA Astrophysics Data System (ADS)

    Chychlowski, M. S.; Nowinowski-Kruszelnicki, E.; Woliński, T. R.

    2011-05-01

    Similarly to liquid crystal displays technology in photonic liquid crystal fibers (PLCFs) a molecular orientation control is a crucial issue that influences proper operation of PLCF-based devices. The paper presents two distinct configurations: planar and radial escaped orientation of the LC molecules inside capillaries as well as methods of their application to photonic liquid crystal fibers. Possibilities of LC orientation control influence both: attenuation and transmitting spectra of the PLCF The orienting method is based on creation of an additional orienting layer on the inner surface of the capillary or air hole of the photonic liquid crystal fiber. Aligning materials used in the experiment are commercially available polyimides SE1211 and SE130 which induce liquid crystal homeotropic and planar anchoring conditions. The orienting layer increase an order parameter of the liquid crystal improving propagation properties and stability of photonic liquid crystal fiber-based devices.

  20. Solid-state 13C NMR study of banana liquid crystals - 3: Alkyl-tail-group packing environments of an acute-angle bent-core molecule in the hexagonal columnar and cubic phases

    NASA Astrophysics Data System (ADS)

    Kurosu, Hiromichi; Endo, Yumi; Kimura, Saori; Hashimoto, Tomoko; Harada, Motoi; Lee, Eun-Woo; Sone, Masato; Watanabe, Junji; Kang, Sungmin

    2016-02-01

    Solid-state 13C nuclear magnetic resonance (NMR) measurements were performed on the hexagonal columnar and cubic phases of an acute-angle banana-shaped molecule, N(1,7)-S30. In the hexagonal columnar phase, three peaks appear at the NMR chemical shifts assigned to the internal methylene carbons of alkyl tails, indicating that the two alkyl tails have different packing structures, and one of the tails has two different conformations within a single molecule. Combined cross-polarization/magic-angle spinning and pulse saturation transfer/magic-angle spinning measurements show that one of the alkyl chains is located inside and the other is located outside the columnar structure. In the cubic phase, pulse saturation transfer/magic-angle spinning measurement shows that only one peak appears at the NMR chemical shifts assigned to the internal methylene carbons of alkyl tails, indicating that both of the alkyl chains are located outside the cubic structure.

  1. Hindered diffusion of coal liquids

    SciTech Connect

    Tsotsis, T.T.; Sahimi, M. . Dept. of Chemical Engineering); Webster, I.A. )

    1992-01-01

    The molecules comprising coal liquids can range from less than 10 to several hundred [angstrom] in diameter. Their size is, therefore, comparable to the average pore size of most hydroprocessing catalysts. Thus, during processing, transport of these molecules into the catalyst occurs mainly by configurational'' or hindered diffusion,'' which is the result of two phenomena occurring in the pores; the distribution of solute molecules in the pores is affected by the pores and the solute molecules experience an increased hydrodynamic drag. The field of hindered diffusion has been reviewed by Deen [16]. The earliest studies in the filed were by Renkin et al. [17].

  2. NMR studies of oriented molecules

    SciTech Connect

    Sinton, S.W.

    1981-11-01

    Deuterium and proton magnetic resonance are used in experiments on a number of compounds which either form liquid crystal mesophases themselves or are dissolved in a liquid crystal solvent. Proton multiple quantum NMR is used to simplify complicated spectra. The theory of nonselective multiple quantum NMR is briefly reviewed. Benzene dissolved in a liquid crystal are used to demonstrate several outcomes of the theory. Experimental studies include proton and deuterium single quantum (..delta..M = +-1) and proton multiple quantum spectra of several molecules which contain the biphenyl moiety. 4-Cyano-4'-n-pentyl-d/sub 11/-biphenyl (5CB-d/sub 11/) is studied as a pure compound in the nematic phase. The obtained chain order parameters and dipolar couplings agree closely with previous results. Models for the effective symmetry of the biphenyl group in 5CB-d/sub 11/ are tested against the experimental spectra. The dihedral angle, defined by the planes containing the rings of the biphenyl group, is found to be 30 +- 2/sup 0/ for 5DB-d/sub 11/. Experiments are also described for 4,4'-d/sub 2/-biphenyl, 4,4' - dibromo-biphenyl, and unsubstituted biphenyl.

  3. Surface vibrational spectroscopy of pure liquids

    SciTech Connect

    Superfine, R.; Huang, J.Y.; Du, Q.; Shen, Y.R.

    1991-03-01

    We report the use of infrared visible sum frequency generation (SFG) to obtain the surface vibrational spectra of pure liquid methanol and water. These are the first surface vibrational spectra ever obtained for pure liquids. We have also deduced from the SFG results the absolute orientations of molecules at the pure liquid/vapor interface. The surface methanol molecules appear to have their CH{sub 3} groups projecting out of the liquid in agreement with the theoretical prediction. For the orientation of surface water molecules, however, different calculations have yielded very different predictions. Our SFG measurement provides clear evidence that the molecules are oriented with an unbonded hydrogen projecting out of the liquid. 9 refs., 3 figs.

  4. Target molecules detection by waveguiding in a photonic silicon membrane

    DOEpatents

    Letant, Sonia E.; Van Buuren, Anthony; Terminello, Louis; Hart, Bradley R.

    2006-12-26

    Disclosed herein is a porous silicon filter capable of binding and detecting biological and chemical target molecules in liquid or gas samples. A photonic waveguiding silicon filter with chemical and/or biological anchors covalently attached to the pore walls bind target molecules. The system uses transmission curve engineering principles to allow measurements to be made in situ and in real time to detect the presence of various target molecules and calculate the concentration of bound target.

  5. Target molecules detection by waveguiding in a photonic silicon membrane

    DOEpatents

    Letant, Sonia; Van Buuren, Anthony; Terminello, Louis

    2004-08-31

    Disclosed herein is a photonic silicon filter capable of binding and detecting biological and chemical target molecules in liquid or gas samples. A photonic waveguiding silicon filter with chemical and/or biological anchors covalently attached to the pore walls selectively bind target molecules. The system uses transmission curve engineering principles to allow measurements to be made in situ and in real time to detect the presence of various target molecules and determine the concentration of bound target.

  6. Electrochemical Single-Molecule Transistors with Optimized Gate Coupling.

    PubMed

    Osorio, Henrry M; Catarelli, Samantha; Cea, Pilar; Gluyas, Josef B G; Hartl, František; Higgins, Simon J; Leary, Edmund; Low, Paul J; Martín, Santiago; Nichols, Richard J; Tory, Joanne; Ulstrup, Jens; Vezzoli, Andrea; Milan, David C; Zeng, Qiang

    2015-11-18

    Electrochemical gating at the single molecule level of viologen molecular bridges in ionic liquids is examined. Contrary to previous data recorded in aqueous electrolytes, a clear and sharp peak in the single molecule conductance versus electrochemical potential data is obtained in ionic liquids. These data are rationalized in terms of a two-step electrochemical model for charge transport across the redox bridge. In this model the gate coupling in the ionic liquid is found to be fully effective with a modeled gate coupling parameter, ξ, of unity. This compares to a much lower gate coupling parameter of 0.2 for the equivalent aqueous gating system. This study shows that ionic liquids are far more effective media for gating the conductance of single molecules than either solid-state three-terminal platforms created using nanolithography, or aqueous media. PMID:26488257

  7. Electrophoretic transport of biomolecules across liquid-liquid interfaces.

    PubMed

    Hahn, Thomas; Münchow, Götz; Hardt, Steffen

    2011-05-11

    The mass transfer resistance of a liquid-liquid interface in an aqueous two-phase system composed of poly(ethylene glycol) and dextran is investigated. Different types of proteins and DNA stained with fluorescent dyes serve as probes to study the transport processes close to the interface. A microfluidic device is employed to enable the electrophoretic transport of biomolecules from one phase to another. The results obtained for proteins can be explained solely via the different electrophoretic mobilities and different affinities of the molecules to the two phases, without any indications of a significant mass transfer resistance of the liquid-liquid interface. By contrast, DNA molecules adsorb to the interface and only desorb under an increased electric field strength. The desorption process carries the signature of a thermally activated escape from a metastable state, as reflected in the exponential decay of the fluorescence intensity at the interface as a function of time. PMID:21508474

  8. Clusters of mobile molecules in supercooled water

    NASA Astrophysics Data System (ADS)

    Giovambattista, Nicolas; Buldyrev, Sergey V.; Stanley, H. Eugene; Starr, Francis W.

    2005-07-01

    We study the spatially heterogeneous dynamics in water via molecular dynamics simulations using the extended simple point charge potential. We identify clusters formed by mobile molecules and study their properties. We find that these clusters grow in size and become more compact as temperature decreases. We analyze the probability density function of cluster size, and we study the cluster correlation length. We find that clusters appear to be characterized by a fractal dimension consistent with that of lattice animals. We relate the cluster size and correlation length to the configurational entropy, Sconf . We find that these quantities depend weakly on 1/Sconf . In particular, the linearity found between the cluster mass n* and 1/Sconf suggests that n* may be interpreted as the mass of the cooperatively rearranging regions that form the basis of the Adam-Gibbs approach to the dynamics of supercooled liquids. We study the motion of molecules within a cluster, and find that each molecule preferentially follows a neighboring molecule in the same cluster. Based on this finding we hypothesize that stringlike cooperative motion may be a general mechanism for molecular rearrangement of complex, as well as simple liquids. By mapping each equilibrium configuration onto its corresponding local potential energy minimum or inherent structure (IS), we are able to compare the mobile molecule clusters in the equilibrium system with the molecules forming the clusters identified in the transitions between IS. We find that (i) mobile molecule clusters obtained by comparing different system configurations and (ii) clusters obtained by comparing the corresponding IS are completely different for short time scales, but are the same on the longer time scales of diffusive motion.

  9. Role of the deposition temperature on the self-assembly of the non-planar molecule benzene-1,3,5-triphosphonic acid (BTP) at the liquid-solid interface.

    PubMed

    Nguyen, Doan Chau Yen; Smykalla, Lars; Nguyen, Thi Ngoc Ha; Mehring, Michael; Hietschold, Michael

    2016-09-21

    Benzene-1,3,5-triphosphonic acid (BTP) contains three non-planar phosphonic acid groups which enable three-dimensional hydrogen bonding. Because of these versatile 3D functional groups, BTP is an interesting intermediate to design both 2D and 3D supramolecular hydrogen-bonded architectures and organic-inorganic hybrid frameworks. However, the adsorption of BTP has surprisingly not been the subject of scanning tunneling microscopy (STM) investigations so far. Here a STM study of the adsorption pattern of BTP as obtained from deposition out of a solution in undecanol on an interface to highly-oriented pyrolytic graphite (HOPG) is presented. Furthermore, the influence of the substrate temperature during the deposition from solution on the self-assembly is investigated. High-resolution STM images reveal that the BTB molecules usually form various structures by co-adsorption with undecanol and that the BTP molecules as parts of self-assembled aggregates adsorb with their benzene ring planes tilted with respect to the substrate plane. The specific supramolecular pattern and the 2D packing density of BTP can be precisely tuned by adjusting the initial substrate temperature during deposition. The experimental results are compared to corresponding model structures obtained from semi-empirical simulations and explained by the influence of temperature on the concentration at the solution-solid interface and the kinetics of the self-assembly process. Based on these results, the control of the deposition substrate temperature has been proven to be a versatile tool to control the polymorphism of molecular patterns deposited out of solutions. PMID:27530556

  10. A supported liquid extraction-LC-MS/MS method for determination of GDC-0980 (Apitolisib), a dual small-molecule inhibitor of class 1A phosphoinositide 3-kinase and mammalian target of rapamycin, in human plasma.

    PubMed

    Ding, X; Li, F; McKnight, J; Schmidt, C; Strooisma, K; Shimizu, H; Faber, K; Ware, J A; Dean, B

    2014-11-01

    A liquid chromatographic-tandem mass spectrometry (LC-MS/MS) method for the determination of GDC-0980 (Apitolisib) concentrations in human plasma has been developed and validated to support clinical development. Supported liquid extraction (SLE) was used to extract plasma samples (80μL) and the resulting samples were analyzed using reverse-phase chromatography and mass spectrometry coupled with a turbo-ionspray interface. The mass analysis of GDC-0980 was performed using multiple reaction monitoring (MRM) transitions in positive ionization mode. The method was validated over the calibration curve range 0.0500-25.0ng/mL using linear regression and 1/x(2) weighting. Within-run relative standard deviation (%RSD) ranged from 0.4 to 3.9%, while the between-run %RSD varied from 1.1 to 1.5% for QCs. The accuracy ranged from 96.1% to 106.7% of nominal for within-run and 96.7-106.7% of nominal for between-run at all concentrations including the LLOQ quality control at 0.0500ng/mL. Extraction recovery of GDC-0980 was between 72.4% and 75.5%. Stability of GDC-0980 was established in human plasma for 547 days at -20°C and -70°C and established in reconstituted sample extracts for 146h when stored at 2-8°C. Stable-labeled internal standard was used to minimize matrix effects. Mean pharmacokinetic parameters determined using this method for the day 1 control group in a phase I trial were: Cmax=11.1ng/mL, AUC0-inf=108ngh/mL, and T1/2=13.1h. PMID:25165011

  11. Enzymatic DNA molecules

    NASA Technical Reports Server (NTRS)

    Joyce, Gerald F. (Inventor); Breaker, Ronald R. (Inventor)

    1998-01-01

    The present invention discloses deoxyribonucleic acid enzymes--catalytic or enzymatic DNA molecules--capable of cleaving nucleic acid sequences or molecules, particularly RNA, in a site-specific manner, as well as compositions including same. Methods of making and using the disclosed enzymes and compositions are also disclosed.

  12. Adhesion molecules and receptors

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Adhesion molecules are necessary for leukocyte trafficking and differentiation. They serve to initiate cell-cell interactions under conditions of shear, and they sustain the cell-cell and cell-matrix interactions needed for cellular locomotion. They also can serve directly as signaling molecules act...

  13. Molecules between the Stars.

    ERIC Educational Resources Information Center

    Verschuur, Gerrit L.

    1987-01-01

    Provides a listing of molecules discovered to date in the vast interstellar clouds of dust and gas. Emphasizes the recent discoveries of organic molecules. Discusses molecular spectral lines, MASERs (microwave amplification by stimulated emission of radiation), molecular clouds, and star birth. (TW)

  14. Energy conversion at liquid/liquid interfaces: artificial photosynthetic systems

    NASA Technical Reports Server (NTRS)

    Volkov, A. G.; Gugeshashvili, M. I.; Deamer, D. W.

    1995-01-01

    This chapter focuses on multielectron reactions in organized assemblies of molecules at the liquid/liquid interface. We describe the thermodynamic and kinetic parameters of such reactions, including the structure of the reaction centers, charge movement along the electron transfer pathways, and the role of electric double layers in artificial photosynthesis. Some examples of artificial photosynthesis at the oil/water interface are considered, including water photooxidation to the molecular oxygen, oxygen photoreduction, photosynthesis of amphiphilic compounds and proton evolution by photochemical processes.

  15. Single-Molecule Electronics: Chemical and Analytical Perspectives.

    PubMed

    Nichols, Richard J; Higgins, Simon J

    2015-01-01

    It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions. Such measurements can be made across a wide range of environments including ambient conditions, organic liquids, ionic liquids, aqueous solutions, electrolytes, and ultra high vacuum. This has given new insights into charge transport across molecule electrical junctions, and these experimental methods have been complemented with increasingly sophisticated theory. This article reviews progress in single-molecule electronics from a chemical perspective and discusses topics such as the molecule-surface coupling in electrical junctions, chemical control, and supramolecular interactions in junctions and gating charge transport. The article concludes with an outlook regarding chemical analysis based on single-molecule conductance. PMID:26048551

  16. Single-Molecule Electronics: Chemical and Analytical Perspectives

    NASA Astrophysics Data System (ADS)

    Nichols, Richard J.; Higgins, Simon J.

    2015-07-01

    It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions. Such measurements can be made across a wide range of environments including ambient conditions, organic liquids, ionic liquids, aqueous solutions, electrolytes, and ultra high vacuum. This has given new insights into charge transport across molecule electrical junctions, and these experimental methods have been complemented with increasingly sophisticated theory. This article reviews progress in single-molecule electronics from a chemical perspective and discusses topics such as the molecule-surface coupling in electrical junctions, chemical control, and supramolecular interactions in junctions and gating charge transport. The article concludes with an outlook regarding chemical analysis based on single-molecule conductance.

  17. Langmuir Films of Polycyclic Molecules on Mercury

    SciTech Connect

    Tamam,L.; Kraack, H.; Sloutskin, E.; Ocko, B.; Pershan, P.; Deutsch, M.

    2007-01-01

    Langmuir films (LFs) of biphenyl and anthracene derivatives on the surface of liquid mercury were studied by surface-specific X-ray and surface tension measurements. Phases of lying-down, side-lying and standing-up molecules were found, some of which exhibit long-range lateral order. The molecular symmetry and the position and nature of the side-, end-, and headgroups are shown to dominate the structural evolution of the LFs with surface coverage.

  18. Soft Landing of Complex Molecules on Surfaces

    SciTech Connect

    Johnson, Grant E.; Hu, Qichi; Laskin, Julia

    2011-07-01

    Mass spectrometry is a versatile technique for identification and structural characterization of large molecules. The advent of soft ionization techniques such as electrospray (ESI) (1-2) has enabled ionization of a wide variety of complex molecules without significant \\fragmentation while non-thermal ion sources such as laser vaporization (3-4) and magnetron sputtering (5-6) have provided access to materials that cannot, currently, be produced through conventional techniques. Most mass spectrometry studies rely on ionization of a molecule of interest or a complex mixture followed by mass analysis. Alternatively, mass spectrometry may be used as a preparatory technique, in which mass-selected ions are deposited onto solid supports or into liquid materials (7-18). Preparatory mass spectrometry offers several unique advantages for deposition of complex molecules on substrates including the ability to generate high-purity uniform films (19-20), unprecedented selectivity and specificity of preparation of deposited species (11, 21-22), the ability to focus and pattern an ion beam (23-24), and flexibility in both ion formation (1, 3, 25-26) and mass selection (27-32) processes. This review will highlight applications of mass-selected deposition of complex molecules for selective immobilization of biological molecules and catalytically active complexes on substrates.

  19. Interactions of biomacromolecules with reverse hexagonal liquid crystals: drug delivery and crystallization applications.

    PubMed

    Libster, Dima; Aserin, Abraham; Garti, Nissim

    2011-04-15

    Recently, self-assembled lyotropic liquid crystals (LLCs) of lipids and water have attracted the attention of both scientific and applied research communities, due to their remarkable structural complexity and practical potential in diverse applications. The phase behavior of mixtures of glycerol monooleate (monoolein, GMO) was particularly well studied due to the potential utilization of these systems in drug delivery systems, food products, and encapsulation and crystallization of proteins. Among the studied lyotropic mesophases, reverse hexagonal LLC (H(II)) of monoolein/water were not widely subjected to practical applications since these were stable only at elevated temperatures. Lately, we obtained stable H(II) mesophases at room temperature by incorporating triacylglycerol (TAG) molecules into the GMO/water mixtures and explored the physical properties of these structures. The present feature article summarizes recent systematic efforts in our laboratory to utilize the H(II) mesophases for solubilization, and potential release and crystallization of biomacromolecules. Such a concept was demonstrated in the case of two therapeutic peptides-cyclosporin A (CSA) and desmopressin, as well as RALA peptide, which is a model skin penetration enhancer, and eventually a larger macromolecule-lysozyme (LSZ). In the course of the study we tried to elucidate relationships between the different levels of organization of LLCs (from the microstructural level, through mesoscale, to macroscopic level) and find feasible correlations between them. Since the structural properties of the mesophase systems are a key factor in drug release applications, we investigated the effects of these guest molecules on their conformations and the way these molecules partition within the domains of the mesophases. The examined H(II) mesophases exhibited great potential as transdermal delivery vehicles for bioactive peptides, enabling tuning the release properties according to their chemical

  20. Ultracold polar KRb molecules

    NASA Astrophysics Data System (ADS)

    Neyenhuis, Brian; Chotia, Amodsen; Moses, Steven; Ye, Jun; Jin, Deborah

    2011-05-01

    Ultracold polar molecules in the quantum degenerate regime open the possibility of realizing quantum gases with long-range, and spatially anisotropic, interparticle interactions. Currently, we can create a gas of ultracold fermionic ground-state KRb molecules in with a peak density of 1012 cm-3 and a temperature just 1.4 times the Fermi temperature. We will report on efforts to further cool this gas of molecules. One possibility is to evaporatively cool a spin-polarized molecular Fermi gas confined in quasi-2D, where we would rely on dipole-dipole interactions for rethermalization. We acknowledge funding from NIST, NSF, and AFOSR-MURI.

  1. Poisson's spot with molecules

    SciTech Connect

    Reisinger, Thomas; Holst, Bodil; Patel, Amil A.; Smith, Henry I.; Reingruber, Herbert; Fladischer, Katrin; Ernst, Wolfgang E.; Bracco, Gianangelo

    2009-05-15

    In the Poisson-spot experiment, waves emanating from a source are blocked by a circular obstacle. Due to their positive on-axis interference an image of the source (the Poisson spot) is observed within the geometrical shadow of the obstacle. In this paper we report the observation of Poisson's spot using a beam of neutral deuterium molecules. The wavelength independence and the weak constraints on angular alignment and position of the circular obstacle make Poisson's spot a promising candidate for applications ranging from the study of large molecule diffraction to patterning with molecules.

  2. Poisson's spot with molecules

    NASA Astrophysics Data System (ADS)

    Reisinger, Thomas; Patel, Amil A.; Reingruber, Herbert; Fladischer, Katrin; Ernst, Wolfgang E.; Bracco, Gianangelo; Smith, Henry I.; Holst, Bodil

    2009-05-01

    In the Poisson-spot experiment, waves emanating from a source are blocked by a circular obstacle. Due to their positive on-axis interference an image of the source (the Poisson spot) is observed within the geometrical shadow of the obstacle. In this paper we report the observation of Poisson’s spot using a beam of neutral deuterium molecules. The wavelength independence and the weak constraints on angular alignment and position of the circular obstacle make Poisson’s spot a promising candidate for applications ranging from the study of large molecule diffraction to patterning with molecules.

  3. Nanosecond liquid crystalline optical modulator

    DOEpatents

    Borshch, Volodymyr; Shiyanovskii, Sergij V.; Lavrentovich, Oleg D.

    2016-07-26

    An optical modulator includes a liquid crystal cell containing liquid crystal material having liquid crystal molecules oriented along a quiescent director direction in the unbiased state, and a voltage source configured to apply an electric field to the liquid crystal material wherein the direction of the applied electric field does not cause the quiescent director direction to change. An optical source is arranged to transmit light through or reflect light off the liquid crystal cell with the light passing through the liquid crystal material at an angle effective to undergo phase retardation in response to the voltage source applying the electric field. The liquid crystal material may have negative dielectric anisotropy, and the voltage source configured to apply an electric field to the liquid crystal material whose electric field vector is transverse to the quiescent director direction. Alternatively, the liquid crystal material may have positive dielectric anisotropy and the voltage source configured to apply an electric field to the liquid crystal material whose electric field vector is parallel with the quiescent director direction.

  4. Single-Molecule Enzymology

    SciTech Connect

    Xie, Xiaoliang; Lu, H PETER.

    1999-06-04

    Viewing a movie of an enzyme molecule made from molecular dynamics (MD) simulation, we see incredible details of molecular motions, be it a change of the conformation or the action of a chemical reaction.

  5. Of Molecules and Models.

    ERIC Educational Resources Information Center

    Brinner, Bonnie

    1992-01-01

    Presents an activity in which models help students visualize both the DNA process and transcription. After constructing DNA, RNA messenger, and RNA transfer molecules; students model cells, protein synthesis, codons, and RNA movement. (MDH)

  6. Polyatomic molecule vibrations

    NASA Technical Reports Server (NTRS)

    1976-01-01

    Polyatomic molecule vibrations are analyzed as harmonic vibrations along normal coordinates. The energy eigenvalues are found for linear and nonlinear symmetric triatomic molecules for valence bond models of the potential function with arbitrary coupling coefficients; such models can usually be fitted to observed energy levels with reasonably good accuracy. Approximate normal coordinates for the H2O molecule are discussed. Degenerate vibrational modes such as occur in CO2 are analyzed and expressions for Fermi resonance between close-lying states of the same symmetry are developed. The bending modes of linear triatomic molecules are expressed in terms of Laguerre polynomials in cylindrical coordinates as well as in terms of Hermite polynomials in Cartesian coordinates. The effects of large-amplitude bending such as occur in the C3 molecule are analyzed, along with anharmonic effects, which split the usually degenerate bending mode energy levels. Finally, the vibrational frequencies, degeneracies, and symmetry properties of XY3, X2Y2, and XY4 type molecules are discussed.

  7. Modeling liquid crystal polymeric devices

    NASA Astrophysics Data System (ADS)

    Gimenez Pinto, Vianney Karina

    The main focus of this work is the theoretical and numerical study of materials that combine liquid crystal and polymer. Liquid crystal elastomers are polymeric materials that exhibit both the ordered properties of the liquid crystals and the elastic properties of rubbers. Changing the order of the liquid crystal molecules within the polymer network can induce shape change. These materials are very valuable for applications such as actuators, sensors, artificial muscles, haptic displays, etc. In this work we apply finite element elastodynamics simulations to study the temperature induced shape deformation in nematic elastomers with complex director microstructure. In another topic, we propose a novel numerical method to model the director dynamics and microstructural evolution of three dimensional nematic and cholesteric liquid crystals. Numerical studies presented in this work are in agreement with experimental observations and provide insight into the design of application devices.

  8. Positron binding to molecules

    NASA Astrophysics Data System (ADS)

    Danielson, J. R.

    2011-05-01

    While there is theoretical evidence that positrons can bind to atoms, calculations for molecules are much less precise. Unfortunately, there have been no measurements of positron-atom binding, due primarily to the difficulty in forming positron-atom bound states in two-body collisions. In contrast, positrons attach to molecules via Feshbach resonances (VFR) in which a vibrational mode absorbs the excess energy. Using a high-resolution positron beam, this VFR process has been studied to measure binding energies for more than 40 molecules. New measurements will be described in two areas: positron binding to relatively simple molecules, for which theoretical calculations appear to be possible; and positron binding to molecules with large permanent dipole moments, which can be compared to analogous, weakly bound electron-molecule (negative-ion) states. Binding energies range from 75 meV for CS2 (no dipole moment) to 180 meV for acetonitrile (CH3CN). Other species studied include aldehydes and ketones, which have permanent dipole moments in the range 2.5 - 3.0 debye. The measured binding energies are surprisingly large (by a factor of 10 to 100) compared to those for the analogous negative ions, and these differences will be discussed. New theoretical calculations for positron-molecule binding are in progress, and a recent result for acetonitrile will be discussed. This ability to compare theory and experiment represents a significant step in attempts to understand positron binding to matter. In collaboration with A. C. L. Jones, J. J. Gosselin, and C. M. Surko, and supported by NSF grant PHY 07-55809.

  9. Characteristics of Liquid Flow Induced by Atmospheric Pressure DC Glow Discharge with Liquid Electrode

    NASA Astrophysics Data System (ADS)

    Tochikubo, Fumiyoshi; Aoki, Takuya; Shirai, Naoki; Uchida, Satoshi

    2015-09-01

    In the application of atmospheric-pressure discharges in contact with liquid, primary reactions are initiated between radicals and liquid molecules at plasma-liquid interface. Since the diffusion in the liquid is very slow, some convective flow is necessary to exchange the chemicals at the plasma-liquid interface for the efficient reactions. In our previous work, we found the appearance of specific downward flow in the liquid just below the dc glow discharge in contact with liquid. This downflow will be effective for exchanging the chemicals at plasma-liquid interface. In this work, we investigated the characteristics of liquid flow induced by atmospheric-pressure dc glow discharge with liquid electrode in detail; the influence of voltage polarity, current amplitude, liquid conductivity, the electrode arrangement, and so on. The spatiotemporal development of liquid flow was visualized by schlieren method, and the temperature distribution was measured using temperature-sensitive liquid crystal particles dispersed in the liquid. The liquid-flow characteristics was reproduced by a fluid simulation considering a downward driving force at liquid surface from plasma. The candidate of the driving force will be the momentum transfer of charged species at the liquid surface. This work is partly supported by JSPS KAKENHI Grant Number 15H03584.

  10. Understanding ultracold polar molecules

    NASA Astrophysics Data System (ADS)

    Julienne, Paul

    2009-05-01

    The successful production of a dense sample of ultracold ground state KRb polar molecules [1] opens the door to a new era of research with dipolar gases and lattices of such species. This feat was achieved by first associating a K and a Rb atom to make a weakly bound Feshbach molecule and then coherently transferring the population to the ground vibrational level of the molecule. This talk focuses on theoretical issues associated with making and using ultracold polar molecules, using KRb as an example [2]. Full understanding of this species and the processes by which it is made requires taking advantage of accurate molecular potentials [3], ab initio calculations [4], and the properties of the long-range potential. A highly accurate model is available for KRb for all bound states below the ground state separated atom limit and could be constructed for other species. The next step is to develop an understanding of the interactions between polar molecules, and their control in the ultracold domain. Understanding long-range interactions and threshold resonances will be crucial for future work. [1] K.-K. Ni, et al, Science 322, 231(2008). [2] P. S. Julienne, arXiv:0812:1233. [3] Pashov et al., Phys. Rev. A76, 022511 (2007). [4] S. Kotochigova, et al., arXiv:0901.1486.

  11. LIQUID-LIQUID EXTRACTION COLUMNS

    DOEpatents

    Thornton, J.D.

    1957-12-31

    This patent relates to liquid-liquid extraction columns having a means for pulsing the liquid in the column to give it an oscillatory up and down movement, and consists of a packed column, an inlet pipe for the dispersed liquid phase and an outlet pipe for the continuous liquid phase located in the direct communication with the liquid in the lower part of said column, an inlet pipe for the continuous liquid phase and an outlet pipe for the dispersed liquid phase located in direct communication with the liquid in the upper part of said column, a tube having one end communicating with liquid in the lower part of said column and having its upper end located above the level of said outlet pipe for the dispersed phase, and a piston and cylinder connected to the upper end of said tube for applying a pulsating pneumatic pressure to the surface of the liquid in said tube so that said surface rises and falls in said tube.

  12. Molecules on ice

    SciTech Connect

    Clary, D.C.

    1996-03-15

    The ozone hole that forms in the spring months over the Antarctic is thought to be produced through a network of chemical reactions catalyzed by the surfaces of ice crystals in polar stratospheric clouds (PSCs). A reaction between chlorine reservoir molecules, such as HCl + ClONO{sub 2} > HNO{sub 3} + Cl{sub 2}, is kinetically forbidden in the gas phase but proceeds quickly on the surface of ice and produces Cl{sub 2} molecules that are photodissociated by sunlight to yield the Cl atoms that destroy ozone. This destructive chain of events begins when HCl molecules stick to the ice crystals, and the mechanism for this crucial sticking process has been the subject of much debate. Recent work describes a mechanism that explains how HCl sticks to ice. This article goes on to detail research focusing surface reactions in stratospheric chemistry. 9 refs., 1 fig.

  13. Positronium ions and molecules

    NASA Technical Reports Server (NTRS)

    Ho, Y. K.

    1990-01-01

    Recent theoretical studies on positronium ions and molecules are discussed. A positronium ion is a three particle system consisting of two electrons in singlet spin state, and a positron. Recent studies include calculations of its binding energy, positron annihilation rate, and investigations of its doubly excited resonant states. A positronium molecule is a four body system consisting of two positrons and two electrons in an overall singlet spin state. The recent calculations of its binding energy against the dissociation into two positronium atoms, and studies of auto-detaching states in positronium molecules are discussed. These auto-dissociating states, which are believed to be part of the Rydberg series as a result of a positron attaching to a negatively charged positronium ion, Ps-, would appear as resonances in Ps-Ps scattering.

  14. Atomic branching in molecules

    NASA Astrophysics Data System (ADS)

    Estrada, Ernesto; Rodríguez-Velázquez, Juan A.; Randić, Milan

    A graph theoretic measure of extended atomic branching is defined that accounts for the effects of all atoms in the molecule, giving higher weight to the nearest neighbors. It is based on the counting of all substructures in which an atom takes part in a molecule. We prove a theorem that permits the exact calculation of this measure based on the eigenvalues and eigenvectors of the adjacency matrix of the graph representing a molecule. The definition of this measure within the context of the Hückel molecular orbital (HMO) and its calculation for benzenoid hydrocarbons are also studied. We show that the extended atomic branching can be defined using any real symmetric matrix, as well as any Hermitian (self-adjoint) matrix, which permits its calculation in topological, geometrical, and quantum chemical contexts.

  15. Single-Molecule Bioelectronics

    PubMed Central

    Rosenstein, Jacob K.; Lemay, Serge G.; Shepard, Kenneth L.

    2014-01-01

    Experimental techniques which interface single biomolecules directly with microelectronic systems are increasingly being used in a wide range of powerful applications, from fundamental studies of biomolecules to ultra-sensitive assays. Here we review several technologies which can perform electronic measurements of single molecules in solution: ion channels, nanopore sensors, carbon nanotube field-effect transistors, electron tunneling gaps, and redox cycling. We discuss the shared features among these techniques that enable them to resolve individual molecules, and discuss their limitations. Recordings from each of these methods all rely on similar electronic instrumentation, and we discuss the relevant circuit implementations and potential for scaling these single-molecule bioelectronic interfaces to high-throughput arrayed sensing platforms. PMID:25529538

  16. Single-molecule bioelectronics.

    PubMed

    Rosenstein, Jacob K; Lemay, Serge G; Shepard, Kenneth L

    2015-01-01

    Experimental techniques that interface single biomolecules directly with microelectronic systems are increasingly being used in a wide range of powerful applications, from fundamental studies of biomolecules to ultra-sensitive assays. In this study, we review several technologies that can perform electronic measurements of single molecules in solution: ion channels, nanopore sensors, carbon nanotube field-effect transistors, electron tunneling gaps, and redox cycling. We discuss the shared features among these techniques that enable them to resolve individual molecules, and discuss their limitations. Recordings from each of these methods all rely on similar electronic instrumentation, and we discuss the relevant circuit implementations and potential for scaling these single-molecule bioelectronic interfaces to high-throughput arrayed sensing platforms. PMID:25529538

  17. Photochemistry of interstellar molecules

    NASA Technical Reports Server (NTRS)

    Stief, L. J.

    1971-01-01

    The photochemistry of two diatomic and eight polyatomic molecules is discussed quantitatively. For an interstellar molecule, the lifetime against photodecomposition depends upon the absorption cross section, the quantum yield or probability of dissociation following photon absorption, and the interstellar radiation field. The constant energy density of Habing is used for the unobserved regions of interstellar radiation field, and the field in obscuring clouds is estimated by combining the constant flux with the observed interstellar extinction curve covering the visible and ultraviolet regions. Lifetimes against photodecomposition in the unobscured regions and as a function of increasing optical thickness in obscuring clouds are calculated for the ten species. The results show that, except for CO, all the molecules have comparable lifetimes of less than one hundred years. Thus they can exist only in dense clouds and can never have been exposed to the unobscured radiation. The calculations further show that the lifetimes in clouds of moderate opacity are of the order of one million years.

  18. Molecules in η Carinae

    NASA Astrophysics Data System (ADS)

    Loinard, Laurent; Menten, Karl M.; Güsten, Rolf; Zapata, Luis A.; Rodríguez, Luis F.

    2012-04-01

    We report the detection toward η Carinae of six new molecules, CO, CN, HCO+, HCN, HNC, and N2H+, and of two of their less abundant isotopic counterparts, 13CO and H13CN. The line profiles are moderately broad (~100 km s-1), indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO+ do not appear to be underabundant in η Carinae. On the other hand, molecules containing nitrogen or the 13C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of η Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

  19. Poisson's Spot with Molecules

    NASA Astrophysics Data System (ADS)

    Reisinger, Thomas; Patel, Amil; Reingruber, Herbert; Fladischer, Katrin; Ernst, Wolfgang E.; Bracco, Gianangelo; Smith, Henry I.; Holst, Bodil

    2009-03-01

    In the Poisson-Spot experiment, waves emanating from a source are blocked by a circular obstacle. Due to their positive on-axis interference an image of the source (the Poisson spot) is observed within the geometrical shadow of the obstacle. The Poisson spot is the last of the classical optics experiments to be realized with neutral matter waves. In this paper we report the observation of Poisson's Spot using a beam of neutral deuterium molecules. The wavelength-independence and the weak constraints on angular alignment and position of the circular obstacle make Poisson's spot a promising candidate for applications ranging from the study of large-molecule diffraction and coherence in atom-lasers to patterning with large molecules.

  20. MOLECULES IN {eta} CARINAE

    SciTech Connect

    Loinard, Laurent; Menten, Karl M.; Guesten, Rolf; Zapata, Luis A.; Rodriguez, Luis F.

    2012-04-10

    We report the detection toward {eta} Carinae of six new molecules, CO, CN, HCO{sup +}, HCN, HNC, and N{sub 2}H{sup +}, and of two of their less abundant isotopic counterparts, {sup 13}CO and H{sup 13}CN. The line profiles are moderately broad ({approx}100 km s{sup -1}), indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO{sup +} do not appear to be underabundant in {eta} Carinae. On the other hand, molecules containing nitrogen or the {sup 13}C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of {eta} Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

  1. Part I. Evaluation of thermodynamic and kinetic parameters for electron transfer and following chemical reaction from a global analysis of current-potential-time data. Part II. Electro-catalytic detection in high-performance liquid chromatography of vitamin B[sub 12] and other molecules of biological and environmental interest

    SciTech Connect

    Kumar, V.T.

    1992-01-01

    Simultaneous evaluation of electron transfer rate constant, k[sup 0], following chemical reaction rate constant, k[sub f], electron transfer coefficient, [alpha] and standard potential, E[sup 0][prime] for an electrochemical reaction following the EC mechanism is described. A mathematical model for the current response to a potential step is developed, starting with the Butler-Volmer equation for electrode kinetics and concentration expressions for the redox couple. The resulting integral equations are solved numerically via the Step Function method. Current-potential and current-time curves are simulated and tested under limiting conditions. The four parameters of the system are evaluated by fitting simulated current-voltage-time (i-E-t) surface to the theoretical equation. The method is applied to study an important biological molecule, viz., methyl cobalamin, in DMSO. Included in the discussion part is the use of kinetic zone diagrams to depict chronoamperometric current response as a function of dimensionless rate constants for the EC reaction scheme. This compact display of the influence of the two rate constants on current in all time windows can be used to select the best data for analysis. Theoretical limits of measurable rate constants can be estimated from the zone diagram. The development of a dropping mercury electrode detector for High Performance Liquid Chromatography (HPLC) and its application to analysis of B[sub 12] and other vitamins is described. This EC detector is able to achieve high levels of sensitivity by exploiting the catalytic hydrogen evolution undergone by many nitrogenous organic molecules. Vitamin B[sub 12], thiamine, riboflavin and niacinamide were analyzed individually and in mixtures on reverse phase C18 column. Preliminary results from the analysis of commercial multivitamin preparations are also discussed.

  2. Towards single molecule switches.

    PubMed

    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

  3. Plasmonic nanostructures: artificial molecules.

    PubMed

    Wang, Hui; Brandl, Daniel W; Nordlander, Peter; Halas, Naomi J

    2007-01-01

    This Account describes a new paradigm for the relationship between the geometry of metallic nanostructures and their optical properties. While the interaction of light with metallic nanoparticles is determined by their collective electronic or plasmon response, a compelling analogy exists between plasmon resonances of metallic nanoparticles and wave functions of simple atoms and molecules. Based on this insight, an entire family of plasmonic nanostructures, artificial molecules, has been developed whose optical properties can be understood within this picture: nanoparticles (nanoshells, nanoeggs, nanomatryushkas, nanorice), multi-nanoparticle assemblies (dimers, trimers, quadrumers), and a nanoparticle-over-metallic film, an electromagnetic analog of the spinless Anderson model. PMID:17226945

  4. Prebiologically Important Interstellar Molecules

    NASA Astrophysics Data System (ADS)

    Kuan, Y.-J.; Huang, H.-C.; Charnley, S. B.; Tseng, W.-L.; Snyder, L. E.; Ehrenfreund, P.; Kisiel, Z.; Thorwirth, S.; Bohn, R. K.; Wilson, T. L.

    2004-06-01

    Understanding the organic chemistry of molecular clouds, particularly the formation of biologically important molecules, is fundamental to the study of the processes which lead to the origin, evolution and distribution of life in the Galaxy. Determining the level of molecular complexity attainable in the clouds, and the nature of the complex organic material available to protostellar disks and the planetary systems that form from them, requires an understanding of the possible chemical pathways and is therefore a central question in astrochemistry. We have thus searched for prebiologically important molecules in the hot molecular cloud cores: Sgr B2(N-LMH), W51 e1/e2 and Orion-KL. Among the molecules searched: Pyrimidine is the unsubstituted ring analogue for three of the DNA and RNA bases. 2H-Azirine and Aziridine are azaheterocyclic compounds. And Glycine is the simplest amino acid. Detections of these interstellar organic molecular species will thus have important implications for Astrobiology. Our preliminary results indicate a tentative detection of interstellar glycine. If confirmed, this will be the first detection of an amino acid in interstellar space and will greatly strengthen the thesis that interstellar organic molecules could have played a pivotal role in the prebiotic chemistry of the early Earth.

  5. Algebraic theory of molecules

    NASA Technical Reports Server (NTRS)

    Iachello, Franco

    1995-01-01

    An algebraic formulation of quantum mechanics is presented. In this formulation, operators of interest are expanded onto elements of an algebra, G. For bound state problems in nu dimensions the algebra G is taken to be U(nu + 1). Applications to the structure of molecules are presented.

  6. Mighty Molecule Models

    ERIC Educational Resources Information Center

    Brown, Tom; Rushton, Greg; Bencomo, Marie

    2008-01-01

    As part of the SMATHematics Project: The Wonder of Science, The Power of Mathematics--a collaborative partnership between Kennesaw State University and two local school districts, fifth graders had the opportunity to puzzle out chemical formulas of propane, methanol, and other important molecules. In addition, they explored properties that…

  7. Diversity in Biological Molecules

    ERIC Educational Resources Information Center

    Newbury, H. John

    2010-01-01

    One of the striking characteristics of fundamental biological processes, such as genetic inheritance, development and primary metabolism, is the limited amount of variation in the molecules involved. Natural selective pressures act strongly on these core processes and individuals carrying mutations and producing slightly sub-optimal versions of…

  8. The Science of Molecules

    ERIC Educational Resources Information Center

    Flory, Paul J.

    1974-01-01

    The author maintains that chemistry has a key role as the science of molecules and rejects the concept of chemistry as a branch of physics. The scope of chemistry, the philosophies underlying its practice, and the teaching of the subject also are discussed. (DT)

  9. OMG: Open Molecule Generator

    PubMed Central

    2012-01-01

    Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck. PMID:22985496

  10. OMG: Open Molecule Generator.

    PubMed

    Peironcely, Julio E; Rojas-Chertó, Miguel; Fichera, Davide; Reijmers, Theo; Coulier, Leon; Faulon, Jean-Loup; Hankemeier, Thomas

    2012-01-01

    Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG), which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck. PMID:22985496

  11. Bacterial invasion reconstructed molecule by molecule

    SciTech Connect

    Werner, James H

    2009-01-01

    We propose to visualize the initial stages of bacterial infection of a human host cell with unmatched spatial and temporal resolution. This work will develop a new capability for the laboratory (super-resolution optical imaging), will test unresolved scientific hypotheses regarding host-pathogen interaction dynamics, and leverages state of the art 3D molecular tracking instrumentation developed recently by our group. There is much to be gained by applying new single molecule tools to the important and familiar problem of pathogen entry into a host cell. For example, conventional fluorescence microscopy has identified key host receptors, such as CD44 and {alpha}5{beta}1 integrin, that aggregate near the site of Salmonella typhimurium infection of human cells. However, due to the small size of the bacteria ({approx} 2 {micro}m) and the diffraction of the emitted light, one just sees a fluorescent 'blob' of host receptors that aggregate at the site of attachment, making it difficult to determine the exact number of receptors present or whether there is any particular spatial arrangement of the receptors that facilitates bacterial adhesion/entry. Using newly developed single molecule based super-resolution imaging methods, we will visualize how host receptors are directed to the site of pathogen adhesion and whether host receptors adopt a specific spatial arrangement for successful infection. Furthermore, we will employ our 3D molecular tracking methods to follow the injection of virulence proteins, or effectors, into the host cell by the pathogen Type III secretion system (TTSS). We expect these studies to provide mechanistic insights into the early events of pathogen infection that have here-to-fore been technically beyond our reach. Our Research Goals are: Goal 1--Construct a super-resolution fluorescence microscope and use this new capability to image the spatial distribution of different host receptors (e.g. CD44, as {alpha}5{beta}1 integrin) at the point of

  12. Water: The Strangest Liquid

    SciTech Connect

    Nilsson, Anders

    2009-02-24

    Water, H2O, is familiar to everyone - it shapes our bodies and our planet. But despite its abundance, water has remained a mystery, exhibiting many strange properties that are still not understood. Why does the liquid have an unusually large capacity to store heat? And why is it denser than ice? Now, using the intense X-ray beams from particle accelerators, investigations into water are leading to fundamental discoveries about the structure and arrangement of water molecules. This lecture will elucidate the many mysteries of water and discuss current studies that are revolutionizing the way we see and understand one of the most fundamental substances of life.

  13. Alkaloid-derived molecules in low rank Argonne premium coals.

    SciTech Connect

    Winans, R. E.; Tomczyk, N. A.; Hunt, J. E.

    2000-11-30

    Molecules that are probably derived from alkaloids have been found in the extracts of the subbituminous and lignite Argonne Premium Coals. High resolution mass spectrometry (HRMS) and liquid chromatography mass spectrometry (LCMS) have been used to characterize pyridine and supercritical extracts. The supercritical extraction used an approach that has been successful for extracting alkaloids from natural products. The first indication that there might be these natural products in coals was the large number of molecules found containing multiple nitrogen and oxygen heteroatoms. These molecules are much less abundant in bituminous coals and absent in the higher rank coals.

  14. Quantum Fluids of Self-Assembled Chains of Polar Molecules

    SciTech Connect

    Wang, D.-W.; Lukin, Mikhail D.; Demler, Eugene

    2006-11-03

    We study polar molecules in a stack of strongly confined pancake traps. When dipole moments point perpendicular to the planes of the traps and are sufficiently strong, the system is stable against collapse but attractive interaction between molecules in different layers leads to the formation of dipolar chains, analogously to the chaining phenomenon in classical rheological electro- and magnetofluids. We analyze properties of the resulting quantum liquid of dipolar chains and show that only the longest chains undergo Bose-Einstein condensation with a strongly reduced condensation temperature. We discuss several experimental methods for studying chains of polar molecules.

  15. Fluorescence correlation spectroscopy: Diagnostics for sparse molecules

    PubMed Central

    Maiti, Sudipta; Haupts, Ulrich; Webb, Watt W.

    1997-01-01

    The robust glow of molecular fluorescence renders even sparse molecules detectable and susceptible to analysis for concentration, mobility, chemistry, and photophysics. Correlation spectroscopy, a statistical-physics-based tool, gleans quantitative information from the spontaneously fluctuating fluorescence signals obtained from small molecular ensembles. This analytical power is available for studying molecules present at minuscule concentrations in liquid solutions (less than one nanomolar), or even on the surfaces of living cells at less than one macromolecule per square micrometer. Indeed, routines are becoming common to detect, locate, and examine individual molecules under favorable conditions. PMID:9342306

  16. ELECTRONS IN NONPOLAR LIQUIDS.

    SciTech Connect

    HOLROYD,R.A.

    2002-10-22

    Excess electrons can be introduced into liquids by absorption of high energy radiation, by photoionization, or by photoinjection from metal surfaces. The electron's chemical and physical properties can then be measured, but this requires that the electrons remain free. That is, the liquid must be sufficiently free of electron attaching impurities for these studies. The drift mobility as well as other transport properties of the electron are discussed here as well as electron reactions, free-ion yields and energy levels, Ionization processes typically produce electrons with excess kinetic energy. In liquids during thermalization, where this excess energy is lost to bath molecules, the electrons travel some distance from their geminate positive ions. In general the electrons at this point are still within the coulombic field of their geminate ions and a large fraction of the electrons recombine. However, some electrons escape recombination and the yield that escapes to become free electrons and ions is termed G{sub fi}. Reported values of G{sub fi} for molecular liquids range from 0.05 to 1.1 per 100 eV of energy absorbed. The reasons for this 20-fold range of yields are discussed here.

  17. Liquids with permanent porosity.

    PubMed

    Giri, Nicola; Del Pópolo, Mario G; Melaugh, Gavin; Greenaway, Rebecca L; Rätzke, Klaus; Koschine, Tönjes; Pison, Laure; Gomes, Margarida F Costa; Cooper, Andrew I; James, Stuart L

    2015-11-12

    Porous solids such as zeolites and metal-organic frameworks are useful in molecular separation and in catalysis, but their solid nature can impose limitations. For example, liquid solvents, rather than porous solids, are the most mature technology for post-combustion capture of carbon dioxide because liquid circulation systems are more easily retrofitted to existing plants. Solid porous adsorbents offer major benefits, such as lower energy penalties in adsorption-desorption cycles, but they are difficult to implement in conventional flow processes. Materials that combine the properties of fluidity and permanent porosity could therefore offer technological advantages, but permanent porosity is not associated with conventional liquids. Here we report free-flowing liquids whose bulk properties are determined by their permanent porosity. To achieve this, we designed cage molecules that provide a well-defined pore space and that are highly soluble in solvents whose molecules are too large to enter the pores. The concentration of unoccupied cages can thus be around 500 times greater than in other molecular solutions that contain cavities, resulting in a marked change in bulk properties, such as an eightfold increase in the solubility of methane gas. Our results provide the basis for development of a new class of functional porous materials for chemical processes, and we present a one-step, multigram scale-up route for highly soluble 'scrambled' porous cages prepared from a mixture of commercially available reagents. The unifying design principle for these materials is the avoidance of functional groups that can penetrate into the molecular cage cavities. PMID:26560299

  18. Liquids with permanent porosity

    NASA Astrophysics Data System (ADS)

    Giri, Nicola; Del Pópolo, Mario G.; Melaugh, Gavin; Greenaway, Rebecca L.; Rätzke, Klaus; Koschine, Tönjes; Pison, Laure; Gomes, Margarida F. Costa; Cooper, Andrew I.; James, Stuart L.

    2015-11-01

    Porous solids such as zeolites and metal-organic frameworks are useful in molecular separation and in catalysis, but their solid nature can impose limitations. For example, liquid solvents, rather than porous solids, are the most mature technology for post-combustion capture of carbon dioxide because liquid circulation systems are more easily retrofitted to existing plants. Solid porous adsorbents offer major benefits, such as lower energy penalties in adsorption-desorption cycles, but they are difficult to implement in conventional flow processes. Materials that combine the properties of fluidity and permanent porosity could therefore offer technological advantages, but permanent porosity is not associated with conventional liquids. Here we report free-flowing liquids whose bulk properties are determined by their permanent porosity. To achieve this, we designed cage molecules that provide a well-defined pore space and that are highly soluble in solvents whose molecules are too large to enter the pores. The concentration of unoccupied cages can thus be around 500 times greater than in other molecular solutions that contain cavities, resulting in a marked change in bulk properties, such as an eightfold increase in the solubility of methane gas. Our results provide the basis for development of a new class of functional porous materials for chemical processes, and we present a one-step, multigram scale-up route for highly soluble ‘scrambled’ porous cages prepared from a mixture of commercially available reagents. The unifying design principle for these materials is the avoidance of functional groups that can penetrate into the molecular cage cavities.

  19. LIQUID TARGET

    DOEpatents

    Martin, M.D.; Salsig, W.W. Jr.

    1959-01-13

    A liquid handling apparatus is presented for a liquid material which is to be irradiated. The apparatus consists essentially of a reservoir for the liquid, a target element, a drain tank and a drain lock chamber. The target is in the form of a looped tube, the upper end of which is adapted to be disposed in a beam of atomic particles. The lower end of the target tube is in communication with the liquid in the reservoir and a means is provided to continuously circulate the liquid material to be irradiated through the target tube. Means to heat the reservoir tank is provided in the event that a metal is to be used as the target material. The apparatus is provided with suitable valves and shielding to provide maximum safety in operation.

  20. Intermolecular interactions of liquid dichloromethane and equilibrium properties of liquid{endash}vapor and liquid{endash}liquid interfaces: A molecular dynamics study

    SciTech Connect

    Dang, L.X.

    1999-05-01

    Extensive molecular dynamics simulations are carried out to study the molecular interactions, liquid states, and liquid/vapor properties of dichloromethane. The study is also extended to the equilibrium properties of the liquid/liquid interface of water-dichloromethane. The intermolecular interactions among water, dichloromethane, and water-dichloromethane are described using our polarizable potential models. The equilibrium properties of liquid dichloromethane, including the radial distribution functions, the intermolecular structural factor, the self-diffusion coefficient, and the dielectric constant, are evaluated. The dielectric constant is computed using Ewald summation techniques and the computed result compared reasonably well with the available experimental data. Properties such as surface tensions and density profiles of liquid/vapor dichloromethane are evaluated. We found that the computed surface tensions for several temperatures are in excellent agreement with experimental data. The computed density profile of the liquid/liquid interface of water-dichloromethane is averaged over 1 ns and we found the computed profile to be quite smooth and stable. The effect of polarization on the liquid/liquid interfacial equilibrium properties is evaluated by computing the dipole moments of water and dichloromethane molecules as a function of the distance normal to the interface. We found that these values deviated significantly from the simulations that are based on nonpolarizable potential models. We attribute these observations to the changes in the electric fields around the water and dichloromethane molecules near the interface. {copyright} {ital 1999 American Institute of Physics.}

  1. A Guided Inquiry Liquid/Liquid Extractions Laboratory for Introductory Organic Chemistry

    ERIC Educational Resources Information Center

    Raydo, Margaret L.; Church, Megan S.; Taylor, Zane W.; Taylor, Christopher E.; Danowitz, Amy M.

    2015-01-01

    A guided inquiry laboratory experiment for teaching liquid/liquid extractions to first semester undergraduate organic chemistry students is described. This laboratory is particularly useful for introductory students as the analytes that are separated are highly colored dye molecules. This allows students to track into which phase each analyte…

  2. Single-molecule electrophoresis

    SciTech Connect

    Castro, A.; Shera, E.B.

    1995-09-15

    A novel method for the detection and identification of single molecules in solution has been devised, computer simulated, and experimentally achieved. The technique involves the determination of electrophoretic velocities by measuring the time required for individual molecules to travel a fixed distance between two laser beams. Computer simulations of the process were performed before-hand in order to estimate the experimental feasibility of the method and to determine the optimum values for the various experimental parameters. Examples of the use of the technique for the ultrasensitive detection and identification of rhodamine-6G, a mixture of DNA restriction fragments, and a mixture of proteins in aqueous solution are presented. 20 refs., 8 figs.

  3. Thermodynamics and Kinetics of Gas Storage in Porous Liquids.

    PubMed

    Zhang, Fei; Yang, Fengchang; Huang, Jingsong; Sumpter, Bobby G; Qiao, Rui

    2016-07-28

    The recent synthesis of organic molecular liquids with permanent porosity opens up exciting new avenues for gas capture, storage, and separation. Using molecular simulations, we study the thermodynamics and kinetics for the storage of CH4, CO2, and N2 molecules in porous liquids consisting of crown-ether-substituted cage molecules in a 15-crown-5 solvent. It is found that the intrinsic gas storage capacity per cage molecule follows the order CH4 > CO2 > N2, which does not correlate simply with the size of gas molecules. Different gas molecules are stored inside the cage differently; e.g., CO2 molecules prefer the cage's core whereas CH4 molecules favor both the core and the branch regions. All gas molecules considered can enter the cage essentially without energy barriers and leave the cage on a nanosecond time scale by overcoming a modest energy penalty. The molecular mechanisms of these observations are clarified. PMID:27379463

  4. Configurations of the amphiphilic molecules in micelles

    SciTech Connect

    Dill, K.A.

    1982-04-29

    Several theoretic models aim to account for the properties of micelles in terms of the configurations of the constituent amphiphilic chain molecules. Recent /sup 13/C NMR measurement of one property of the configuration distribution of the the hydrocarbon chain segments allows critical evaluation of these theories. It is concluded that the interphase and singly-bent chain theories, which fully account for chain continuity and for intermolecular constraints imposed by hydrophobic and steric forces, give a more satisfactory description of micellar molecular organization than models in which chains are ordered and radially aligned, or in which they have the complete disorder characteristic of an amorphous hydrocarbon liquid.

  5. Strange skyrmion molecules

    NASA Astrophysics Data System (ADS)

    Kopeliovich, Vladimir B.; Stern, Boris E.

    1997-05-01

    Composed skyrmions with B=2, strangeness content close to 0.5 and the binding energy of several tens of Mev are described. These skyrmions are obtained starting from the system of two B=1 hedgehogs located in different SU(2) subgroups of SU(3) and have the mass and baryon number distribution of molecular (dipole) type. The quantization of zero modes of skyrmion molecules and physics consequences of their existence are discussed.

  6. Strange skyrmion molecules

    SciTech Connect

    Kopeliovich, Vladimir B.; Stern, Boris E.

    1997-05-20

    Composed skyrmions with B=2, strangeness content close to 0.5 and the binding energy of several tens of Mev are described. These skyrmions are obtained starting from the system of two B=1 hedgehogs located in different SU(2) subgroups of SU(3) and have the mass and baryon number distribution of molecular (dipole) type. The quantization of zero modes of skyrmion molecules and physics consequences of their existence are discussed.

  7. Single Molecule Mechanochemistry

    NASA Astrophysics Data System (ADS)

    Li, Shaowei; Zhang, Yanxing; Ho, Wilson; Wu, Ruqian; Ruqian Wu, Yanxing Zhang Team; Wilson Ho, Shaowei Li Team

    Mechanical forces can be used to trigger chemical reactions through bending and stretching of chemical bonds. Using the reciprocating movement of the tip of a scanning tunneling microscope (STM), mechanical energy can be provided to a single molecule sandwiched between the tip and substrate. When the mechanical pulse center was moved to the outer ring feature of a CO molecule, the reaction rate was significantly increased compared with bare Cu surface and over Au atoms. First, DFT calculations show that the presence of CO makes the Cu cavity more attractive toward H2 Second, H2 prefers the horizontal adsorption geometry in the Cu-Cu and Au-Cu cavities and no hybridization occurs between the antibonding states of H2 and states of Cu atoms. While H2 loses electrons from its bonding state in all three cavities, the filling of its anti-bonding state only occurs in the CO-Cu cavity. Both make the CO-Cu cavity much more effectively to chop the H2 molecule. Work was supported by the National Science Foundation Center for Chemical Innovation on Chemistry at the Space-Time Limit (CaSTL) under Grant No. CHE-1414466.

  8. Model molecules mimicking asphaltenes.

    PubMed

    Sjöblom, Johan; Simon, Sébastien; Xu, Zhenghe

    2015-04-01

    Asphalthenes are typically defined as the fraction of petroleum insoluble in n-alkanes (typically heptane, but also hexane or pentane) but soluble in toluene. This fraction causes problems of emulsion formation and deposition/precipitation during crude oil production, processing and transport. From the definition it follows that asphaltenes are not a homogeneous fraction but is composed of molecules polydisperse in molecular weight, structure and functionalities. Their complexity makes the understanding of their properties difficult. Proper model molecules with well-defined structures which can resemble the properties of real asphaltenes can help to improve this understanding. Over the last ten years different research groups have proposed different asphaltene model molecules and studied them to determine how well they can mimic the properties of asphaltenes and determine the mechanisms behind the properties of asphaltenes. This article reviews the properties of the different classes of model compounds proposed and present their properties by comparison with fractionated asphaltenes. After presenting the interest of developing model asphaltenes, the composition and properties of asphaltenes are presented, followed by the presentation of approaches and accomplishments of different schools working on asphaltene model compounds. The presentation of bulk and interfacial properties of perylene-based model asphaltene compounds developed by Sjöblom et al. is the subject of the next part. Finally the emulsion-stabilization properties of fractionated asphaltenes and model asphaltene compounds is presented and discussed. PMID:25638443

  9. Photonic Molecule Lasers Revisited

    NASA Astrophysics Data System (ADS)

    Gagnon, Denis; Dumont, Joey; Déziel, Jean-Luc; Dubé, Louis J.

    2014-05-01

    Photonic molecules (PMs) formed by coupling two or more optical resonators are ideal candidates for the fabrication of integrated microlasers, photonic molecule lasers. Whereas most calculations on PM lasers have been based on cold-cavity (passive) modes, i.e. quasi-bound states, a recently formulated steady-state ab initio laser theory (SALT) offers the possibility to take into account the spectral properties of the underlying gain transition, its position and linewidth, as well as incorporating an arbitrary pump profile. We will combine two theoretical approaches to characterize the lasing properties of PM lasers: for two-dimensional systems, the generalized Lorenz-Mie theory will obtain the resonant modes of the coupled molecules in an active medium described by SALT. Not only is then the theoretical description more complete, the use of an active medium provides additional parameters to control, engineer and harness the lasing properties of PM lasers for ultra-low threshold and directional single-mode emission. We will extend our recent study and present new results for a number of promising geometries. The authors acknowledge financial support from NSERC (Canada) and the CERC in Photonic Innovations of Y. Messaddeq.

  10. Molecules in interstellar clouds

    NASA Astrophysics Data System (ADS)

    Irvine, W. M.; Hjalmarson, A.; Rydbeck, O. E. H.

    The physical conditions and chemical compositions of the gas in interstellar clouds are reviewed in light of the importance of interstellar clouds for star formation and the origin of life. The Orion A region is discussed as an example of a giant molecular cloud where massive stars are being formed, and it is pointed out that conditions in the core of the cloud, with a kinetic temperature of about 75 K and a density of 100,000-1,000,000 molecules/cu cm, may support gas phase ion-molecule chemistry. The Taurus Molecular Clouds are then considered as examples of cold, dark, relatively dense interstellar clouds which may be the birthplaces of solar-type stars and which have been found to contain the heaviest interstellar molecules yet discovered. The molecular species identified in each of these regions are tabulated, including such building blocks of biological monomers as H2O, NH3, H2CO, CO, H2S, CH3CN and H2, and more complex species such as HCOOCH3 and CH3CH2CN.

  11. Epithelial Cell Adhesion Molecule

    PubMed Central

    Trzpis, Monika; McLaughlin, Pamela M.J.; de Leij, Lou M.F.H.; Harmsen, Martin C.

    2007-01-01

    The epithelial cell adhesion molecule (EpCAM, CD326) is a glycoprotein of ∼40 kd that was originally identified as a marker for carcinoma, attributable to its high expression on rapidly proliferating tumors of epithelial origin. Normal epithelia express EpCAM at a variable but generally lower level than carcinoma cells. In early studies, EpCAM was proposed to be a cell-cell adhesion molecule. However, recent insights revealed a more versatile role for EpCAM that is not limited only to cell adhesion but includes diverse processes such as signaling, cell migration, proliferation, and differentiation. Cell surface expression of EpCAM may actually prevent cell-cell adhesion. Here, we provide a comprehensive review of the current knowledge on EpCAM biology in relation to other cell adhesion molecules. We discuss the implications of the newly identified functions of EpCAM in view of its prognostic relevance in carcinoma, inflammatory pathophysiology, and tissue development and regeneration as well as its role in normal epithelial homeostasis. PMID:17600130

  12. Sodium dimers on the surface of liquid {sup 4}He

    SciTech Connect

    Ancilotto, F.; DeToffol, G.; Toigo, F.

    1995-12-01

    We have studied the structure of a sodium dimer interacting with liquid {sup 4}He. We calculated the equilibrium configuration and binding energy of a Na{sub 2} molecule solvated in a bulk liquid {sup 4}He ``bubble`` and near the liquid-vapor interface ``dimple`` by using a density-functional approach. We find that the solvated molecule is a metastable state, while the the lowest energy bound state occurs when the molecule lies flat on the surface of the liquid. The binding energy for the ``erect`` dimer is only {similar_to}1 K higher than the flat dimer, with no potential energy barrier between the two orientations, implying relatively free rotations of the molecule on the surface. The small effects of the liquid environment on the vibrational properties of the dimer are investigated.

  13. Slow dynamics and aging in small molecule liquids

    NASA Astrophysics Data System (ADS)

    Shi, Xiang F.; McKenna, Gregory B.; Mandanici, Andrea; Cutroni, Maria

    2004-03-01

    The dynamics of m-toluidine and sucrose benzoate have been studied near to and below the glass transition using dynamic-mechanical measurements. The results at each temperature are analyzed in terms of both the KWW stretched exponential function and by the Cole-Davidson function. Both functions provide adequate fits to the mechanical data. However, even though time-temperature superposition appears to hold, the function 'shape' parameters vary with temperature which indicates that neither the KWW function nor the Cole-Davidson function is a true descriptor of the material mechanical dynamics. In addition, from studies of the material response below the glass transition temperature we show that both materials exhibit classical physical aging behavior due to the structural recovery of the non-equilibrium glass towards equilibrium.

  14. Negative ions of polyatomic molecules.

    PubMed Central

    Christophorou, L G

    1980-01-01

    In this paper general concepts relating to, and recent advances in, the study of negative ions of polyatomic molecules area discussed with emphasis on halocarbons. The topics dealt with in the paper are as follows: basic electron attachment processes, modes of electron capture by molecules, short-lived transient negative ions, dissociative electron attachment to ground-state molecules and to "hot" molecules (effects of temperature on electron attachment), parent negative ions, effect of density, nature, and state of the medium on electron attachment, electron attachment to electronically excited molecules, the binding of attached electrons to molecules ("electron affinity"), and the basic and the applied significance of negative-ion studies. PMID:7428744

  15. Liquid atomization

    NASA Astrophysics Data System (ADS)

    Bayvel, L.; Orzechowski, Z.

    The present text defines the physical processes of liquid atomization, the primary types of atomizers and their design, and ways of measuring spray characteristics; it also presents experimental investigation results on atomizers and illustrative applications for them. Attention is given to the macrostructural and microstructural parameters of atomized liquids; swirl, pneumatic, and rotary atomizers; and optical drop sizing methods, with emphasis on nonintrusive optical methods.

  16. Molecular reorientation of a nematic liquid crystal by thermal expansion

    PubMed Central

    Kim, Young-Ki; Senyuk, Bohdan; Lavrentovich, Oleg D.

    2012-01-01

    A unique feature of nematic liquid crystals is orientational order of molecules that can be controlled by electromagnetic fields, surface modifications and pressure gradients. Here we demonstrate a new effect in which the orientation of nematic liquid crystal molecules is altered by thermal expansion. Thermal expansion (or contraction) causes the nematic liquid crystal to flow; the flow imposes a realigning torque on the nematic liquid crystal molecules and the optic axis. The optical and mechanical responses activated by a simple temperature change can be used in sensing, photonics, microfluidic, optofluidic and lab-on-a-chip applications as they do not require externally imposed gradients of temperature, pressure, surface realignment, nor electromagnetic fields. The effect has important ramifications for the current search of the biaxial nematic phase as the optical features of thermally induced structural changes in the uniaxial nematic liquid crystal mimic the features expected of the biaxial nematic liquid crystal. PMID:23072803

  17. Watching single molecules dance

    NASA Astrophysics Data System (ADS)

    Mehta, Amit Dinesh

    Molecular motors convert chemical energy, from ATP hydrolysis or ion flow, into mechanical motion. A variety of increasingly precise mechanical probes have been developed to monitor and perturb these motors at the single molecule level. Several outstanding questions can be best approached at the single molecule level. These include: how far does a motor progress per energy quanta consumed? how does its reaction cycle respond to load? how many productive catalytic cycles can it undergo per diffusional encounter with its track? and what is the mechanical stiffness of a single molecule connection? A dual beam optical trap, in conjunction with in vitro ensemble motility assays, has been used to characterize two members of the myosin superfamily: muscle myosin II and chick brain myosin V. Both move the helical polymer actin, but myosin II acts in large ensembles to drive muscle contraction or cytokinesis, while myosin V acts in small numbers to transport vesicles. An optical trapping apparatus was rendered sufficiently precise to identify a myosin working stroke with 1nm or so, barring systematic errors such as those perhaps due to random protein orientations. This and other light microscopic motility assays were used to characterize myosin V: unlike myosin II this vesicle transport protein moves through many increments of travel while remaining strongly bound to a single actin filament. The step size, stall force, and travel distance of myosin V reveal a remarkably efficient motor capable of moving along a helical track for over a micrometer without significantly spiraling around it. Such properties are fully consistent with the putative role of an organelle transport motor, present in small numbers to maintain movement over long ranges relative to cellular size scales. The contrast between myosin II and myosin V resembles that between a human running on the moon and one walking on earth, where the former allows for faster motion when in larger ensembles but for less

  18. Leucocyte cellular adhesion molecules.

    PubMed

    Yong, K; Khwaja, A

    1990-12-01

    Leucocytes express adhesion promoting receptors which mediate cell-cell and cell-matrix interactions. These adhesive interactions are crucial to the regulation of haemopoiesis and thymocyte maturation, the direction and control of leucocyte traffic and migration through tissues, and in the development of immune and non-immune inflammatory responses. Several families of adhesion receptors have been identified (Table). The leucocyte integrin family comprises 3 alpha beta heterodimeric membrane glycoproteins which share a common beta subunit, designated CD18. The alpha subunits of each of the 3 members, lymphocyte function associated antigen-1 (LFA-1), macrophage antigen-1 (Mac-1) and p150,95 are designated CD11a, b and c respectively. These adhesion molecules play a critical part in the immune and inflammatory responses of leucocytes. The leucocyte integrin family is, in turn, part of the integrin superfamily, members of which are evolutionally, structurally and functionally related. Another Integrin subfamily found on leucocytes is the VLA group, so-called because the 'very late activation antigens' VLA-1 and VLA-2 were originally found to appear late in T-cell activation. Members of this family function mainly as extracellular matrix adhesion receptors and are found both on haemopoietic and non-haemopoietic cells. They play a part in diverse cellular functions including tissue organisation, lymphocyte recirculation and T-cell immune responses. A third integrin subfamily, the cytoadhesins, are receptors on platelets and endothelial cells which bind extracellular matrix proteins. A second family of adhesion receptors is the immunoglobulin superfamily, members of which include CD2, LFA-3 and ICAM-1, which participate in T-cell adhesive interactions, and the antigen-specific receptors of T and B cells, CD4, CD8 and the MHC Class I and II molecules. A recently recognised family of adhesion receptors is the selectins, characterised by a common lectin domain. Leucocyte

  19. Single Molecule Transcription Elongation

    PubMed Central

    Galburt, Eric A.; Grill, Stephan W.; Bustamante, Carlos

    2009-01-01

    Single molecule optical trapping assays have now been applied to a great number of macromolecular systems including DNA, RNA, cargo motors, restriction enzymes, DNA helicases, chromosome remodelers, DNA polymerases and both viral and bacterial RNA polymerases. The advantages of the technique are the ability to observe dynamic, unsynchronized molecular processes, to determine the distributions of experimental quantities and to apply force to the system while monitoring the response over time. Here, we describe the application of these powerful techniques to study the dynamics of transcription elongation by RNA polymerase II from Saccharomyces cerevisiae. PMID:19426807

  20. Ultra-cold molecule production.

    SciTech Connect

    Ramirez-Serrano, Jamie; Chandler, David W.; Strecker, Kevin; Rahn, Larry A.

    2005-12-01

    The production of Ultra-cold molecules is a goal of many laboratories through out the world. Here we are pursuing a unique technique that utilizes the kinematics of atomic and molecular collisions to achieve the goal of producing substantial numbers of sub Kelvin molecules confined in a trap. Here a trap is defined as an apparatus that spatially localizes, in a known location in the laboratory, a sample of molecules whose temperature is below one degree absolute Kelvin. Further, the storage time for the molecules must be sufficient to measure and possibly further cool the molecules. We utilize a technique unique to Sandia to form cold molecules from near mass degenerate collisions between atoms and molecules. This report describes the progress we have made using this novel technique and the further progress towards trapping molecules we have cooled.

  1. Molecules for Fluorescence Detection of Specific Chemicals

    NASA Technical Reports Server (NTRS)

    Fedor, Steve

    2008-01-01

    A family of fluorescent dye molecules has been developed for use in on-off fluorescence detection of specific chemicals. By themselves, these molecules do not fluoresce. However, when exposed to certain chemical analytes in liquid or vapor forms, they do fluoresce (see figure). These compounds are amenable to fixation on or in a variety of substrates for use in fluorescence-based detection devices: they can be chemically modified to anchor them to porous or non-porous solid supports or can be incorporated into polymer films. Potential applications for these compounds include detection of chemical warfare agents, sensing of acidity or alkalinity, and fluorescent tagging of proteins in pharmaceutical research and development. These molecules could also be exploited for use as two-photon materials for photodynamic therapy in the treatment of certain cancers and other diseases. A molecule in this family consists of a fluorescent core (such as an anthracene or pyrene) attached to two end groups that, when the dye is excited by absorption of light, transfer an electron to the core, thereby quenching the fluorescence. The end groups can be engineered so that they react chemically with certain analytes. Upon reaction, electrons on the end groups are no longer available for transfer to the core and, consequently, the fluorescence from the core is no longer quenched. The chemoselectivity of these molecules can be changed by changing the end groups. For example, aniline end groups afford a capability for sensing acids or acid halides (including those contained in chemical warfare agents). Pyridine or bipyridyl end groups would enable sensing of metal ions. Other chemicals that can be selectively detected through suitable choice of end groups include glucose and proteins. Moreover, the fluorescent cores can be changed to alter light-absorption and -emission characteristics: anthracene cores fluoresce at wavelengths around 500 nm, whereas perylene cores absorb and emit at

  2. Covalent Chemistry beyond Molecules.

    PubMed

    Jiang, Juncong; Zhao, Yingbo; Yaghi, Omar M

    2016-03-16

    Linking molecular building units by covalent bonds to make crystalline extended structures has given rise to metal-organic frameworks (MOFs) and covalent organic frameworks (COFs), thus bringing the precision and versatility of covalent chemistry beyond discrete molecules to extended structures. The key advance in this regard has been the development of strategies to overcome the "crystallization problem", which is usually encountered when attempting to link molecular building units into covalent solids. Currently, numerous MOFs and COFs are made as crystalline materials in which the large size of the constituent units provides for open frameworks. The molecular units thus reticulated become part of a new environment where they have (a) lower degrees of freedom because they are fixed into position within the framework; (b) well-defined spatial arrangements where their properties are influenced by the intricacies of the pores; and (c) ordered patterns onto which functional groups can be covalently attached to produce chemical complexity. The notion of covalent chemistry beyond molecules is further strengthened by the fact that covalent reactions can be carried out on such frameworks, with full retention of their crystallinity and porosity. MOFs are exemplars of how this chemistry has led to porosity with designed metrics and functionality, chemically-rich sequences of information within their frameworks, and well-defined mesoscopic constructs in which nanoMOFs enclose inorganic nanocrystals and give them new levels of spatial definition, stability, and functionality. PMID:26863450

  3. Static heterogeneities in liquid water

    NASA Astrophysics Data System (ADS)

    Stanley, H. Eugene; Buldyrev, Sergey V.; Giovambattista, Nicolas

    2004-10-01

    The thermodynamic behavior of water seems to be closely related to static heterogeneities. These static heterogeneities are related to the local structure of water molecules, and when properly characterized, may offer an economical explanation of thermodynamic data. The key feature of liquid water is not so much that the existence of hydrogen bonds, first pointed out by Linus Pauling, but rather the local geometry of the liquid molecules is not spherical or oblong but tetrahedral. In the consideration of static heterogeneities, this local geometry is critical. Recent experiments suggested more than one phase of amorphous solid water, while simulations suggest that one of these phases is metastable with respect to another, so that in fact there are only two stable phases.

  4. Light-induced liquid crystallinity.

    PubMed

    Kosa, Tamas; Sukhomlinova, Ludmila; Su, Linli; Taheri, Bahman; White, Timothy J; Bunning, Timothy J

    2012-05-17

    Liquid crystals are traditionally classified as thermotropic, lyotropic or polymeric, based on the stimulus that governs the organization and order of the molecular system. The most widely known and applied class of liquid crystals are a subset of thermotropic liquid crystals known as calamitic, in which adding heat can result in phase transitions from or into the nematic, cholesteric and smectic mesophases. Photoresponsive liquid-crystal materials and mixtures can undergo isothermal phase transitions if light affects the order parameter of the system within a mesophase sufficiently. In nearly all previous examinations, light exposure of photoresponsive liquid-crystal materials and mixtures resulted in order-decreasing photo-induced isothermal phase transitions. Under specialized conditions, an increase in order with light exposure has been reported, despite the tendency of the photoresponsive liquid-crystal system to reduce order in the exposed state. A direct, photo-induced transition from the isotropic to the nematic phase has been observed in a mixture of spiropyran molecules and a nematic liquid crystal. Here we report a class of naphthopyran-based materials that exhibit photo-induced conformational changes in molecular structure capable of yielding order-increasing phase transitions. Appropriate functionalization of the naphthopyran molecules leads to an exceedingly large order parameter in the open form, which results in a clear to strongly absorbing dichroic state. The increase in order with light exposure has profound implications in optics, photonics, lasing and displays and will merit further consideration for applications in solar energy harvesting. The large, photo-induced dichroism exhibited by the material system has been long sought in ophthalmic applications such as photochromic and polarized variable transmission sunglasses. PMID:22596158

  5. Quantum theory of cholesteric liquid crystals

    NASA Astrophysics Data System (ADS)

    Issaenko, Sergei A.

    A long standing and central problem in cholesteric liquid crystals is to relate the macroscopic pitch to the underlying microscopic interactions. These interactions are of two types which we call quantum (dispersion) and classical. Here we show that, contrary to common belief, intermolecular biaxial correlations usually play an important role for dispersion forces. To understand the microscopic picture of cholesteric liquid crystal we first analyze the effective chiral interaction between molecules arising front long-range quantum interactions between fluctuating charge moments in terms of a simple model of a chiral molecule. This model is based on the approximations that (a) the dominant excited states of a molecule form a band whose width is small compared to the average energy of excitation above the ground state and (b) biaxial orientational correlation between adjacent molecules can be neglected. We consider a system consisted of elongated molecules and, although we invoke the expansion in terms of coordinates transverse to the long axis of constituent molecules, we treat the longitudinal coordinate exactly. We identify two distinct physical limits depending on whether one or both of the interacting molecules are excited in the virtual state. The two-molecule interaction can be interpreted in terms of a superposition of pairwise interactions between individual atoms (or local chiral centers) on a chiral molecule and centers of anisotropic part of polarizability on the other molecule, while the one-molecule term involves three-body interactions between two local dipole moments of a chiral molecule and centers of anisotropic part of polarizability on the other, possibly nonchiral molecule. The numerical estimates of the pitch appeared from the above mechanism even without the Taylor expansion of the potential turns out to be considerably larger than experimental results and so it appears that the mean field treatment of these interactions can be used only in

  6. Local lateral environment of the molecules at the surface of DMSO-water mixtures.

    PubMed

    Fábián, Balázs; Idrissi, Abdenacer; Marekha, Bogdan; Jedlovszky, Pál

    2016-10-12

    Molecular dynamics simulations of the liquid-vapour interface of dimethyl sulphoxide (DMSO)-water mixtures of 11 different compositions, including two neat systems are performed on the canonical (N, V, T) ensemble at 298 K. The molecules constituting the surface layer of these systems are selected by means of the identification of the truly interfacial molecules (ITIM) method, and their local lateral environment at the liquid surface is investigated by performing Voronoi analysis. The obtained results reveal that both molecules prefer to be in a mixed local environment, consisting of both kinds of molecules, at the liquid surface, and this preference is even stronger here than in the bulk liquid phase. Neat-like patches, in which a molecule is surrounded by like neighbours, are not found. However, vacancies that are surrounded solely by water molecules are observed at the liquid surface. Our results show that strongly hydrogen bonded DMSO·H2O complexes, known to exist in the bulk phase of these mixtures, are absent from the liquid surface. PMID:27506283

  7. The Nematic Phases of Bent-Core Liquid Crystals

    PubMed Central

    Gleeson, Helen F; Kaur, Sarabjot; Görtz, Verena; Belaissaoui, Abdel; Cowling, Stephen; Goodby, John W

    2014-01-01

    Over the last ten years, the nematic phases of liquid crystals formed from bent-core structures have provoked considerable research because of their remarkable properties. This Minireview summarises some recent measurements of the physical properties of these systems, as well as describing some new data. We concentrate on oxadiazole-based materials as exemplars of this class of nematogens, but also describe some other bent-core systems. The influence of molecular structure on the stability of the nematic phase is described, together with progress in reducing the nematic transition temperatures by modifications to the molecular structure. The physical properties of bent-core nematic materials have proven difficult to study, but patterns are emerging regarding their optical and dielectric properties. Recent breakthroughs in understanding the elastic and flexoelectric behaviour are summarised. Finally, some exemplars of unusual electric field behaviour are described. PMID:24700653

  8. Two-Dimensional Microrheology of Freely Suspended Liquid Crystal Films

    NASA Astrophysics Data System (ADS)

    Eremin, A.; Baumgarten, S.; Harth, K.; Stannarius, R.; Nguyen, Z. H.; Goldfain, A.; Park, C. S.; Maclennan, J. E.; Glaser, M. A.; Clark, N. A.

    2011-12-01

    Smectic liquid crystals form freely-suspended, fluid films of highly uniform structure and thickness, making them ideal systems for studies of hydrodynamics in two dimensions. We have measured particle mobility and shear viscosity by direct observation of the gravitational drift of silica spheres and smectic islands included in these fluid membranes. In thick films, we observe a hydrodynamic regime dominated by lateral confinement effects, with the mobility of the inclusion determined predominantly by coupling of the fluid flow to the fixed boundaries of the film. In thin films, the mobility of inclusions is governed primarily by coupling of the fluid to the surrounding air, as predicted by Saffman-Delbrück theory.

  9. Liquid marbles

    NASA Astrophysics Data System (ADS)

    Aussillous, Pascale; Quéré, David

    2001-06-01

    The transport of a small amount of liquid on a solid is not a simple process, owing to the nature of the contact between the two phases. Setting a liquid droplet in motion requires non-negligible forces (because the contact-angle hysteresis generates a force opposing the motion), and often results in the deposition of liquid behind the drop. Different methods of levitation-electrostatic, electromagnetic, acoustic, or even simpler aerodynamic techniques-have been proposed to avoid this wetting problem, but all have proved to be rather cumbersome. Here we propose a simple alternative, which consists of encapsulating an aqueous liquid droplet with a hydrophobic powder. The resulting `liquid marbles' are found to behave like a soft solid, and show dramatically reduced adhesion to a solid surface. As a result, motion can be generated using gravitational, electrical and magnetic fields. Moreover, because the viscous friction associated with motion is very small, we can achieve quick displacements of the droplets without any leaks. All of these features are of potential benefit in microfluidic applications, and also permit the study of a drop in a non-wetting situation-an issue of renewed interest following the recent achievement of super-hydrophobic substrates.

  10. Liquid Crystals

    NASA Astrophysics Data System (ADS)

    1990-01-01

    Thermochromic liquid crystals, or TLCs, are a type of liquid crystals that react to changes in temperature by changing color. The Hallcrest/NASA collaboration involved development of a new way to visualize boundary layer transition in flight and in wind tunnel testing of aircraft wing and body surfaces. TLCs offered a new and potentially better method of visualizing the boundary layer transition in flight. Hallcrest provided a liquid crystal formulation technique that afforded great control over the sensitivity of the liquid crystals to varying conditions. Method is of great use to industry, government and universities for aerodynamic and hydrodynamic testing. Company's principal line is temperature indicating devices for industrial use, such as non-destructive testing and flaw detection in electric/electronic systems, medical application, such as diagnostic systems, for retail sale, such as room, refrigerator, baby bath and aquarium thermometers, and for advertising and promotion specials. Additionally, Hallcrest manufactures TLC mixtures for cosmetic applications, and liquid crystal battery tester for Duracell batteries.

  11. Liquid marbles.

    PubMed

    Aussillous, P; Quéré, D

    2001-06-21

    The transport of a small amount of liquid on a solid is not a simple process, owing to the nature of the contact between the two phases. Setting a liquid droplet in motion requires non-negligible forces (because the contact-angle hysteresis generates a force opposing the motion), and often results in the deposition of liquid behind the drop. Different methods of levitation-electrostatic, electromagnetic, acoustic, or even simpler aerodynamic techniques-have been proposed to avoid this wetting problem, but all have proved to be rather cumbersome. Here we propose a simple alternative, which consists of encapsulating an aqueous liquid droplet with a hydrophobic powder. The resulting 'liquid marbles' are found to behave like a soft solid, and show dramatically reduced adhesion to a solid surface. As a result, motion can be generated using gravitational, electrical and magnetic fields. Moreover, because the viscous friction associated with motion is very small, we can achieve quick displacements of the droplets without any leaks. All of these features are of potential benefit in microfluidic applications, and also permit the study of a drop in a non-wetting situation-an issue of renewed interest following the recent achievement of super-hydrophobic substrates. PMID:11418851

  12. Electrically rotating suspended films of polar liquids

    NASA Astrophysics Data System (ADS)

    Shirsavar, R.; Amjadi, A.; Tonddast-Navaei, A.; Ejtehadi, M. R.

    2011-02-01

    Controlled rotation of a suspended soap water film, simply generated by applying an electric field, has been reported recently. The film rotates when the applied electric field exceeds a certain threshold. In this study, we investigate the phenomenon in films made of a number of other liquids with various physical and chemical properties. Our measurements show that the intrinsic electrical dipole moments of the liquid molecules seems to be vital for the corresponding film rotation. All the investigated rotating liquids have a molecular electric dipole moment of above 1 Debye, while weakly polar liquids do not rotate. However, the liquids investigated here cover a wide range of physical parameters (e.g. viscosity, density, conductivity, etc.). So far, no significant correlation has been observed between the electric field thresholds and macroscopic properties of the liquids.

  13. Why molecules move along a temperature gradient

    PubMed Central

    Duhr, Stefan; Braun, Dieter

    2006-01-01

    Molecules drift along temperature gradients, an effect called thermophoresis, the Soret effect, or thermodiffusion. In liquids, its theoretical foundation is the subject of a long-standing debate. By using an all-optical microfluidic fluorescence method, we present experimental results for DNA and polystyrene beads over a large range of particle sizes, salt concentrations, and temperatures. The data support a unifying theory based on solvation entropy. Stated in simple terms, the Soret coefficient is given by the negative solvation entropy, divided by kT. The theory predicts the thermodiffusion of polystyrene beads and DNA without any free parameters. We assume a local thermodynamic equilibrium of the solvent molecules around the molecule. This assumption is fulfilled for moderate temperature gradients below a fluctuation criterion. For both DNA and polystyrene beads, thermophoretic motion changes sign at lower temperatures. This thermophilicity toward lower temperatures is attributed to an increasing positive entropy of hydration, whereas the generally dominating thermophobicity is explained by the negative entropy of ionic shielding. The understanding of thermodiffusion sets the stage for detailed probing of solvation properties of colloids and biomolecules. For example, we successfully determine the effective charge of DNA and beads over a size range that is not accessible with electrophoresis. PMID:17164337

  14. Molecules in the Spotlight

    SciTech Connect

    Cryan, James

    2010-01-26

    SLAC has just unveiled the world's first X-ray laser, the LCLS. This machine produces pulses of X-rays that are ten billion times brighter than those from conventional sources. One of the goals of this machine is to make movies of chemical reactions, including reactions necessary for life and reactions that might power new energy technologies. This public lecture will show the first results from the LCLS. As a first target, we have chosen nitrogen gas, the main component of the air we breathe. Using the unprecedented power of the LCLS X-rays as a blasting torch, we have created new forms of this molecule and with unique electronic arrangements. Please share with us the first insights from this new technology.

  15. Emerging small molecule drugs.

    PubMed

    Colin, Sophie; Chinetti-Gbaguidi, Giulia; Kuivenhoven, Jan A; Staels, Bart

    2015-01-01

    Dyslipidaemia is a major risk factor for cardiovascular diseases. Pharmacological lowering of LDL-C levels using statins reduces cardiovascular risk. However, a substantial residual risk persists especially in patients with type 2 diabetes mellitus. Because of the inverse association observed in epidemiological studies of HDL-C with the risk for cardiovascular diseases, novel therapeutic strategies to raise HDL-C levels or improve HDL functionality are developed as complementary therapy for cardiovascular diseases. However, until now most therapies targeting HDL-C levels failed in clinical trials because of side effects or absence of clinical benefits. This chapter will highlight the emerging small molecules currently developed and tested in clinical trials to pharmacologically modulate HDL-C and functionality including new CETP inhibitors (anacetrapib, evacetrapib), novel PPAR agonists (K-877, CER-002, DSP-8658, INT131 and GFT505), LXR agonists (ATI-111, LXR-623, XL-652) and RVX-208. PMID:25523004

  16. Biochips - Can molecules compute?

    NASA Astrophysics Data System (ADS)

    Tucker, J. B.

    1984-02-01

    In recent years the possibility has been considered to build 'biochip' computers, in which the silicon transistors of present machines would be replaced by large organic molecules or genetically engineered proteins. Two major advantages of such biochips over current devices would be related to vastly increased densities of computing elements, and entirely new styles of data processing, suited to such high-level tasks as pattern recognition and context-dependent analysis. The limitations of the semiconductor chip with respect to the density of elementary units due to size considerations and heat development could be overcome by making use of molecular switches. Attention is given to soliton switching, soliton logic, bulk molecular devices, analog biochips, 'intelligent' switches based on the employment of enzymes, robot vision, questions of biochip fabrication, protein engineering, and a strategy for the development of biochips.

  17. Forces in molecules.

    PubMed

    Hernández-Trujillo, Jesús; Cortés-Guzmán, Fernando; Fang, De-Chai; Bader, Richard F W

    2007-01-01

    Chemistry is determined by the electrostatic forces acting within a collection of nuclei and electrons. The attraction of the nuclei for the electrons is the only attractive force in a molecule and is the force responsible for the bonding between atoms. This is the attractive force acting on the electrons in the Ehrenfest force and on the nuclei in the Feynman force, one that is countered by the repulsion between the electrons in the former and by the repulsion between the nuclei in the latter. The virial theorem relates these forces to the energy changes resulting from interactions between atoms. All bonding, as signified by the presence of a bond path, has a common origin in terms of the mechanics determined by the Ehrenfest, Feynman and virial theorems. This paper is concerned in particular with the mechanics of interaction encountered in what are classically described as 'nonbonded interactions'--are atoms that 'touch' bonded or repelling one another? PMID:17328425

  18. Simulation of self-organization processes in crystal-forming systems: Supramolecular cyclic R6 cluster precursors and self-assembly of TeO2- TEL ( Tellurite) and TeO2- PAR ( Paratellurite) structures

    NASA Astrophysics Data System (ADS)

    Ilyushin, G. D.

    2014-11-01

    The supramolecular chemistry of oxides of sp elements (SO2, SeO2, and TeO2) is considered. The self-assembly of TeO2- TEL ( Tellurite) and TeO2- PAR ( Paratellurite) crystal structures is simulated. Methods of combinatorial and topological analysis (TOPOS program package) are applied which are based on constructing a basis 3D network of the structure in the form of a graph, the sites of which correspond to the positions of centroids of TeO2 molecules and the edges characterize bonds between them. The topological type of the basis 2D network in the TeO2- TEL structure corresponds to graphite (C- GRA), while in the TeO2- PAR structure the basis network corresponds to the 3D diamond network (C- DIA). A nanocluster precursor of cyclic type ( R6) composed of six covalently bound TeO2 molecules (chair conformation) is established for both structures. The desymmetrization of the cyclic structure of the R6 cluster in TeO2- PAR is related to the formation of Te-Te bonds with lengths of 3.824 and 4.062 Å. The symmetry and topology code of the processes of self-assembly of 3D structures from nanocluster precursors is completely reconstructed into the form "primary chain → microlayer → microframework." In both structures R6 clusters form 2D packings with a coordination number of 6. The cluster self-assembly model explains the specific features of the morphogenesis of TeO2- TEL and TeO2- PAR (phases with low and high crystallization temperatures, respectively): platelike shape, perfect cleavage in the (110) plane, and preferred growth in the primar-chain direction [100] in the former case and growth in the direction of the primary [001] axis with the preferred formation of tetragonal prism faces (110) in the latter case.

  19. Liquid-Liquid Phase Transitions of Phosphorus via Constant-Pressure First-Principles Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Morishita, Tetsuya

    2001-09-01

    Pressure-induced phase transitions in liquid phosphorus have been studied by constant-pressure first-principles molecular dynamics simulations. By compressing a low-pressure liquid which consists of the tetrahedral P4 molecules, a structural phase transition from the molecular to polymeric liquid (a high-pressure phase) observed in the recent experiment by Katayama et al. [Nature (London) 403, 170 (2000)] was successfully realized. It is found that this transition is caused by a breakup of the tetrahedral molecules with large volume contraction. The same transition is also realized by heating. This indicates that only the polymeric liquid can stably exist at high temperature.

  20. Dispersion properties of transverse anisotropic liquid crystal core photonic crystal fibers

    NASA Astrophysics Data System (ADS)

    Karasawa, Naoki

    2016-04-01

    The dispersion properties of liquid crystal core photonic crystal fibers for different core diameters have been calculated by a full vectorial finite difference method. In calculations, air holes are assumed to be arranged in a regular hexagonal array in fused silica and a central hole is filled with liquid crystal to create a core. In this study, three types of transverse anisotropic configurations, where liquid crystal molecules are oriented in a transverse plane, and a planar configuration, where liquid crystal molecules are oriented in a propagation direction, are considered. The large changes of the dispersion properties are found when the orientation of the liquid crystal molecules is changed from a planar configuration to a uniform configuration, where all molecules are oriented in the same direction in a transverse plane. Since the orientation of liquid crystal molecules may be controlled by applying an electric field, it could be utilized for various applications including the spectral control of supercontinuum generation.

  1. Quantum Behavior of Water Molecules Confined to Nanocavities in Gemstones.

    PubMed

    Gorshunov, Boris P; Zhukova, Elena S; Torgashev, Victor I; Lebedev, Vladimir V; Shakurov, Gil'man S; Kremer, Reinhard K; Pestrjakov, Efim V; Thomas, Victor G; Fursenko, Dimitry A; Dressel, Martin

    2013-06-20

    When water is confined to nanocavities, its quantum mechanical behavior can be revealed by terahertz spectroscopy. We place H2O molecules in the nanopores of a beryl crystal lattice and observe a rich and highly anisotropic set of absorption lines in the terahertz spectral range. Two bands can be identified, which originate from translational and librational motions of the water molecule isolated within the cage; they correspond to the analogous broad bands in liquid water and ice. In the present case of well-defined and highly symmetric nanocavities, the observed fine structure can be explained by macroscopic tunneling of the H2O molecules within a six-fold potential caused by the interaction of the molecule with the cavity walls. PMID:26283245

  2. A mechanism for supercooling in organic liquids

    SciTech Connect

    Thoma, P.E.

    1996-12-31

    In this investigation, a mechanism for supercooling inorganic liquids is formulated. By comparing the melting temperature and spontaneous freezing temperature of the chemicals evaluated with their molecular characteristics, the factors promoting supercooling are developed. The results obtained indicate that the following molecular characteristics promote supercooling in organic liquids: an unequal sharing of electrons between the atoms of a molecule; a three-dimensional chemical structure; a permanent, three-dimensional, and partially charged pocket within the chemical structure; a partially charged projection having a charge opposite that of the pocket and located on the side of the molecule opposite that of the pocket.

  3. Macromolecular liquids

    SciTech Connect

    Safinya, C.R.; Safran, S.A. ); Pincus, P.A. )

    1990-01-01

    Liquids include a broad range of material systems which are of high scientific and technological interest. Generally speaking, these are partially ordered or disordered phases where the individual molecular species have organized themselves on length scales which are larger than simple fluids, typically between 10 Angstroms and several microns. The specific systems reported on in this book include membranes, microemulsions, micelles, liquid crystals, colloidal suspensions, and polymers. They have a major impact on a broad spectrum of technological industries such as displays, plastics, soap and detergents, chemicals and petroleum, and pharmaceuticals.

  4. Nanoconstructions based on double-stranded DNA molecules and their applications as optical biosensing units

    NASA Astrophysics Data System (ADS)

    Zakharov, M. A.; Kazankov, G. M.; Sergeeva, V. S.; Yevdokimov, Yu. M.

    2006-02-01

    We describe the formation and the properties of biosensing units based on the cholesteric liquid-crystalline dispersions of the double-stranded nucleic acid molecules. The resulting biosensing units are proved to be sensitive to the presence of some relevant chemical or biological compounds in a liquid to be analyzed.

  5. Photosensitive dopants for liquid noble gases

    DOEpatents

    Anderson, David F.

    1988-01-01

    In an ionization type detector for high energy radiation wherein the energy of incident radiation is absorbed through the ionization of a liquid noble gas and resulting free charge is collected to form a signal indicative of the energy of the incident radiation, an improvement comprising doping the liquid noble gas with photosensitive molecules to convert scintillation light due to recombination of ions, to additional free charge.

  6. Liquid crystalline thermotropic and lyotropic nanohybrids

    NASA Astrophysics Data System (ADS)

    Saliba, Sarmenio; Mingotaud, Christophe; Kahn, Myrtil L.; Marty, Jean-Daniel

    2013-07-01

    This review is meant to give the reader an insight into hybrids incorporating different types of nanoparticles, e.g. metallic or metal oxides, within different types of lyotropic and thermotropic liquid crystals, from relatively small calamitic molecules to the larger discotics and polymers. In particular, this review highlights the importance of nanoparticle-liquid crystal interactions in accessing hybrid materials that exhibit synergetic properties.

  7. Geranyl diphosphate synthase molecules, and nucleic acid molecules encoding same

    SciTech Connect

    Croteau, Rodney Bruce; Burke, Charles Cullen

    2008-06-24

    In one aspect, the present invention provides isolated nucleic acid molecules that each encode a geranyl diphosphate synthase protein, wherein each isolated nucleic acid molecule hybridizes to a nucleic acid molecule consisting of the sequence set forth in SEQ ID NO:1 under conditions of 5.times.SSC at 45.degree. C. for one hour. The present invention also provides isolated geranyl diphosphate synthase proteins, and methods for altering the level of expression of geranyl diphosphate synthase protein in a host cell.

  8. Organic Molecules in Meteorites

    NASA Astrophysics Data System (ADS)

    Martins, Zita

    2015-08-01

    Carbonaceous meteorites are primitive samples from the asteroid belt, containing 3-5wt% organic carbon. The exogenous delivery of organic matter by carbonaceous meteorites may have contributed to the organic inventory of the early Earth. The majority (>70%) of the meteoritic organic material consist of insoluble organic matter (IOM) [1]. The remaining meteoritic organic material (<30%) consists of a rich organic inventory of soluble organic compounds, including key compounds important in terrestrial biochemistry [2-4]. Different carbonaceous meteorites contain soluble organic molecules with different abundances and distributions, which may reflect the extension of aqueous alteration or thermal metamorphism on the meteorite parent bodies. Extensive aqueous alteration on the meteorite parent body may result on 1) the decomposition of α-amino acids [5, 6]; 2) synthesis of β- and γ-amino acids [2, 6-9]; 3) higher relative abundances of alkylated polycyclic aromatic hydrocarbons (PAHs) [6, 10]; and 4) higher L-enantiomer excess (Lee) value of isovaline [6, 11, 12].The soluble organic content of carbonaceous meteorites may also have a contribution from Fischer-Tropsch/Haber-Bosch type gas-grain reactions after the meteorite parent body cooled to lower temperatures [13, 14].The analysis of the abundances and distribution of the organic molecules present in meteorites helps to determine the physical and chemical conditions of the early solar system, and the prebiotic organic compounds available on the early Earth.[1] Cody and Alexander (2005) GCA 69, 1085. [2] Cronin and Chang (1993) in: The Chemistry of Life’s Origin. pp. 209-258. [3] Martins and Sephton (2009) in: Amino acids, peptides and proteins in organic chemistry. pp. 1-42. [4] Martins (2011) Elements 7, 35. [5] Botta et al. (2007) MAPS 42, 81. [6] Martins et al. (2015) MAPS, in press. [7] Cooper and Cronin (1995) GCA 59, 1003. [8] Glavin et al. (2006) MAPS. 41, 889. [9] Glavin et al. (2011) MAPS 45, 1948. [10

  9. Structure of the catalytic chain of Methanococcus jannaschii aspartate transcarbamoylase in a hexagonal crystal form: Insights into the path of carbamoyl phosphate to the active site of the enzyme

    SciTech Connect

    Vitali J.; Soares A.; Singh, A. K.; Colaneri, M. J.

    2012-05-01

    Crystals of the catalytic chain of Methanococcus jannaschii aspartate transcarbamoylase (ATCase) grew in the presence of the regulatory chain in the hexagonal space group P6{sub 3}22, with one monomer per asymmetric unit. This is the first time that crystals with only one monomer in the asymmetric unit have been obtained; all known structures of the catalytic subunit contain several crystallographically independent monomers. The symmetry-related chains form the staggered dimer of trimers observed in the other known structures of the catalytic subunit. The central channel of the catalytic subunit contains a sulfate ion and a K{sup +} ion as well as a glycerol molecule at its entrance. It is possible that it is involved in channeling carbamoyl phosphate (CP) to the active site of the enzyme. A second sulfate ion near Arg164 is near the second CP position in the wild-type Escherichia coli ATCase structure complexed with CP. It is suggested that this position may also be in the path that CP takes when binding to the active site in a partial diffusion process at 310 K. Additional biochemical studies of carbamoylation and the molecular organization of this enzyme in M. jannaschii will provide further insight into these points.

  10. Structure of the catalytic chain of Methanococcus jannaschii aspartate transcarbamoylase in a hexagonal crystal form: insights into the path of carbamoyl phosphate to the active site of the enzyme

    PubMed Central

    Vitali, Jacqueline; Singh, Aditya K.; Soares, Alexei S.; Colaneri, Michael J.

    2012-01-01

    Crystals of the catalytic chain of Methanococcus jannaschii aspartate trans­carbamoylase (ATCase) grew in the presence of the regulatory chain in the hexagonal space group P6322, with one monomer per asymmetric unit. This is the first time that crystals with only one monomer in the asymmetric unit have been obtained; all known structures of the catalytic subunit contain several crystallographically independent monomers. The symmetry-related chains form the staggered dimer of trimers observed in the other known structures of the catalytic subunit. The central channel of the catalytic subunit contains a sulfate ion and a K+ ion as well as a glycerol molecule at its entrance. It is possible that it is involved in channeling carbamoyl phosphate (CP) to the active site of the enzyme. A second sulfate ion near Arg164 is near the second CP position in the wild-type Escherichia coli ATCase structure complexed with CP. It is suggested that this position may also be in the path that CP takes when binding to the active site in a partial diffusion process at 310 K. Additional biochemical studies of carbamoylation and the molecular organization of this enzyme in M. janna­schii will provide further insight into these points. PMID:22691781

  11. Reliable anchoring groups for single-molecule junctions

    NASA Astrophysics Data System (ADS)

    González, M. Teresa; Leary, Edmund; Evangeli, Charalambos; Arroyo, Carlos; Rubio-Bollinger, Gabino; Agraïit, Nicolás

    2012-02-01

    In the field of molecular electronics, thiols have been extensively used as the most common anchoring groups to bind molecules to gold electrodes. However, other anchoring groups as amines can provide interesting advantages. Recently, C-60 has been also proposed as a possible very efficient binding group. In this talk, I will present our studies on molecular junctions formed by thiol-, amine-, and C-60-terminated molecules. We use a STM (scanning tunneling microscope) break-junction technique to create and characterized single-molecule junctions both in ambient and liquid environment. We compare thiols and amines on the alkane family and an oligo(phenylene ethynylene). Our study of the molecular-junction stretching length allows us to conclude that thiols affect atomic rearrangement at the electrodes significantly more than amines. Using C-60-terminated molecules, we have recently introduced a new technique for controllably wiring one molecule at a time. We first get STM images to located isolated molecules on a gold substrate, which are then specifically targeted and contacted using a STM gold tip. This technique offers a significant improvement over other techniques, as it guaranties that one and only one molecule is contacted at a time between the electrodes.

  12. Electrochromic graphene molecules.

    PubMed

    Ji, Zhiqiang; Doorn, Stephen K; Sykora, Milan

    2015-04-28

    Polyclic aromatic hydrocarbons also called Graphene Molecules (GMs), with chemical composition C132H36(COOH)2 were synthesized in situ on the surface of transparent nanocrystalline indium tin oxide (nc-ITO) electrodes and their electronic structure was studied electrochemically and spectro-electrochemically. Variations in the potential applied onto the nc-ITO/GM electrodes induce only small changes in the observed current, but they produce dramatic changes in the absorption of the GMs, which are associated with their oxidation and reduction. Analysis of the absorption changes using a modified Nernst equation is used to determine standard potentials associated with the individual charge transfer processes. For the GMs prepared here, these were found to be E1,ox(0) = 0.77 ± 0.01 V and E2,ox(0) = 1.24 ± 0.02 V vs NHE for the first and second oxidation and E1,red(0) = -1.50 ± 0.04 V for the first reduction. The charge transfer processes are found to be nonideal. The nonideality factors associated with the oxidation and reduction processes are attributed to strong interactions between the GM redox centers. Under the conditions of potential cycling, GMs show rapid (seconds) color change with high contrast and stability. An electrochromic application is demonstrated wherein the GMs are used as the optically active component. PMID:25768313

  13. Electrochromic Graphene Molecules

    DOE PAGESBeta

    Ji, Zhiqiang; Doorn, Stephen K.; Sykora, Milan

    2015-03-13

    Polyclic aromatic hydrocarbons, also called Graphene Molecules (GMs), with chemical composition C132H36(COOH)2 were synthesized in-situ on the surface of transparent nanocrystaline indium tin oxide (nc-ITO) electrodes. Their electronic structure was studied electrochemically and spectro-electrochemically. Variations in the potential applied onto the nc-ITO/GM electrodes induce only small changes in the observed current but they produce dramatic changes in the absorption of the GMs, which are associated with their oxidation and reduction. Analysis of the absorption changes using modified Nernst equation is used to determine standard potentials associated with the individual charge transfer processes. For the GMs prepared here these were foundmore » to be E1,ox 0 = 0.77± 0.01 V and E2,ox 0 = 1.24 ± 0.02 V vs. NHE for the first and second oxidation and E1,red 0 = -1.50 ± 0.04 V for the first reduction. The charge transfer processes are found to be non-ideal. The non-ideality factors associated with the oxidation and reduction processes suggest presence of strong interactions between the GM redox centers. Under the conditions of potential cycling GMs show rapid (seconds) color change with high contrast and stability. An electrochromic application is demonstrated wherein the GMs are used as the optically active component.« less

  14. Reactions of oriented molecules.

    PubMed

    Brooks, P R

    1976-07-01

    Beams of oriented molecules have been used to directly study geometrical requirements in chemical reactions. These studies have shown that reactivity is much greater in some orientations than others and demonstrated the existence of steric effects. For some reactions portions of the orientation results are in good accord with traditional views of steric hindrance, but for others it is clear that our chemical intuition needs recalibrating. Indeed, the information gained from simultaneously orienting the reactants and observing the scattering angle of the products may lead to new insights about the detailed mechanism of certain reactions. Further work must be done to extend the scope and detail of the studies described here. More detailed information is needed on the CH(3)I reaction and the CF(3)I reaction. The effects of alkyl groups of various sizes and alkali metals of various sizes are of interest. In addition, reactions where a long-lived complex is formed should be studied to see if orientation is important. Finally, it would be of interest to apply the technique to the sort of reactions that led to our interest in the first place: the S(N)2 displacements in alkyl halides where the fascinating Walden inversion occurs. PMID:17793988

  15. Single molecule tracking

    DOEpatents

    Shera, E. Brooks

    1988-01-01

    A detection system is provided for identifying individual particles or molecules having characteristic emission in a flow train of the particles in a flow cell. A position sensitive sensor is located adjacent the flow cell in a position effective to detect the emissions from the particles within the flow cell and to assign spatial and temporal coordinates for the detected emissions. A computer is then enabled to predict spatial and temporal coordinates for the particle in the flow train as a function of a first detected emission. Comparison hardware or software then compares subsequent detected spatial and temporal coordinates with the predicted spatial and temporal coordinates to determine whether subsequently detected emissions originate from a particle in the train of particles. In one embodiment, the particles include fluorescent dyes which are excited to fluoresce a spectrum characteristic of the particular particle. Photones are emitted adjacent at least one microchannel plate sensor to enable spatial and temporal coordinates to be assigned. The effect of comparing detected coordinates with predicted coordinates is to define a moving sample volume which effectively precludes the effects of background emissions.

  16. Single molecule tracking

    DOEpatents

    Shera, E.B.

    1987-10-07

    A detection system is provided for identifying individual particles or molecules having characteristic emission in a flow train of the particles in a flow cell. A position sensitive sensor is located adjacent the flow cell in a position effective to detect the emissions from the particles within the flow cell and to assign spatial and temporal coordinates for the detected emissions. A computer is then enabled to predict spatial and temporal coordinates for the particle in the flow train as a function of a first detected emission. Comparison hardware or software then compares subsequent detected spatial and temporal coordinates with the predicted spatial and temporal coordinates to determine whether subsequently detected emissions originate from a particle in the train of particles. In one embodiment, the particles include fluorescent dyes which are excited to fluoresce a spectrum characteristic of the particular particle. Photons are emitted adjacent at least one microchannel plate sensor to enable spatial and temporal coordinates to be assigned. The effect of comparing detected coordinates with predicted coordinates is to define a moving sample volume which effectively precludes the effects of background emissions. 3 figs.

  17. Strongly interacting ultracold polar molecules

    NASA Astrophysics Data System (ADS)

    Gadway, Bryce; Yan, Bo

    2016-08-01

    This paper reviews recent advances in the study of strongly interacting systems of dipolar molecules. Heteronuclear molecules feature large and tunable electric dipole moments, which give rise to long-range and anisotropic dipole–dipole interactions. Ultracold samples of dipolar molecules with long-range interactions offer a unique platform for quantum simulations and the study of correlated many-body physics. We provide an introduction to the physics of dipolar quantum gases, both electric and magnetic, and summarize the multipronged efforts to bring dipolar molecules into the quantum regime. We discuss in detail the recent experimental progress in realizing and studying strongly interacting systems of polar molecules trapped in optical lattices, with particular emphasis on the study of interacting spin systems and non-equilibrium quantum magnetism. Finally, we conclude with a brief discussion of the future prospects for studies of strongly interacting dipolar molecules.

  18. Adsorption kinetics of diatomic molecules.

    PubMed

    Burde, Jared T; Calbi, M Mercedes

    2014-05-01

    The adsorption dynamics of diatomic molecules on solid surfaces is examined by using a Kinetic Monte Carlo algorithm. Equilibration times at increasing loadings are obtained, and explained based on the elementary processes that lead to the formation of the adsorbed film. The ability of the molecules to change their orientation accelerates the overall uptake and leads to competitive kinetic behaviour between the different orientations. The dependence of the equilibration time on coverage follows the same decreasing trend obtained experimentally for ethane adsorption on closed-end carbon nanotube bundles. The exploration of molecule-molecule interaction effects on this trend provides relevant insights to understand the kinetic behaviour of other species, from simpler molecules to larger polyatomic molecules, adsorbing on surfaces with different binding strength. PMID:24654004

  19. General nature of liquid-liquid transition in aqueous organic solutions

    NASA Astrophysics Data System (ADS)

    Murata, Ken-Ichiro; Tanaka, Hajime

    2013-11-01

    The presence or absence of a liquid-liquid transition in water is one of the hot topics in liquid science, and while a liquid-liquid transition in water/glycerol mixtures is known, its generality in aqueous solutions has remained elusive. Here we reveal that 14 aqueous solutions of sugar and polyol molecules, which have an ability to form hydrogen bonding with water molecules, exhibit liquid-liquid transitions. We find evidence that both melting of ice and liquid-liquid transitions in all these aqueous solutions are controlled solely by water activity, which is related to the difference in the chemical potential between an aqueous solution and pure water at the same temperature and pressure. Our theory shows that water activity is determined by the degree of local tetrahedral ordering, indicating that both phenomena are driven by structural ordering towards ice-like local structures. This has a significant implication on our understanding of the low-temperature behaviour of water.

  20. Trapping Single Molecules by Dielectrophoresis

    NASA Astrophysics Data System (ADS)

    Hölzel, Ralph; Calander, Nils; Chiragwandi, Zackary; Willander, Magnus; Bier, Frank F.

    2005-09-01

    We have trapped single protein molecules of R-phycoerythrin in an aqueous solution by an alternating electric field. A radio frequency voltage is applied to sharp nanoelectrodes and hence produces a strong electric field gradient. The resulting dielectrophoretic forces attract freely diffusing protein molecules. Trapping takes place at the electrode tips. Switching off the field immediately releases the molecules. The electric field distribution is computed, and from this the dielectrophoretic response of the molecules is calculated using a standard polarization model. The resulting forces are compared to the impact of Brownian motion. Finally, we discuss the experimental observations on the basis of the model calculations.

  1. Aromatic molecules as spintronic devices

    SciTech Connect

    Ojeda, J. H.; Orellana, P. A.; Laroze, D.

    2014-03-14

    In this paper, we study the spin-dependent electron transport through aromatic molecular chains attached to two semi-infinite leads. We model this system taking into account different geometrical configurations which are all characterized by a tight binding Hamiltonian. Based on the Green's function approach with a Landauer formalism, we find spin-dependent transport in short aromatic molecules by applying external magnetic fields. Additionally, we find that the magnetoresistance of aromatic molecules can reach different values, which are dependent on the variations in the applied magnetic field, length of the molecules, and the interactions between the contacts and the aromatic molecule.

  2. Electrical Transport through Organic Molecules

    NASA Astrophysics Data System (ADS)

    Lau, C. N.; Chang, Shun-Chi; Williams, Stan

    2003-03-01

    We investigate electrical transport properties of single organic molecules using electromigration break junctions[1]. A self-assembled monolayer of various organic molecules such as 1,4-di(phenylethynyl-4'-methanethiol)benzene was grown on narrow metal wires, and single or a few molecules were incorporated into the junctions which were created by applying a large voltage and breaking the wires. The transport properties of these molecules were then measured at low temperatures. Latest experimental results will be discussed. [1] Park, J. et al, Nature, 417, 722 (2002); Liang W. et al, Nature, 417, 725 (2002).

  3. Electrochromic Graphene Molecules

    SciTech Connect

    Ji, Zhiqiang; Doorn, Stephen K.; Sykora, Milan

    2015-03-13

    Polyclic aromatic hydrocarbons, also called Graphene Molecules (GMs), with chemical composition C132H36(COOH)2 were synthesized in-situ on the surface of transparent nanocrystaline indium tin oxide (nc-ITO) electrodes. Their electronic structure was studied electrochemically and spectro-electrochemically. Variations in the potential applied onto the nc-ITO/GM electrodes induce only small changes in the observed current but they produce dramatic changes in the absorption of the GMs, which are associated with their oxidation and reduction. Analysis of the absorption changes using modified Nernst equation is used to determine standard potentials associated with the individual charge transfer processes. For the GMs prepared here these were found to be E1,ox 0 = 0.77± 0.01 V and E2,ox 0 = 1.24 ± 0.02 V vs. NHE for the first and second oxidation and E1,red 0 = -1.50 ± 0.04 V for the first reduction. The charge transfer processes are found to be non-ideal. The non-ideality factors associated with the oxidation and reduction processes suggest presence of strong interactions between the GM redox centers. Under the conditions of potential cycling GMs show rapid (seconds) color change with high contrast and stability. An electrochromic application is demonstrated wherein the GMs are used as the optically active component.

  4. Phase behavior of ionic liquid crystals

    NASA Astrophysics Data System (ADS)

    Kondrat, S.; Bier, M.; Harnau, L.

    2010-05-01

    Bulk properties of ionic liquid crystals are investigated using density functional theory. The liquid crystal molecules are represented by ellipsoidal particles with charges located in their center or at their tails. Attractive interactions are taken into account in terms of the Gay-Berne pair potential. Rich phase diagrams involving vapor, isotropic and nematic liquid, as well as smectic phases are found. The dependence of the phase behavior on various parameters such as the length of the particles and the location of charges on the particles is studied.

  5. Liquid atomization

    SciTech Connect

    Walzel, P. )

    1993-01-01

    A systematic review of different liquid atomizers is presented, accompanied by a discussion of various mechanisms of droplet formation in a gas atmosphere as a function of the liquid flow-regime and the geometry of the atomizer. Equations are presented for the calculation of the mean droplet-diameter. In many applications, details of the droplet size distribution are, also, important, e.g., approximate values of the breadth of the droplet formation are given. The efficiency of utilization of mechanical energy in droplet formation is indicated for the different types of atomizers. Atomization is used, in particular, for the following purposes: (1) atomization of fuels; (2) making granular products; (3) carrying out mass-transfer operations; and (4) coating of surfaces.

  6. Adhesion molecules in cutaneous inflammation.

    PubMed

    Barker, J N

    1995-01-01

    As in other organs, leukocyte adhesion molecules and their ligands play a major role in cutaneous inflammatory events both by directing leukocyte trafficking and by their effects on antigen presentation. Skin biopsies of inflamed skin from patients with diseases such as as psoriasis or atopic dermatitis reveal up-regulation of endothelial cell expression of P- and E-selectin, vascular cell adhesion molecule 1 and intercellular adhesion molecule 1. Studies of evolving lesions following UVB irradiation, Mantoux reaction or application of contact allergen, demonstrate that expression of these adhesion molecules parallels leukocyte infiltration into skin. When cutaneous inflammation is widespread (e.g. in erythroderma), soluble forms of these molecules are detectable in serum. In vitro studies predict that peptide mediators are important regulatory factors for endothelial adhesion molecules. Intradermal injection of the cytokines interleukin 1, tumour necrosis factor alpha and interferon gamma into normal human skin leads to induction of endothelial adhesion molecules with concomitant infiltration of leukocytes. In addition, neuropeptides rapidly induce P-selectin translocation to the cell membrane and expression of E-selectin. Adhesion molecules also play a crucial role as accessory molecules in the presentation of antigen to T lymphocytes by Langerhans' cells. Expression of selectin ligands by Langerhans' cells is up-regulated by various inflammatory stimuli, suggesting that adhesion molecules may be important in Langerhans' cell migration. The skin, because of its accessibility, is an ideal organ in which to study expression of adhesion molecules and their relationship to inflammatory events. Inflammatory skin diseases are common and inhibition of lymphocyte accumulation in skin is likely to prove of great therapeutic benefit. PMID:7587640

  7. Liquid electrode

    DOEpatents

    Ekechukwu, Amy A.

    1994-01-01

    A dropping electrolyte electrode for use in electrochemical analysis of non-polar sample solutions, such as benzene or cyclohexane. The liquid electrode, preferably an aqueous salt solution immiscible in the sample solution, is introduced into the solution in dropwise fashion from a capillary. The electrolyte is introduced at a known rate, thus, the droplets each have the same volume and surface area. The electrode is used in making standard electrochemical measurements in order to determine properties of non-polar sample solutions.

  8. Single-molecule spectroscopy using microfluidic platforms.

    PubMed

    Kim, Samuel; Zare, Richard N

    2010-01-01

    Microfluidics serves as a convenient platform for single-molecule experiments by providing manipulation of small amounts of liquids and micron-sized particles. An adapted version of capillary electrophoresis (CE) on a microchip can be utilized to separate chemical species with high resolution based on their ionic mobilities (i.e., charges and sizes), but identification of separated species is not trivial, especially for complex mixtures of sticky biomolecules. We describe here how to use a surfactant mixture system for CE on a poly(dimethylsiloxane) (PDMS) microchip, capture separated peaks within a 50-pl chamber using microvalves, analyze the fluorescence signals with correlation spectroscopy to extract molecular diffusion characteristics, and to identify the biomolecular clusters in a model immunocomplex system. PMID:20580962

  9. Micro-Kelvin cold molecules.

    SciTech Connect

    Strecker, Kevin E.; Chandler, David W.

    2009-10-01

    We have developed a novel experimental technique for direct production of cold molecules using a combination of techniques from atomic optical and molecular physics and physical chemistry. The ability to produce samples of cold molecules has application in a broad spectrum of technical fields high-resolution spectroscopy, remote sensing, quantum computing, materials simulation, and understanding fundamental chemical dynamics. Researchers around the world are currently exploring many techniques for producing samples of cold molecules, but to-date these attempts have offered only limited success achieving milli-Kelvin temperatures with low densities. This Laboratory Directed Research and Development project is to develops a new experimental technique for producing micro-Kelvin temperature molecules via collisions with laser cooled samples of trapped atoms. The technique relies on near mass degenerate collisions between the molecule of interest and a laser cooled (micro-Kelvin) atom. A subset of collisions will transfer all (nearly all) of the kinetic energy from the 'hot' molecule, cooling the molecule at the expense of heating the atom. Further collisions with the remaining laser cooled atoms will thermally equilibrate the molecules to the micro-Kelvin temperature of the laser-cooled atoms.

  10. Featured Molecules: Sucrose and Vanillin

    NASA Astrophysics Data System (ADS)

    Coleman, William F.; Wildman, Randall J.

    2003-04-01

    The WebWare molecules of the month for April relate to the sense of taste. Apple Fool, the JCE Classroom Activity, mentions sucrose and vanillin and their use as flavorings. Fully manipulable (Chime) versions of these and other molecules are available at Only@JCE Online.

  11. Proregenerative Properties of ECM Molecules

    PubMed Central

    Plantman, Stefan

    2013-01-01

    After traumatic injuries to the nervous system, regrowing axons encounter a complex microenvironment where mechanisms that promote regeneration compete with inhibitory processes. Sprouting and axonal regrowth are key components of functional recovery but are often counteracted by inhibitory molecules. This review covers extracellular matrix molecules that support neuron axonal outgrowth. PMID:24195084

  12. Loosely-Bound Diatomic Molecules.

    ERIC Educational Resources Information Center

    Balfour, W. J.

    1979-01-01

    Discusses concept of covalent bonding as related to homonuclear diatomic molecules. Article draws attention to the existence of bound rare gas and alkaline earth diatomic molecules. Summarizes their molecular parameters and offers spectroscopic data. Strength and variation with distance of interatomic attractive forces is given. (Author/SA)

  13. Frequency Modulation Atomic Force Microscopy in Liquids

    NASA Astrophysics Data System (ADS)

    Kobayashi, Kei; Yamada, Hirofumi

    Atomic force microscopy (AFM) using frequency modulation (FM) detection has been widely used for the atomic-scale investigations of various materials. However, high-resolution imaging in liquids by FM-AFM is severely deteriorated by the extreme reduction of the Q-factor due to the hydrodynamic interaction between the cantilever and the liquid. Recently, the use of the small amplitude mode and the large noise reduction in the cantilever deflection sensor brought great progress in FM-AFM imaging in liquids. In this chapter viscous damping of the cantilever and the electric double layer force are discussed in detail. Following the detailed analysis of the frequency noise in FM-AFM, instrumentation of the optical beam deflection sensor for FM-AFM in liquid environments is described. Finally high-resolution FM-AFM images of muscovite mica, purple membranes, and isolated protein molecules in liquids are presented.

  14. Neutron Scattering of Aromatic and Aliphatic Liquids

    PubMed Central

    Falkowska, Marta; Bowron, Daniel T.; Manyar, Haresh G.

    2016-01-01

    Abstract Organic solvents, such as cyclohexane, cyclohexene, methylcyclohexane, benzene and toluene, are widely used as both reagents and solvents in industrial processes. Despite the ubiquity of these liquids, the local structures that govern the chemical properties have not been studied extensively. Herein, we report neutron diffraction measurements on liquid cyclohexane, cyclohexene, methylcyclohexane, benzene and toluene at 298 K to obtain a detailed description of the local structure in these compounds. The radial distribution functions of the centres of the molecules, as well as the partial distribution functions for the double bond for cyclohexene and methyl group for methylcyclohexane and toluene have been calculated. Additionally, probability density functions and angular radial distribution functions were extracted to provide a full description of the local structure within the chosen liquids. Structural motifs are discussed and compared for all liquids, referring specifically to the functional group and aromaticity present in the different liquids. PMID:26990367

  15. Neutron Scattering of Aromatic and Aliphatic Liquids.

    PubMed

    Falkowska, Marta; Bowron, Daniel T; Manyar, Haresh G; Hardacre, Christopher; Youngs, Tristan G A

    2016-07-01

    Organic solvents, such as cyclohexane, cyclohexene, methylcyclohexane, benzene and toluene, are widely used as both reagents and solvents in industrial processes. Despite the ubiquity of these liquids, the local structures that govern the chemical properties have not been studied extensively. Herein, we report neutron diffraction measurements on liquid cyclohexane, cyclohexene, methylcyclohexane, benzene and toluene at 298 K to obtain a detailed description of the local structure in these compounds. The radial distribution functions of the centres of the molecules, as well as the partial distribution functions for the double bond for cyclohexene and methyl group for methylcyclohexane and toluene have been calculated. Additionally, probability density functions and angular radial distribution functions were extracted to provide a full description of the local structure within the chosen liquids. Structural motifs are discussed and compared for all liquids, referring specifically to the functional group and aromaticity present in the different liquids. PMID:26990367

  16. Electron paramagnetic resonance study of two smectic A liquid crystals.

    NASA Technical Reports Server (NTRS)

    Fryburg, G. C.; Gelerinter, E.; Fishel, D. L.

    1972-01-01

    Study of the molecular ordering in two smectic A liquid crystals using vanadyl acetylacetonate as a paramagnetic probe. The average hyperfine splitting of the spectrum in the smectic A mesophase is measured as a function of the orientation relative to the dc magnetic field of the spectrometer after alignment of the molecules of the liquid crystal.

  17. Demonstrations of Some Optical Properties of Liquid Crystals.

    ERIC Educational Resources Information Center

    Nicastro, Anthony J.

    1983-01-01

    Discusses several properties of liquid crystal displays. Includes instructions for demonstrating liquid crystalline phase, ordering of the long axes of molecules along one direction, and electro-optic effects. The latter is accomplished with the use of an overhead projector following preparation of a sandwich cell. (JN)

  18. Pump for Saturated Liquids

    NASA Technical Reports Server (NTRS)

    Elliott, D. G.

    1986-01-01

    Boiling liquids pumped by device based on proven components. Expanding saturated liquid in nozzle and diverting its phases along separate paths in liquid/vapor separator raises pressure of liquid. Liquid cooled in process. Pump makes it unnecessary to pressurize cryogenic liquids in order to pump them. Problems of introducing noncondensable pressurizing gas avoided.

  19. Enzyme molecules in solitary confinement.

    PubMed

    Liebherr, Raphaela B; Gorris, Hans H

    2014-01-01

    Large arrays of homogeneous microwells each defining a femtoliter volume are a versatile platform for monitoring the substrate turnover of many individual enzyme molecules in parallel. The high degree of parallelization enables the analysis of a statistically representative enzyme population. Enclosing individual enzyme molecules in microwells does not require any surface immobilization step and enables the kinetic investigation of enzymes free in solution. This review describes various microwell array formats and explores their applications for the detection and investigation of single enzyme molecules. The development of new fabrication techniques and sensitive detection methods drives the field of single molecule enzymology. Here, we introduce recent progress in single enzyme molecule analysis in microwell arrays and discuss the challenges and opportunities. PMID:25221867

  20. Magnetoassociation of KRb Feshbach molecules

    NASA Astrophysics Data System (ADS)

    Cumby, Tyler; Perreault, John; Shewmon, Ruth; Jin, Deborah

    2010-03-01

    I will discuss experiments in which we study the creation of ^40K^87Rb Feshbach molecules via magnetoassociation. We measure the molecule number as a function of the magnetic-field sweep rate through the interspecies Feshbach resonance and explore the dependence of association on the initial atom gas conditions. This study of the Feshbach molecule creation process may be relevant to the production of ultracold polar molecules, where magnetoassociated Feshbach molecules can be a crucial first step [1].[4pt] [1] K.-K. Ni, S. Ospelkaus, M. H. G. de Miranda, A. Peer, B. Neyenhuis, J. J. Zirbel, S. Kotochigova, P. S. Julienne, D. S. Jin, and J. Ye, Science, 2008, 322, 231- 235.

  1. Magnetoassociation of KRb Feshbach molecules

    NASA Astrophysics Data System (ADS)

    Cumby, Tyler; Perreault, John; Shewmon, Ruth; Jin, Deborah

    2010-03-01

    I will discuss experiments in which we study the creation of ^40K^87Rb Feshbach molecules via magnetoassociation. We measure the molecule number as a function of the magnetic-field sweep rate through the interspecies Feshbach resonance and explore the dependence of association on the initial atom gas conditions. This study of the Feshbach molecule creation process may be relevant to the production of ultracold polar molecules, where magnetoassociated Feshbach molecules can be a crucial first step [1].[4pt] [1] K.-K. Ni, S. Ospelkaus, M. H. G. de Miranda, A. Peer, B. Neyenhuis, J. J. Zirbel, S. Kotochigova, P. S. Julienne, D. S. Jin, and J. Ye, Science, 2008, 322, 231-235.

  2. Molecule-hugging graphene nanopores.

    PubMed

    Garaj, Slaven; Liu, Song; Golovchenko, Jene A; Branton, Daniel

    2013-07-23

    It has recently been recognized that solid-state nanopores in single-atomic-layer graphene membranes can be used to electronically detect and characterize single long charged polymer molecules. We have now fabricated nanopores in single-layer graphene that are closely matched to the diameter of a double-stranded DNA molecule. Ionic current signals during electrophoretically driven translocation of DNA through these nanopores were experimentally explored and theoretically modeled. Our experiments show that these nanopores have unusually high sensitivity (0.65 nA/Å) to extremely small changes in the translocating molecule's outer diameter. Such atomically short graphene nanopores can also resolve nanoscale-spaced molecular structures along the length of a polymer, but do so with greatest sensitivity only when the pore and molecule diameters are closely matched. Modeling confirms that our most closely matched pores have an inherent resolution of ≤ 0.6 nm along the length of the molecule. PMID:23836648

  3. Cold molecules, collisions and reactions

    NASA Astrophysics Data System (ADS)

    Hecker Denschlag, Johannes

    2016-05-01

    I will report on recent experiments of my group where we have been studying the formation of ultracold diatomic molecules and their subsequent inelastic/reactive collisions. For example, in one of these experiments we investigate collisions of triplet Rb2 molecules in the rovibrational ground state. We observe fast molecular loss and compare the measured loss rates to predictions based on universality. In another set of experiments we investigate the formation of (BaRb)+ molecules after three-body recombination of a single Ba+ ion with two Rb atoms in an ultracold gas of Rb atoms. Our investigations indicate that the formed (BaRb)+ molecules are weakly bound and that several secondary processes take place ranging from photodissociation of the (BaRb)+ molecule to reactive collisions with Rb atoms. I will explain how we can experimentally distinguish these processes and what the typical reaction rates are. Support from the German Research foundation DFG and the European Community is acknowledged.

  4. Fluorinated monolayers at liquid-liquid and liquid-vapor interfaces

    NASA Astrophysics Data System (ADS)

    Zhang, Zhongjian

    Microscopic structure of several fluorinated monolayers at water-vapor and water-oil interfaces were examined using x-ray specular reflectivity and grazing incidence diffraction (GID) techniques. Grazing incidence x-ray diffraction measurements of monolayers of perfluoro-n-eicosane (F(CFsb2)sb{20}F) and F(CFsb2)sb{m}(CHsb2)sb{n}H (denoted as Fsb{m}Hsb{n}) supported at the air-water interface demonstrated that even without the conventional polar head group, the surfactant molecules are capable of forming ordered in-plane structures defined by hexagonal close packing of the fluorinated blocks of adsorbed molecules due to the stronger chain-chain interaction between fluorocarbon chains than the corresponding hydrocarbons. The specular reflectivity data reveals a hydrocarbon-down, fluorocarbon-up orientation for Fsb{12}Hsb{18}. In contrast to the conventional expectation that soluble surfactants form disordered monolayers at the liquid-liquid interface, the studies on a fluoroalcohol (F(CFsb2)sb{10}(CHsb2)sb2OH) monolayer at water-hexane interface indicate that the surfactants are in a close packed hexagonal phase, similar to the in-plane structure of other fluorocarbon molecules at water-air interface. Above a transition temperature the monolayer is in a low density gas phase. Preliminary study shows that hysteresis effect occurs around the transition temperature. The first measurements of microscopic structure at common high interfacial tension liquid-liquid interfaces such as a simple oil-water (hexane-water) interface is also reported. Thermal expansion coefficient measurements indicate subtle structural differences in these monolayers.

  5. Dynamics of capillary-driven liquid-liquid displacement in open microchannels.

    PubMed

    Yang, D; Krasowska, M; Priest, C; Ralston, J

    2014-11-28

    The dynamics of the spontaneous spreading of a liquid droplet along an open hydrophilic microchannel filled with another immiscible liquid is primarily determined by the competition between the capillary driving force and the viscous drag. While the former force depends on the channel cross-section and dimensions, interfacial tension between two liquids and the contact angle formed between the channel's wall and the two liquids, the latter arises from the motion of fluid molecules in the two bulk liquids. This paper focuses on the influence of the outer (displaced) phase viscosity. In general, as the viscosity of the displaced phase increases relative to the viscosity of the displacing phase, the velocity of the liquid-liquid meniscus decreases. The experiments were interpreted by extending a previously established correlation for liquid-vapour systems (J. Phys. Chem. C, 2011, 115(38), 18761-18769) in open microchannels of the same geometry. The relationship between the liquid-liquid flow dynamics and the properties of the liquids (e.g. viscosities) is still unclear. Nonetheless, by taking a self-consistent empirical approach to estimate the influence of the viscosities on the flow kinetics for a given system, it is possible to obtain a reasonable theoretical description for the experimental system over a specific range of viscosity ratios. PMID:25308905

  6. Nonlinear optical studies of liquid crystal alignment on a rubbed polyvinyl alcohol surface

    NASA Astrophysics Data System (ADS)

    Wei, Xing; Hong, Seok-Cheol; Zhuang, Xiaowei; Goto, Tomohisa; Shen, Y. R.

    2000-10-01

    Sum-frequency vibrational spectroscopy and second-harmonic generation have been used to measure the orientational distributions of the polymer chains and adsorbed 8CB liquid crystal molecules on a rubbed polyvinyl alcohol surface. Results show that the polymer chains at the surface appear to be well aligned by rubbing, and the adsorbed liquid crystal molecules are aligned, in turn, by the surface polymer chains. Strong correlation exists between the orientational distributions of the polymer chains and the liquid crystal molecules, indicating that the surface-induced bulk alignment of a liquid crystal film by rubbed polymer surfaces is via an orientational epitaxylike mechanism.

  7. Chemical and biological sensing using liquid crystals

    PubMed Central

    Carlton, Rebecca J.; Hunter, Jacob T.; Miller, Daniel S.; Abbasi, Reza; Mushenheim, Peter C.; Tan, Lie Na; Abbott, Nicholas L.

    2014-01-01

    The liquid crystalline state of matter arises from orientation-dependent, non-covalent interaction between molecules within condensed phases. Because the balance of intermolecular forces that underlies formation of liquid crystals is delicate, this state of matter can, in general, be easily perturbed by external stimuli (such as an electric field in a display). In this review, we present an overview of recent efforts that have focused on exploiting the responsiveness of liquid crystals as the basis of chemical and biological sensors. In this application of liquid crystals, the challenge is to design liquid crystalline systems that undergo changes in organization when perturbed by targeted chemical and biological species of interest. The approaches described below revolve around the design of interfaces that selectively bind targeted species, thus leading to surface-driven changes in the organization of the liquid crystals. Because liquid crystals possess anisotropic optical and dielectric properties, a range of different methods can be used to read out the changes in organization of liquid crystals that are caused by targeted chemical and biological species. This review focuses on principles for liquid crystal-based sensors that provide an optical output. PMID:24795857

  8. Clusterization of water molecules as deduced from statistical mechanical approach

    NASA Astrophysics Data System (ADS)

    Krasnoholovets, Volodymyr

    2004-12-01

    Using the methods of statistical mechanics we have shown that a homogeneous water network is unstable and spontaneously disintegrates to the nonhomogeneous state (i.e. peculiar clusters), which can be treated as an ordinary state of liquid water. The major peculiarity of the concept is that it separates the paired potential into two independent components—the attractive potential and the repulsive one, which in turn should feature a very different dependence on the distance from the particle (a water molecule in the present case). We choose the interaction potential as a combination of the ionic crystal potential and the vibratory potential associated with the elastic properties of the water system as a whole. The number ℵ of water molecules that enters a cluster is calculated as a function of several parameters, such as the dielectric constant, the mass of a water molecule, the distance between nearest molecules, and the vibrations of nearest molecules in their nodes. The number of H2O molecules that comprise a cluster is estimated as about ℵ ≈ 900, which agrees with the available experimental data.

  9. Liquid crystalline order in mucus

    NASA Technical Reports Server (NTRS)

    Viney, C.; Huber, A. E.; Verdugo, P.

    1993-01-01

    Mucus plays an exceptionally wide range of important biological roles. It operates as a protective, exchange, and transport medium in the digestive, respiratory, and reproductive systems of humans and other vertebrates. Mucus is a polymer hydrogel. It is secreted as discrete packages (secretory granules) by specialized secretory cells. Mucus hydrogel is stored in a condensed state inside the secretory granules. Depending upon the architecture of their constituent macromolecules and on the composition of the solvent, polymer gels can form liquid crystalline microstructures, with orientational order being exhibited over optically resolvable distances. Individual mucin molecules consist of alternating rigid segments (heavily glycosylated; hydrophilic) and flexible segments (nonglycosylated; hydrophobic). Polymer molecules consisting of rigid units linked by flexible spacers are frequently associated with liquid crystalline behavior, which again raises the possibility that mucus could form anisotropic fluid phases. Suggestions that mucins may be self-associating in dilute solution have previously been challenged on the basis of sedimentation-equilibrium studies performed on mucus in which potential sites of association were competitively blocked with inhibitors. However, the formation of stable liquid crystalline phases does not depend on the existence of inter- or intramolecular associations; these phases can form on the basis of steric considerations alone.

  10. Liquid electrode

    DOEpatents

    Ekechukwu, A.A.

    1994-07-05

    A dropping electrolyte electrode is described for use in electrochemical analysis of non-polar sample solutions, such as benzene or cyclohexane. The liquid electrode, preferably an aqueous salt solution immiscible in the sample solution, is introduced into the solution in dropwise fashion from a capillary. The electrolyte is introduced at a known rate, thus, the droplets each have the same volume and surface area. The electrode is used in making standard electrochemical measurements in order to determine properties of non-polar sample solutions. 2 figures.

  11. Single Molecule Electronics and Devices

    PubMed Central

    Tsutsui, Makusu; Taniguchi, Masateru

    2012-01-01

    The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule. PMID:22969345

  12. A liquid crystalline chirality balance for vapours

    NASA Astrophysics Data System (ADS)

    Ohzono, Takuya; Yamamoto, Takahiro; Fukuda, Jun-Ichi

    2014-04-01

    Chiral discrimination of vapours plays an important role in olfactory perception of biological systems and its realization by artificial sensors has been an intriguing challenge. Here, we report a simple method that tangibly visualizes the chirality of a diverse variety of molecules dissolved from vapours with high sensitivity, by making use of a structural change in a periodic microstructure of a nematic liquid crystal confined in open microchannels. This microstructure is accompanied by a topological line defect of a zigzag form with equal lengths of ‘zig’ and ‘zag.’ We find that a tiny amount of vapour of chiral molecules injected onto the liquid crystal induces the imbalance of ‘zig’ and ‘zag’ depending on its enantiomeric excess within a few seconds. Our liquid-crystal-based ‘chirality balance’ offers a simple, quick and versatile chirality-sensing/-screening method for gas-phase analysis (for example, for odours, environmental chemicals or drugs).

  13. Mobile and static molecular disorder in liquids

    NASA Astrophysics Data System (ADS)

    Huyskens, Pierre L.

    1992-11-01

    The fraction of time during which a molecule of a pure alcohol does not undergo H-bonding, estimated from the vapor pressure, is two orders of magnitude larger than the fraction of molecules that at a given time are not bound by an H-bond to their neighbors, as deduced from IR spectroscopic data. This obviously "anti-ergodic" statement renders questionable all the thermodynamic treatments of H-bonding in liquids, which are based on the usual Boltzmann expression. This expression equates the thermodynamic probability of a system with the static probability of distribution of the various states and, as outlined by Einstein, does not hold for non-ergodic systems. As pointed out by Pais (A. Pais, Subtle is the Lord. The Science and the Life of Albert Einstein, Oxford University Press, 1982), another Boltzmann relation relates the thermodynamic probability of a state to the fraction of time during which the system is found in that state. The latter definition was used by Einstein in his treatment of the ergodic problem. Similarly, the theory of the thermodynamics of mobile order in H-bonded liquids, of Huyskens and Siegel (P.L. Huyskens and G.G. Siegel, Bull. Soc. Chim. Belg., 97 (1988) 821), considers not the static configurations of the liquid, but the fraction of time during which an OH proton follows the oxygen atom of one or another neighboring molecules in its motion through the liquid. This coordination lowers the entropy and this reduction can be evaluated quantitatively. The present paper establishes a distinction between the static disorder, which is due to the possibility of exchange between the positions of the molecules and exists in mixed crystals, and the mobile disorder, which is due to the enlargement of the domain available for the motions of a given molecule, provoked by the mixing of two real gases. The mixing of two liquids allows an exchange in the positions, but also an expansion of the individual domains available for the motions. Thus, the

  14. Chiral analysis and mixtures of cold, large molecules

    NASA Astrophysics Data System (ADS)

    Eibenberger, Sandra; Drayna, Garrett K.; Wang, Kenneth; Hallas, Christian; Doyle, John M.; Patterson, David

    2016-05-01

    We show new avenues for ultra-specific chemical analysis of buffer-gas cooled molecules via microwave spectroscopy. Buffer gas cooling provides a continuous, mixture compatible, solution compatible source, where the cold environment is controllable and the cooling process is separate from the production of the gas phase molecules. We demonstrate the analysis of complex molecular mixtures by introducing a new liquid injection source with microwave spectroscopy in a cryogenic buffer gas environment. Chirality plays a fundamental role in the activity of many biological molecules and in broad classes of chemical reactions. Recently, we have demonstrated species and enantiomer sensitive microwave spectroscopic methods. We seek to apply these methods not just to the analysis of chemical mixtures, but also to the manipulation of mixtures.

  15. Relative Sizes of Organic Molecules

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This computer graphic depicts the relative complexity of crystallizing large proteins in order to study their structures through x-ray crystallography. Insulin is a vital protein whose structure has several subtle points that scientists are still trying to determine. Large molecules such as insuline are complex with structures that are comparatively difficult to understand. For comparison, a sugar molecule (which many people have grown as hard crystals in science glass) and a water molecule are shown. These images were produced with the Macmolecule program. Photo credit: NASA/Marshall Space Flight Center (MSFC)

  16. Quantum transport through aromatic molecules

    SciTech Connect

    Ojeda, J. H.; Rey-González, R. R.; Laroze, D.

    2013-12-07

    In this paper, we study the electronic transport properties through aromatic molecules connected to two semi-infinite leads. The molecules are in different geometrical configurations including arrays. Using a nearest neighbor tight-binding approach, the transport properties are analyzed into a Green's function technique within a real-space renormalization scheme. We calculate the transmission probability and the Current-Voltage characteristics as a function of a molecule-leads coupling parameter. Our results show different transport regimes for these systems, exhibiting metal-semiconductor-insulator transitions and the possibility to employ them in molecular devices.

  17. Organic heterocyclic molecules become superalkalis.

    PubMed

    Reddy, G Naaresh; Giri, Santanab

    2016-09-21

    An organic molecule which behaves like a superalkali has been designed from an aromatic heterocyclic molecule, pyrrole. Using first-principles calculation and a systematic two-step approach, we can have superalkali molecules with a low ionization energy, even lower than that of Cs. Couple cluster (CCSD) calculation reveals that a new heterocycle, C3N2(CH3)5 derived from a well-known aromatic heterocycle, pyrrole (C4H5N) has an ionization energy close to 3.0 eV. A molecular dynamics calculation on C3N2(CH3)5 reveals that the structure is dynamically stable. PMID:27530344

  18. Nonsequential double ionization of molecules

    SciTech Connect

    Prauzner-Bechcicki, Jakub S.; Sacha, Krzysztof; Zakrzewski, Jakub; Eckhardt, Bruno

    2005-03-01

    Double ionization of diatomic molecules by short linearly polarized laser pulses is analyzed. We consider the final stage of the ionization process, that is the decay of a highly excited two electron molecule, which is formed after rescattering. The saddles of the effective adiabatic potential energy close to which simultaneous escape of electrons takes place are identified. Numerical simulations of the ionization of molecules show that the process can be dominated by either sequential or nonsequential events. In order to increase the ratio of nonsequential to sequential ionizations very short laser pulses should be applied.

  19. Resolving metal-molecule interfaces at single-molecule junctions

    PubMed Central

    Komoto, Yuki; Fujii, Shintaro; Nakamura, Hisao; Tada, Tomofumi; Nishino, Tomoaki; Kiguchi, Manabu

    2016-01-01

    Electronic and structural detail at the electrode-molecule interface have a significant influence on charge transport across molecular junctions. Despite the decisive role of the metal-molecule interface, a complete electronic and structural characterization of the interface remains a challenge. This is in no small part due to current experimental limitations. Here, we present a comprehensive approach to obtain a detailed description of the metal-molecule interface in single-molecule junctions, based on current-voltage (I-V) measurements. Contrary to conventional conductance studies, this I-V approach provides a correlated statistical description of both, the degree of electronic coupling across the metal-molecule interface, and the energy alignment between the conduction orbital and the Fermi level of the electrode. This exhaustive statistical approach was employed to study single-molecule junctions of 1,4-benzenediamine (BDA), 1,4-butanediamine (C4DA), and 1,4-benzenedithiol (BDT). A single interfacial configuration was observed for both BDA and C4DA junctions, while three different interfacial arrangements were resolved for BDT. This multiplicity is due to different molecular adsorption sites on the Au surface namely on-top, hollow, and bridge. Furthermore, C4DA junctions present a fluctuating I-V curve arising from the greater conformational freedom of the saturated alkyl chain, in sharp contrast with the rigid aromatic backbone of both BDA and BDT. PMID:27221947

  20. Resolving metal-molecule interfaces at single-molecule junctions

    NASA Astrophysics Data System (ADS)

    Komoto, Yuki; Fujii, Shintaro; Nakamura, Hisao; Tada, Tomofumi; Nishino, Tomoaki; Kiguchi, Manabu

    2016-05-01

    Electronic and structural detail at the electrode-molecule interface have a significant influence on charge transport across molecular junctions. Despite the decisive role of the metal-molecule interface, a complete electronic and structural characterization of the interface remains a challenge. This is in no small part due to current experimental limitations. Here, we present a comprehensive approach to obtain a detailed description of the metal-molecule interface in single-molecule junctions, based on current-voltage (I-V) measurements. Contrary to conventional conductance studies, this I-V approach provides a correlated statistical description of both, the degree of electronic coupling across the metal-molecule interface, and the energy alignment between the conduction orbital and the Fermi level of the electrode. This exhaustive statistical approach was employed to study single-molecule junctions of 1,4-benzenediamine (BDA), 1,4-butanediamine (C4DA), and 1,4-benzenedithiol (BDT). A single interfacial configuration was observed for both BDA and C4DA junctions, while three different interfacial arrangements were resolved for BDT. This multiplicity is due to different molecular adsorption sites on the Au surface namely on-top, hollow, and bridge. Furthermore, C4DA junctions present a fluctuating I-V curve arising from the greater conformational freedom of the saturated alkyl chain, in sharp contrast with the rigid aromatic backbone of both BDA and BDT.

  1. Formulating liquid ethers for microtubular SOFCs

    NASA Astrophysics Data System (ADS)

    Kendall, Kevin; Slinn, Matthew; Preece, John

    One of the key problems of applying solid oxide fuel cells (SOFCs) in transportation is that conventional fuels like kerosene and diesel do not operate directly in SOFCs without prereforming to hydrogen and carbon monoxide which can be handled by the nickel cermet anode. SOFCs can internally reform certain hydrocarbon molecules such as methanol and methane. However, other liquid fuels usable in petrol or diesel internal combustion engines (ICEs) have not easily been reformable directly on the anode. This paper describes a search for liquid fuels which can be mixed with petrol or diesel and also injected directly into an SOFC without destroying the nickel anode. When fuel molecules such as octane are injected onto the conventional nickel/yttria stabilised zirconia (Ni/YSZ) SOFC fuel electrode, the anode rapidly becomes blocked by carbon deposition and the cell power drops to near zero in minutes. This degeneration of the anode can be inhibited by injection of air or water into the anode or by some upstream reforming just before entry to the SOFC. Some smaller molecules such as methane, methanol and methanoic acid produce a slight tendency to carbon deposition but not sufficient to prevent long term operation. In this project we have investigated a large number of molecules and now found that some liquid ethers do not significantly damage the anode when directly injected. These molecules and formulations with other components have been evaluated in this study. The theory put forward in this paper is that carbon-carbon bonds in the fuel are the main reason for anode damage. By testing a number of fuels without such bonds, particularly liquid ethers such as methyl formate and dimethoxy methane, it has been shown that SOFCs can run without substantial carbon formation. The proposal is that conventional fuels can be doped with these molecules to allow hybrid operation of an ICE/SOFC device.

  2. Moving Molecules and Mothball Madness.

    ERIC Educational Resources Information Center

    Strain, John

    1993-01-01

    Describes concrete demonstrations on the states of matter. In the first demonstration, students represent molecules; and, in the second demonstration, moth balls are heated to produce a change of state. (PR)

  3. Surface chemistry of deuterated molecules

    NASA Astrophysics Data System (ADS)

    Tielens, A. G. G. M.

    1983-03-01

    The chemical composition of grain mantles is calculated in order to determine the concentration of deuterated molecules relative to their hydrogenated counterparts in grain mantles. The computation takes into account reactions involving deuterium in the gas phase and on grain surfaces. The results show that the abundance of deuterium molecules in grain mantles is much higher than expected on the basis of the cosmic abundance ratio of D to H. HDCO has a relatively high abundance in grain mantles as compared to other deuterated molecules, due to the fact that H abstraction from HDCO has a lower activation barrier than D abstraction. The infrared characteristics of the calculated grain mantles are discussed and observational tests of the model calcultions are suggested. The contribution of grain surface chemistry to the concentration of molecules in the gas phase is briefly considered.

  4. Cobalt single-molecule magnet

    NASA Astrophysics Data System (ADS)

    Yang, En-Che; Hendrickson, David N.; Wernsdorfer, Wolfgang; Nakano, Motohiro; Zakharov, Lev N.; Sommer, Roger D.; Rheingold, Arnold L.; Ledezma-Gairaud, Marisol; Christou, George

    2002-05-01

    A cobalt molecule that functions as a single-molecule magnet, [Co4(hmp)4(MeOH)4Cl4], where hmp- is the anion of hydroxymethylpyridine, is reported. The core of the molecule consists of four Co(II) cations and four hmp- oxygen atom ions at the corners of a cube. Variable-field and variable-temperature magnetization data have been analyzed to establish that the molecule has a S=6 ground state with considerable negative magnetoanisotropy. Single-ion zero-field interactions (DSz2) at each cobalt ion are the origin of the negative magnetoanisotropy. A single crystal of the compound was studied by means of a micro-superconducting quantum interference device magnetometer in the range of 0.040-1.0 K. Hysteresis was found in the magnetization versus magnetic field response of this single crystal.

  5. Spin tunneling in magnetic molecules

    NASA Astrophysics Data System (ADS)

    Kececioglu, Ersin

    In this thesis, we will focus on spin tunneling in a family of systems called magnetic molecules such as Fe8 and Mn12. This is comparatively new, in relation to other tunneling problems. Many issues are not completely solved and/or understood yet. The magnetic molecule Fe 8 has been observed to have a rich pattern of degeneracies in its magnetic spectrum. We focus on these degeneracies from several points of view. We start with the simplest anisotropy Hamiltonian to describe the Fe 8 molecule and extend our discussion to include higher order anisotropy terms. We give analytical expressions as much as we can, for the degeneracies in the semi-classical limit in both cases. We reintroduce jump instantons to the instanton formalism. Finally, we discuss the effect of the environment on the molecule. Our results, for all different models and techniques, agree well with both experimental and numerical results.

  6. Molecule-hugging graphene nanopores

    PubMed Central

    Garaj, Slaven; Liu, Song; Golovchenko, Jene A.; Branton, Daniel

    2013-01-01

    It has recently been recognized that solid-state nanopores in single-atomic-layer graphene membranes can be used to electronically detect and characterize single long charged polymer molecules. We have now fabricated nanopores in single-layer graphene that are closely matched to the diameter of a double-stranded DNA molecule. Ionic current signals during electrophoretically driven translocation of DNA through these nanopores were experimentally explored and theoretically modeled. Our experiments show that these nanopores have unusually high sensitivity (0.65 nA/Å) to extremely small changes in the translocating molecule’s outer diameter. Such atomically short graphene nanopores can also resolve nanoscale-spaced molecular structures along the length of a polymer, but do so with greatest sensitivity only when the pore and molecule diameters are closely matched. Modeling confirms that our most closely matched pores have an inherent resolution of ≤0.6 nm along the length of the molecule. PMID:23836648

  7. Single-Molecule DNA Analysis

    NASA Astrophysics Data System (ADS)

    Efcavitch, J. William; Thompson, John F.

    2010-07-01

    The ability to detect single molecules of DNA or RNA has led to an extremely rich area of exploration of the single most important biomolecule in nature. In cases in which the nucleic acid molecules are tethered to a solid support, confined to a channel, or simply allowed to diffuse into a detection volume, novel techniques have been developed to manipulate the DNA and to examine properties such as structural dynamics and protein-DNA interactions. Beyond the analysis of the properties of nucleic acids themselves, single-molecule detection has enabled dramatic improvements in the throughput of DNA sequencing and holds promise for continuing progress. Both optical and nonoptical detection methods that use surfaces, nanopores, and zero-mode waveguides have been attempted, and one optically based instrument is already commercially available. The breadth of literature related to single-molecule DNA analysis is vast; this review focuses on a survey of efforts in molecular dynamics and nucleic acid sequencing.

  8. Fluorescence Microscopy of Single Molecules

    ERIC Educational Resources Information Center

    Zimmermann, Jan; van Dorp, Arthur; Renn, Alois

    2004-01-01

    The investigation of photochemistry and photophysics of individual quantum systems is described with the help of a wide-field fluorescence microscopy approach. The fluorescence single molecules are observed in real time.

  9. Ultrastable Liquid-Liquid Interface as Viable Route for Controlled Deposition of Biodegradable Polymer Nanocapsules.

    PubMed

    Vecchione, Raffaele; Iaccarino, Giulia; Bianchini, Paolo; Marotta, Roberto; D'autilia, Francesca; Quagliariello, Vincenzo; Diaspro, Alberto; Netti, Paolo A

    2016-06-01

    Liquid-liquid interfaces are highly dynamic and characterized by an elevated interfacial tension as compared to solid-liquid interfaces. Therefore, they are gaining an increasing interest as viable templates for ordered assembly of molecules and nanoparticles. However, liquid-liquid interfaces are more difficult to handle compared to solid-liquid interfaces; their intrinsic instability may affect the assembly process, especially in the case of multiple deposition. Indeed, some attempts have been made in the deposition of polymer multilayers at liquid-liquid interfaces, but with limited control over size and stability. This study reports on the preparation of an ultrastable liquid-liquid interface based on an O/W secondary miniemulsion and its possible use as a template for the self-assembly of polymeric multilayer nanocapsules. Such polymer nanocapsules are made of entirely biodegradable materials, with highly controlled size-well under 200 nm-and multi-compartment and multifunctional features enriching their field of application in drug delivery, as well as in other bionanotechnology fields. PMID:27060934

  10. Biosensing using smectic and cholesteric liquid crystals

    NASA Astrophysics Data System (ADS)

    Popov, Piotr; Mann, Elizabeth; Jakli, Antal

    2015-03-01

    Liquid-crystal-based biosensors utilize liquid crystal alignment's high sensitivity to the presence of lipids and proteins self-assembled at the liquid crystal/aqueous solution interface. The optical response of the bulk liquid crystal to the interface offers inexpensive, easy optical detection of such biologically relevant molecules. Present technique uses nematic liquid crystal phase state that typically has a planar-to-homeotropic response only. Here we show that smectic and cholesteric phase states of liquid crystals can be used as new sensing modes that can provide additional information or improve the characteristics of a potential biosensor device. Smectic-A phase extends the detection range both toward the lower and higher concentration. Cholesteric phase (nematic with a chiral dopant) may be sensitive to the chirality of biological surface-active molecules such as phospholipids. Additionally, the ``finger-print'' texture of a cholesteric phase may show the differences between biomolecule homologues, thus providing a promising way of distinguishing between subtle differences of hydrocarbon chain or head-group size and structure.

  11. Collisional decoherence of polar molecules

    NASA Astrophysics Data System (ADS)

    Walter, Kai; Stickler, Benjamin A.; Hornberger, Klaus

    2016-06-01

    The quantum state of motion of a large and rotating polar molecule can lose coherence through the collisions with gas atoms. We show how the associated quantum master equation for the center of mass can be expressed in terms of the orientationally averaged differential and total scattering cross sections, for which we provide approximate analytic expressions. The master equation is then utilized to quantify collisional decoherence in a interference experiment with polar molecules.

  12. Morphology-induced low temperature conductivity in ionic liquids

    NASA Astrophysics Data System (ADS)

    Erbas, Aykut; Olvera de La Cruz, Monica; Olvera de la Cruz Team

    Ionic liquids exhibit nano-scale liquid crystalline order depending on the polymeric details of salt molecules. The resulting morphology and temperature behavior are key factors in determining the room temperature conductivity of ionic liquids. Here we discuss the phase behavior and related ionic conductivities of dry ionic liquids with volume fractions close to unity by using extensive molecular dynamics simulations. Temperature dependence, effective persistence length of tails, and excluded volume symmetry of amphiphilic ionic liquid molecules are investigated in large scale systems with short and long-range electrostatics. Our results suggest that by adjusting stiffness of the amphiphilic molecules and excluded volume interactions, lamellar or interconnected 3D phases can be obtained. Resulting phases have significant effects on the conductive properties. If there is no excluded volume asymmetry along the molecules, mostly lamellar phases with anisotropic conductivities emerge. If the excluded volume interactions become asymmetric, lamellar phases are replaced by interconnected phases consist of charged groups. Within temperature ranges that morphological phases are observed, conductivities exhibit low-temperature maxima in accord with experiments of ionic liquid-based liquid Center of Bio-inspried Energy Center (CBES).

  13. Nanochannel Based Single Molecule Recycling

    PubMed Central

    Lesoine, John F.; Venkataraman, Prahnesh A.; Maloney, Peter C.; Dumont, Mark

    2012-01-01

    We present a method for measuring the fluorescence from a single molecule hundreds of times without surface immobilization. The approach is based on the use of electroosmosis to repeatedly drive a single target molecule in a fused silica nanochannel through a stationary laser focus. Single molecule fluorescence detected during the transit time through the laser focus is used to repeatedly reverse the electrical potential controlling the flow direction. Our method does not rely on continuous observation and therefore is less susceptible to fluorescence blinking than existing fluorescence-based trapping schemes. The variation in the turnaround times can be used to measure the diffusion coefficient on a single molecule level. We demonstrate the ability to recycle both proteins and DNA in nanochannels and show that the procedure can be combined with single-pair Förster energy transfer. Nanochannel-based single molecule recycling holds promise for studying conformational dynamics on the same single molecule in solution and without surface tethering. PMID:22662745

  14. What Is a Simple Liquid?

    NASA Astrophysics Data System (ADS)

    Ingebrigtsen, Trond S.; Schrøder, Thomas B.; Dyre, Jeppe C.

    2012-01-01

    different ways: (1) chemically by the fact that the liquid’s properties are fully determined by interactions from the molecules within the FCS, (2) physically by the fact that there are isomorphs in the phase diagram, i.e., curves along which several properties like excess entropy, structure, and dynamics, are invariant in reduced units, and (3) mathematically by the fact that throughout the phase diagram the reduced-coordinate constant-potential-energy hypersurfaces define a one-parameter family of compact Riemannian manifolds. No proof is given that the chemical characterization follows from the strong correlation property, but we show that this FCS characterization is consistent with the existence of isomorphs in strongly correlating liquids’ phase diagram. Finally, we note that the FCS characterization of simple liquids calls into question the physical basis of standard perturbation theory, according to which the repulsive and attractive forces play fundamentally different roles for the physics of liquids.

  15. Molecular catalytic coal liquid conversion

    SciTech Connect

    Stock, L.M.; Yang, Shiyong

    1995-12-31

    This research, which is relevant to the development of new catalytic systems for the improvement of the quality of coal liquids by the addition of dihydrogen, is divided into two tasks. Task 1 centers on the activation of dihydrogen by molecular basic reagents such as hydroxide ion to convert it into a reactive adduct (OH{center_dot}H{sub 2}){sup {minus}} that can reduce organic molecules. Such species should be robust withstanding severe conditions and chemical poisons. Task 2 is focused on an entirely different approach that exploits molecular catalysts, derived from organometallic compounds that are capable of reducing monocyclic aromatic compounds under very mild conditions. Accomplishments and conclusions are discussed.

  16. Floating liquid bridge charge dynamics

    NASA Astrophysics Data System (ADS)

    Teschke, Omar; Soares, David Mendez; Gomes, Whyllerson Evaristo; Valente Filho, Juracyr Ferraz

    2016-01-01

    The interaction of liquid with electric fields is investigated in a configuration where up to 13 kV are applied between electrodes resulting in a 106 V/m electric field in the capillaries and where there is the formation of a free-standing fluid bridge in the interelectrode gap. The Mott-Gurney equation was fitted to the measured ionization current vs applied voltage curve which indicates that the ionization rate at the high-voltage anode electrode dimethylsulfoxide (DMSO) interface and space charging in the interelectrode gap determine the floating liquid bridge current for a given cathode-to-anode voltage. Space charge effects were measured in the cathode becker and also at the liquid bridge since the ionized charges at the anode migrate to the bridge outer surface and decrease the interfacial tension from 43 mJ/m2 to 29 mJ/m2. Two distinct structural regions then form the bridge, a charged plastic (bulk modulus ˜100 MPa) conducting outer layer with a surface conductivity of ˜10-9 Ω-1, which shapes and supports the floating fluid structure, and an inner liquid cylinder, where DMSO molecules flow.

  17. Combining single-molecule manipulation and single-molecule detection.

    PubMed

    Cordova, Juan Carlos; Das, Dibyendu Kumar; Manning, Harris W; Lang, Matthew J

    2014-10-01

    Single molecule force manipulation combined with fluorescence techniques offers much promise in revealing mechanistic details of biomolecular machinery. Here, we review force-fluorescence microscopy, which combines the best features of manipulation and detection techniques. Three of the mainstay manipulation methods (optical traps, magnetic traps and atomic force microscopy) are discussed with respect to milestones in combination developments, in addition to highlight recent contributions to the field. An overview of additional strategies is discussed, including fluorescence based force sensors for force measurement in vivo. Armed with recent exciting demonstrations of this technology, the field of combined single-molecule manipulation and single-molecule detection is poised to provide unprecedented views of molecular machinery. PMID:25255052

  18. Raman Optical Activity Spectra for Large Molecules through Molecules-in-Molecules Fragment-Based Approach.

    PubMed

    Jovan Jose, K V; Raghavachari, Krishnan

    2016-02-01

    We present an efficient method for the calculation of the Raman optical activity (ROA) spectra for large molecules through the molecules-in-molecules (MIM) fragment-based method. The relevant higher energy derivatives from smaller fragments are used to build the property tensors of the parent molecule to enable the extension of the MIM method for evaluating ROA spectra (MIM-ROA). Two factors were found to be particularly important in yielding accurate results. First, the link-atom tensor components are projected back onto the corresponding host and supporting atoms through the Jacobian projection method, yielding a mathematically rigorous method. Second, the long-range interactions between fragments are taken into account by using a less computationally expensive lower level of theory. The performance of the MIM-ROA model is calibrated on the enantiomeric pairs of 10 carbohydrate benchmark molecules, with strong intramolecular interactions. The vibrational frequencies and ROA intensities are accurately reproduced relative to the full, unfragmented, results for these systems. In addition, the MIM-ROA method is employed to predict the ROA spectra of d-maltose, α-D-cyclodextrin, and cryptophane-A, yielding spectra in excellent agreement with experiment. The accuracy and performance of the benchmark systems validate the MIM-ROA model for exploring ROA spectra of large molecules. PMID:26760444

  19. Reversible switching of liquid crystal micro-particles in a nematic liquid crystal.

    PubMed

    Imamura, Koki; Yoshida, Hiroyuki; Ozaki, Masanori

    2016-01-21

    Liquid crystal micro-particles are functional materials possessing optical and dielectric anisotropies originating from the arrangement of rod-like molecules within the particles. Although they can be switched by an electric field, particles dispersed in isotropic hosts usually cannot return to their original state, because there is no restoration force acting on the particles. Here, we describe reversible switching of liquid crystal micro-particles by dispersing them in a nematic liquid crystal host. We fabricate square micro-particles with unidirectional molecular alignment and investigate their static and dynamic electro-optic properties by applying an in-plane electric field. The behavior of the micro-particles is well-described by the theoretical model we construct, making this study potentially useful for the development of liquid crystal-liquid crystal particle composites with engineered properties. PMID:26514389

  20. Measuring an antibody affinity distribution molecule by molecule

    SciTech Connect

    Bradbury, Andrew M; Werner, James H; Temirov, Jamshid

    2008-01-01

    Single molecule fluorescence mIcroscopy was used to observe the binding and unbinding of hapten decorated quantum dots with individual surface immobilized antibodies. The fluorescence time history from an individual antibody site can be used to calculate its binding affinity. While quantum dot blinking occurs during these measurements, we describe a simple empirical method to correct the apparent/observed affinity to account for the blinking contribution. The combination of many single molecule affinity measurements from different antibodies yields not only the average affinity, it directly measures the full shape and character of the surface affinity distribution function.

  1. Isotropization of nematic liquid crystals by TMDSC

    SciTech Connect

    Chen, Wei; Dadmun, M.; Zhang, Ge; Boller, A.; Wunderlich, B. |

    1997-12-01

    Temperature-modulated differential scanning calorimetry (TMDSC) and traditional DSC are used to study the transition between the nematic liquid crystalline state and the isotropic liquid for two small molecules [4,4{prime}-azoxyanisole and N,N`-bis(4-n-octyloxybenzal)-1,4-phenylenediamine] and one macromolecule (4,4{prime}-dihydroxy-{alpha}-methylstilbene copolymerized with a 1:1 molar mixture of 1,7-dibromoheptane and 1,9-dibromononane). The DSC measurements with 4,4{prime}-azoxyanisole were used for temperature calibration with varying heating and cooling rates. Quasi-isothermal TMDSC with small temperature amplitude and standard TMDSC with underlying heating and cooling rates were utilized to analyze the breadth of the transitions. It could be verified that the isotropization transition of a nematic liquid crystal is, indeed, reversible for all three molecules. The nature of the transition changes, however, from relatively sharp, for small, rigid molecules, to about three kelvins wide for the small molecule with flexible ends, to as broad as 20 K for the macromolecule. It was also demonstrated that quantitative heats of fusion of sharp transitions can be extracted from TMDSC, but only from the time-domain heat-flow signal.

  2. Automation of AMOEBA polarizable force field parameterization for small molecules

    PubMed Central

    Wu, Johnny C.; Chattree, Gaurav

    2012-01-01

    A protocol to generate parameters for the AMOEBA polarizable force field for small organic molecules has been established, and polarizable atomic typing utility, Poltype, which fully automates this process, has been implemented. For validation, we have compared with quantum mechanical calculations of molecular dipole moments, optimized geometry, electrostatic potential, and conformational energy for a variety of neutral and charged organic molecules, as well as dimer interaction energies of a set of amino acid side chain model compounds. Furthermore, parameters obtained in gas phase are substantiated in liquid-phase simulations. The hydration free energy (HFE) of neutral and charged molecules have been calculated and compared with experimental values. The RMS error for the HFE of neutral molecules is less than 1 kcal/mol. Meanwhile, the relative error in the predicted HFE of salts (cations and anions) is less than 3% with a correlation coefficient of 0.95. Overall, the performance of Poltype is satisfactory and provides a convenient utility for applications such as drug discovery. Further improvement can be achieved by the systematic study of various organic compounds, particularly ionic molecules, and refinement and expansion of the parameter database. PMID:22505837

  3. Increased Hydrogel Swelling Induced by Absorption of Small Molecules.

    PubMed

    Nam, Changwoo; Zimudzi, Tawanda J; Geise, Geoffrey M; Hickner, Michael A

    2016-06-01

    The water and small molecule uptake behavior of amphiphilic diacrylate terminated poly(dimethylsiloxane) (PDMSDA)/poly(ethylene glycol diacrylate) (PEGDA) cross-linked hydrogels were studied using attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. These hydrogel networks absorbed more water as the PEGDA content of the network increased. In contrast to typical osmotic deswelling behavior that occurs when liquid water equilibrated hydrogels are immersed in small molecule solutions with water activities less than unity, water-swollen gels immersed in 2-acrylamido-2-methylpropanesulfonic acid (AMPS-H) solutions rapidly regained their water content within 4 min following an initial deswelling response. In situ ATR-FTIR analysis of the hydrogel film during the dynamic swelling experiment indicated that small molecule absorption into the gel played an important role in inducing gel reswelling in low water activity solutions. This aspect of polymer gel water uptake and interaction with small molecules is important for optimizing hydrogel coatings and hydrophilic polymer applications where there is an interaction between the internal chemical structure of the gel and electrolytes or other molecules in solution. PMID:27159118

  4. Key Developments in Ionic Liquid Crystals

    PubMed Central

    Alvarez Fernandez, Alexandra; Kouwer, Paul H. J.

    2016-01-01

    Ionic liquid crystals are materials that combine the classes of liquid crystals and ionic liquids. The first one is based on the multi-billion-dollar flat panel display industry, whilst the latter quickly developed in the past decades into a family of highly-tunable non-volatile solvents. The combination yields materials with a unique set of properties, but also with many challenges ahead. In this review, we provide an overview of the key concepts in ionic liquid crystals, particularly from a molecular perspective. What are the important molecular parameters that determine the phase behavior? How should they be introduced into the molecules? Finally, which other tools does one have to realize specific properties in the material? PMID:27196890

  5. Liquid crystal on subwavelength metal gratings

    SciTech Connect

    Palto, S. P.; Barnik, M. I.; Artemov, V. V.; Shtykov, N. M.; Geivandov, A. R.; Yudin, S. G.; Gorkunov, M. V.

    2015-06-14

    Optical and electrooptical properties of a system consisting of subwavelength metal gratings and nematic liquid crystal layer are studied. Aluminium gratings that also act as interdigitated electrodes are produced by focused ion beam lithography. It is found that a liquid crystal layer strongly influences both the resonance and light polarization properties characteristic of the gratings. Enhanced transmittance is observed not only for the TM-polarized light in the near infrared spectral range but also for the TE-polarized light in the visible range. Although the electrodes are separated by nanosized slits, and the electric field is strongly localized near the surface, a pronounced electrooptical effect is registered. The effect is explained in terms of local reorientation of liquid crystal molecules at the grating surface and propagation of the orientational deformation from the surface into the bulk of the liquid crystal layer.

  6. Liquid Crystal Devices.

    ERIC Educational Resources Information Center

    Bradshaw, Madeline J.

    1983-01-01

    The nature of liquid crystals and several important liquid crystal devices are described. Ideas for practical experiments to illustrate the properties of liquid crystals and their operation in devices are also described. (Author/JN)

  7. Liquid Crystal Inquiries.

    ERIC Educational Resources Information Center

    Marroum, Renata-Maria

    1996-01-01

    Discusses the properties and classification of liquid crystals. Presents a simple experiment that illustrates the structure of liquid crystals and the differences between the various phases liquid crystals can assume. (JRH)

  8. Electron Collisions with Large Molecules

    NASA Astrophysics Data System (ADS)

    McKoy, Vincent

    2006-10-01

    In recent years, interest in electron-molecule collisions has increasingly shifted to large molecules. Applications within the semiconductor industry, for example, require electron collision data for molecules such as perfluorocyclobutane, while almost all biological applications involve macromolecules such as DNA. A significant development in recent years has been the realization that slow electrons can directly damage DNA. This discovery has spurred studies of low-energy collisions with the constituents of DNA, including the bases, deoxyribose, the phosphate, and larger moieties assembled from them. In semiconductor applications, a key goal is development of electron cross section sets for plasma chemistry modeling, while biological studies are largely focused on understanding the role of localized resonances in inducing DNA strand breaks. Accurate calculations of low-energy electron collisions with polyatomic molecules are computationally demanding because of the low symmetry and inherent many-electron nature of the problem; moreover, the computational requirements scale rapidly with the size of the molecule. To pursue such studies, we have adapted our computational procedure, known as the Schwinger multichannel method, to run efficiently on highly parallel computers. In this talk, we will present some of our recent results for fluorocarbon etchants used in the semiconductor industry and for constituents of DNA and RNA. In collaboration with Carl Winstead, California Institute of Technology.

  9. REDISTRIBUTOR FOR LIQUID-LIQUID EXTRACTION COLUMNS

    DOEpatents

    Bradley, J.G.

    1957-10-29

    An improved baffle plate construction to intimately mix immiscible liquid solvents for solvent extraction processes in a liquid-liquid pulse column is described. To prevent the light and heavy liquids from forming separate continuous homogeneous vertical channels through sections of the column, a baffle having radially placed rectangular louvers with deflection plates opening upon alternate sides of the baffle is placed in the column, normal to the axis. This improvement substantially completely reduces strippiig losses due to poor mixing.

  10. Hydrogen bonding in liquid methanol, methylamine, and methanethiol studied by molecular-dynamics simulations

    NASA Astrophysics Data System (ADS)

    Kosztolányi, T.; Bakó, I.; Pálinkás, G.

    2003-03-01

    Molecular-dynamics computer simulations have been carried out on liquid methanol, methylamine, and methanethiol. The local structure of the liquids was studied based on radial distribution functions and the density projections of the neighboring molecules obtained on the basis of simulated molecular configurations. The extent of hydrogen bonding was investigated by direct analysis of the connectivity of molecules forming hydrogen-bonded clusters in these liquids. By this analysis, the methanol molecules were found to form linear chainlike structures. The local structure of hydrogen-bonded molecules of methylamine proved to be rather space filling due to the great extent of chain branching. Methanethiol molecules also proved to form hydrogen bonds forming small compact clusters. No evidence was found, however, for the clustering of hydrophobic methyl groups in any of the liquids. The quality of simulations was checked by derivation of neutron total and composite radial distribution functions and by comparison of those with available experimental data.

  11. On the phase-field modelling of a miscible liquid/liquid boundary.

    PubMed

    Xie, Ruilin; Vorobev, Anatoliy

    2016-02-15

    Mixing of miscible liquids is essential for numerous processes in industry and nature. Mixing, i.e. interpenetration of molecules through the liquid/liquid boundary, occurs via interfacial diffusion. Mixing can also involve externally or internally driven hydrodynamic flows, and can lead to deformation or disintegration of the liquid/liquid boundary. At the moment, the mixing dynamics remains poorly understood. The classical Fick's law, generally accepted for description of the diffusion process, does not explain the experimental observations, in particular, the recent experiments with dissolution of a liquid solute by a liquid solvent within a horizontal capillary (Stevar and Vorobev, 2012). We present the results of the numerical study aimed at development of an advanced model for the dissolution dynamics of liquid/liquid binary mixtures. The model is based on the phase-field (Cahn-Hilliard) approach that is used as a physics-based model for the thermo- and hydrodynamic evolution of binary mixtures. Within this approach, the diffusion flux is defined through the gradient of chemical potential, and, in particular, includes the effect of barodiffusion. The dynamic interfacial stresses at the miscible interface are also taken into account. The simulations showed that such an approach can accurately reproduce the shape of the solute/solvent boundary, and some aspects of the diffusion dynamics. Nevertheless, all experimentally-observed features of the diffusion motion of the solute/solvent boundary, were not reproduced. PMID:26609922

  12. Thermal Degradation of Small Molecules: A Global Metabolomic Investigation

    PubMed Central

    2015-01-01

    Thermal processes are widely used in small molecule chemical analysis and metabolomics for derivatization, vaporization, chromatography, and ionization, especially in gas chromatography mass spectrometry (GC/MS). In this study the effect of heating was examined on a set of 64 small molecule standards and, separately, on human plasma metabolite extracts. The samples, either derivatized or underivatized, were heated at three different temperatures (60, 100, and 250 °C) at different exposure times (30 s, 60 s, and 300 s). All the samples were analyzed by liquid chromatography coupled to electrospray ionization mass spectrometry (LC/MS) and the data processed by XCMS Online (xcmsonline.scripps.edu). The results showed that heating at an elevated temperature of 100 °C had an appreciable effect on both the underivatized and derivatized molecules, and heating at 250 °C created substantial changes in the profile. For example, over 40% of the molecular peaks were altered in the plasma metabolite analysis after heating (250 °C, 300s) with a significant formation of degradation and transformation products. The analysis of 64 small molecule standards validated the temperature-induced changes observed on the plasma metabolites, where most of the small molecules degraded at elevated temperatures even after minimal exposure times (30 s). For example, tri- and diorganophosphates (e.g., adenosine triphosphate and adenosine diphosphate) were readily degraded into a mono-organophosphate (e.g., adenosine monophosphate) during heating. Nucleosides and nucleotides (e.g., inosine and inosine monophosphate) were also found to be transformed into purine derivatives (e.g., hypoxanthine). A newly formed transformation product, oleoyl ethyl amide, was identified in both the underivatized and derivatized forms of the plasma extracts and small molecule standard mixture, and was likely generated from oleic acid. Overall these analyses show that small molecules and metabolites undergo

  13. Thermal Degradation of Small Molecules: A Global Metabolomic Investigation.

    PubMed

    Fang, Mingliang; Ivanisevic, Julijana; Benton, H Paul; Johnson, Caroline H; Patti, Gary J; Hoang, Linh T; Uritboonthai, Winnie; Kurczy, Michael E; Siuzdak, Gary

    2015-11-01

    Thermal processes are widely used in small molecule chemical analysis and metabolomics for derivatization, vaporization, chromatography, and ionization, especially in gas chromatography mass spectrometry (GC/MS). In this study the effect of heating was examined on a set of 64 small molecule standards and, separately, on human plasma metabolite extracts. The samples, either derivatized or underivatized, were heated at three different temperatures (60, 100, and 250 °C) at different exposure times (30 s, 60 s, and 300 s). All the samples were analyzed by liquid chromatography coupled to electrospray ionization mass spectrometry (LC/MS) and the data processed by XCMS Online ( xcmsonline.scripps.edu ). The results showed that heating at an elevated temperature of 100 °C had an appreciable effect on both the underivatized and derivatized molecules, and heating at 250 °C created substantial changes in the profile. For example, over 40% of the molecular peaks were altered in the plasma metabolite analysis after heating (250 °C, 300s) with a significant formation of degradation and transformation products. The analysis of 64 small molecule standards validated the temperature-induced changes observed on the plasma metabolites, where most of the small molecules degraded at elevated temperatures even after minimal exposure times (30 s). For example, tri- and diorganophosphates (e.g., adenosine triphosphate and adenosine diphosphate) were readily degraded into a mono-organophosphate (e.g., adenosine monophosphate) during heating. Nucleosides and nucleotides (e.g., inosine and inosine monophosphate) were also found to be transformed into purine derivatives (e.g., hypoxanthine). A newly formed transformation product, oleoyl ethyl amide, was identified in both the underivatized and derivatized forms of the plasma extracts and small molecule standard mixture, and was likely generated from oleic acid. Overall these analyses show that small molecules and metabolites undergo

  14. Liquid supercoiling

    NASA Astrophysics Data System (ADS)

    Ribe, Neil; Habibi, Mehdi; Hosseini, Hossein; Hassan Khatami, Mohammad

    2011-11-01

    Supercoiling is defined as the large-scale secondary coiling of a slender body that is already coiled at a smaller scale (e.g., telephone cords and DNA strands). We demonstrate experimentally a novel fluid-mechanical form of supercoiling that occurs in the context of the familiar ``liquid rope coiling'' instability of a thin thread of viscous fluid falling onto a rigid surface. Under appropriate conditions, the coiling instability generates a tall pile of coils in the form of a hollow cylindrical column, which in turn becomes unstable to a secondary coiling instability with a frequency ~ 10 % of the primary one. To place this phenomenon in a broader context, we determine experimentally the phase diagram for the different possible behaviors of the thread (stagnation flow, simple coiling, rotatory folding, periodic column collapse, supercoiling) in the space of the fluid viscosity, the flow rate, and the fall height. We formulate a mathematical model for supercoiling by combining a thin-shell description of the column wall with a slender-thread description of the column as a whole. This leads to a set of coupled ordinary differential equations in one space dimension (the arclength along the axis of the coiling column) that we solve numerically using a continuation method. A comparison of the predicted and observed frequencies of secondary coiling will be shown.

  15. Liquid annulus

    NASA Technical Reports Server (NTRS)

    Ludewig, Hans

    1991-01-01

    It is shown that the specific impulse varies with the square root of the temperature and inversely with the square root of the molecular weight of the propellant. Typical values for specific impulse corresponding to various rocket concepts are shown. The Liquid Annulus core concept consists of a fuel element which will be arranged in a moderator block. The advantages as seen for the system are: high specific impulse; structural material will all run at low temperature; and lower fission product inventory because of evaporation. It is felt that this concept is worth at least a first look because of the promise of very high specific impulse. Because of the low thrust, one would probably need a cluster of engines. This is not necessarily bad because there would be some redundancy, but because of the low thrust one might have to refuel while running. Depending on the fuel vaporization, material can be included in the uranium that is injected as one is running along.

  16. Room temperature single molecule microscopes

    SciTech Connect

    Ambrose, W.P.; Goodwin, P.M.; Enderlein, G.; Semin, D.J.; Keller, R.A.

    1997-12-31

    We have developed three capabilities to image the locations of and interrogate immobilized single fluorescent molecules: near-field scanning optical, confocal scanning optical, and wide-field epi-fluorescence microscopy. Each microscopy has its own advantages. Near-field illumination can beat the diffraction limit. Confocal microscopy has high brightness and temporal resolution. Wide-field has the quickest (parallel) imaging capability. With confocal microscopy, we have verified that single fluorescent spots in our images are due to single molecules by observing photon antibunching. Using all three microscopies, we have observed that xanthene molecules dispersed on dry silica curiously exhibit intensity fluctuations on millisecond to minute time scales. We are exploring the connection between the intensity fluctuations and fluctuations in individual photophysical parameters. The fluorescence lifetimes of Rhodamine 6G on silica fluctuate. The complex nature of the intensity and lifetime fluctuations is consistent with a mechanism that perturbs more than one photophysical parameter.

  17. Guidance molecules in lung cancer

    PubMed Central

    Nasarre, Patrick; Potiron, Vincent; Drabkin, Harry

    2010-01-01

    Guidance molecules were first described in the nervous system to control axon outgrowth direction. They are also widely expressed outside the nervous system where they control cell migration, tissue development and establishment of the vascular network. In addition, they are involved in cancer development, tumor angiogenesis and metastasis. This review is primarily focused on their functions in lung cancer and their involvement in lung development is also presented. Five guidance molecule families and their corresponding receptors are described, including the semaphorins/neuropilins/plexins, ephrins and Eph receptors, netrin/DCC/UNC5, Slit/Robo and Notch/Delta. In addition, the possibility to target these molecules as a therapeutic approach in cancer is discussed. PMID:20139699

  18. Solvation of a probe molecule by fluid supercooled water in a hydrogel at 200 K.

    PubMed

    Santangelo, Maria Grazia; Levantino, Matteo; Cupane, Antonio; Jeschke, Gunnar

    2008-12-11

    By combining electron paramagnetic resonance (EPR) measurements on a nitroxide probe and differential scanning calorimetry (DSC), we demonstrate existence of liquid supercooled water in a silica hydrogel with high hydration level down to temperatures of at least 198 K. Besides the major fraction of liquid supercooled water, a minor fraction crystallizes at about 236 K during cooling and melts at 246 K during heating. The liquid domains are of sufficient size to solvate the nearly spherical paramagnetic probe molecule TEMPO with a diameter of about 6 A. Analysis of EPR spectra provides the rotational correlation time of the probe that is further used to compare the viscosity of the supercooled water with the one of bulk water. In the temperature interval investigated, the supercooled water behaves as a fragile liquid and eventually solidifies at 120 K to a glass that incorporates the probe molecules. PMID:19053683

  19. Methods of making composite optical devices employing polymer liquid crystal

    DOEpatents

    Jacobs, S.D.; Marshall, K.L.; Cerqua, K.A.

    1991-10-08

    Composite optical devices are disclosed using polymer liquid crystal materials both as optical and adhesive elements. The devices are made by assembling a heated polymer liquid crystal compound, while in a low viscosity form between optically transparent substrates. The molecules of the polymer are oriented, while in the liquid crystalline state and while above the glass transition temperature (T[sub g]) of the polymer, to provide the desired optical effects, such as polarization, and selective reflection. The liquid crystal polymer cements the substrates together to form an assembly providing the composite optical device. 7 figures.

  20. Methods of making composite optical devices employing polymer liquid crystal

    DOEpatents

    Jacobs, Stephen D.; Marshall, Kenneth L.; Cerqua, Kathleen A.

    1991-01-01

    Composite optical devices using polymer liquid crystal materials both as optical and adhesive elements. The devices are made by assembling a heated polymer liquid crystal compound, while in a low viscosity form between optically transparent substrates. The molecules of the polymer are oriented, while in the liquid crystalline state and while above the glass transition temperature (T.sub.g) of the polymer, to provide the desired optical effects, such as polarization, and selective reflection. The liquid crystal polymer cements the substrates together to form an assembly providing the composite optical device.

  1. Phase behavior and local structure of liquid crystalline polymers

    NASA Astrophysics Data System (ADS)

    Fynewever, Herb

    In this work we use a combination of theory and computer simulation to study the phase behavior of liquid crystalline polymers and the local structure of polymer melts. We review experimental and simulation evidence which shows that long and stiff molecules form orientationally ordered phases at packing fractions intermediate between the liquid and the solid. With the aid of a two-molecule simulation, we are able to apply Onsager's theory [Ann. N. Y. Acad. Sci. 51, 627 (1949)] for liquid crystal formation to flexible molecules without any additional approximations. Our results have a quantitative advantage over other theories in comparison with computer simulation data such as for the liquid-liquid crystal phase diagram. We also study the local structure of polymer melts using a two-molecule simulation to apply the density functional theories of Donley, Curro, and McCoy [J. Chem. Phys. 101 , 3205 (1994)1; and Yethiraj and Woodward [J. Chem. Phys 102 , 5499 (1995)]. The accuracy of these methods rivals that of integral equation theories in their predictions of local order. Further, the two-molecule simulation facilitates a more direct calculation of the equation of state via the monitoring of orientational correlations.

  2. Phase structure of soliton molecules

    SciTech Connect

    Hause, A.; Hartwig, H.; Seifert, B.; Stolz, H.; Boehm, M.; Mitschke, F.

    2007-06-15

    Temporal optical soliton molecules were recently demonstrated; they potentially allow further increase of data rates in optical telecommunication. Their binding mechanism relies on the internal phases, but these have not been experimentally accessible so far. Conventional frequency-resolved optical gating techniques are not suited for measurement of their phase profile: Their algorithms fail to converge due to zeros both in their temporal and their spectral profile. We show that the VAMPIRE (very advanced method of phase and intensity retrieval of E-fields) method performs reliably. With VAMPIRE the phase profile of soliton molecules has been measured, and further insight into the mechanism is obtained.

  3. Phase structure of soliton molecules

    NASA Astrophysics Data System (ADS)

    Hause, A.; Hartwig, H.; Seifert, B.; Stolz, H.; Böhm, M.; Mitschke, F.

    2007-06-01

    Temporal optical soliton molecules were recently demonstrated; they potentially allow further increase of data rates in optical telecommunication. Their binding mechanism relies on the internal phases, but these have not been experimentally accessible so far. Conventional frequency-resolved optical gating techniques are not suited for measurement of their phase profile: Their algorithms fail to converge due to zeros both in their temporal and their spectral profile. We show that the VAMPIRE (very advanced method of phase and intensity retrieval of E -fields) method performs reliably. With VAMPIRE the phase profile of soliton molecules has been measured, and further insight into the mechanism is obtained.

  4. Orbital molecules in electronic materials

    SciTech Connect

    Attfield, J. Paul

    2015-04-01

    Orbital molecules are made up of coupled orbital states on several metal ions within an orbitally ordered (and sometimes also charge-ordered) solid such as a transition metal oxide. Spin-singlet dimers are known in many materials, but recent discoveries of more exotic species such as 18-electron heptamers in AlV{sub 2}O{sub 4} and magnetic 3-atom trimerons in magnetite (Fe{sub 3}O{sub 4}) have shown that orbital molecules constitute a general new class of quantum electronic states in solids.

  5. Dipolar molecules in optical lattices.

    PubMed

    Sowiński, Tomasz; Dutta, Omjyoti; Hauke, Philipp; Tagliacozzo, Luca; Lewenstein, Maciej

    2012-03-16

    We study the extended Bose-Hubbard model describing an ultracold gas of dipolar molecules in an optical lattice, taking into account all on-site and nearest-neighbor interactions, including occupation-dependent tunneling and pair tunneling terms. Using exact diagonalization and the multiscale entanglement renormalization ansatz, we show that these terms can destroy insulating phases and lead to novel quantum phases. These considerable changes of the phase diagram have to be taken into account in upcoming experiments with dipolar molecules. PMID:22540482

  6. Nonadiabatic reaction of energetic molecules.

    PubMed

    Bhattacharya, Atanu; Guo, Yuanqing; Bernstein, Elliot R

    2010-12-21

    Energetic materials store a large amount of chemical energy that can be readily converted into mechanical energy via decomposition. A number of different ignition processes such as sparks, shocks, heat, or arcs can initiate the excited electronic state decomposition of energetic materials. Experiments have demonstrated the essential role of excited electronic state decomposition in the energy conversion process. A full understanding of the mechanisms for the decomposition of energetic materials from excited electronic states will require the investigation and analysis of the specific topography of the excited electronic potential energy surfaces (PESs) of these molecules. The crossing of multidimensional electronic PESs creates a funnel-like topography, known as conical intersections (CIs). CIs are well established as a controlling factor in the excited electronic state decomposition of polyatomic molecules. This Account summarizes our current understanding of the nonadiabatic unimolecular chemistry of energetic materials through CIs and presents the essential role of CIs in the determination of decomposition pathways of these energetic systems. Because of the involvement of more than one PES, a decomposition process involving CIs is an electronically nonadiabatic mechanism. Based on our experimental observations and theoretical calculations, we find that a nonadiabatic reaction through CIs dominates the initial decomposition process of energetic materials from excited electronic states. Although the nonadiabatic behavior of some polyatomic molecules has been well studied, the role of nonadiabatic reactions in the excited electronic state decomposition of energetic molecules has not been well investigated. We use both nanosecond energy-resolved and femtosecond time-resolved spectroscopic techniques to determine the decomposition mechanism and dynamics of energetic species experimentally. Subsequently, we employ multiconfigurational methodologies (such as, CASSCF

  7. Piezoresistivity in single DNA molecules

    PubMed Central

    Bruot, Christopher; Palma, Julio L.; Xiang, Limin; Mujica, Vladimiro; Ratner, Mark A.; Tao, Nongjian

    2015-01-01

    Piezoresistivity is a fundamental property of materials that has found many device applications. Here we report piezoresistivity in double helical DNA molecules. By studying the dependence of molecular conductance and piezoresistivity of single DNA molecules with different sequences and lengths, and performing molecular orbital calculations, we show that the piezoresistivity of DNA is caused by force-induced changes in the π–π electronic coupling between neighbouring bases, and in the activation energy of hole hopping. We describe the results in terms of thermal activated hopping model together with the ladder-based mechanical model for DNA proposed by de Gennes. PMID:26337293

  8. Piezoresistivity in single DNA molecules

    NASA Astrophysics Data System (ADS)

    Bruot, Christopher; Palma, Julio L.; Xiang, Limin; Mujica, Vladimiro; Ratner, Mark A.; Tao, Nongjian

    2015-09-01

    Piezoresistivity is a fundamental property of materials that has found many device applications. Here we report piezoresistivity in double helical DNA molecules. By studying the dependence of molecular conductance and piezoresistivity of single DNA molecules with different sequences and lengths, and performing molecular orbital calculations, we show that the piezoresistivity of DNA is caused by force-induced changes in the π-π electronic coupling between neighbouring bases, and in the activation energy of hole hopping. We describe the results in terms of thermal activated hopping model together with the ladder-based mechanical model for DNA proposed by de Gennes.

  9. Piezoresistivity in single DNA molecules.

    PubMed

    Bruot, Christopher; Palma, Julio L; Xiang, Limin; Mujica, Vladimiro; Ratner, Mark A; Tao, Nongjian

    2015-01-01

    Piezoresistivity is a fundamental property of materials that has found many device applications. Here we report piezoresistivity in double helical DNA molecules. By studying the dependence of molecular conductance and piezoresistivity of single DNA molecules with different sequences and lengths, and performing molecular orbital calculations, we show that the piezoresistivity of DNA is caused by force-induced changes in the π-π electronic coupling between neighbouring bases, and in the activation energy of hole hopping. We describe the results in terms of thermal activated hopping model together with the ladder-based mechanical model for DNA proposed by de Gennes. PMID:26337293

  10. From single molecule to single tubules

    NASA Astrophysics Data System (ADS)

    Guo, Chin-Lin

    2012-02-01

    Biological systems often make decisions upon conformational changes and assembly of single molecules. In vivo, epithelial cells (such as the mammary gland cells) can respond to extracellular matrix (ECM) molecules, type I collagen (COL), and switch their morphology from a lobular lumen (100-200 micron) to a tubular lumen (1mm-1cm). However, how cells make such a morphogenetic decision through interactions with each other and with COL is unclear. Using a temporal control of cell-ECM interaction, we find that epithelial cells, in response to a fine-tuned percentage of type I collagen (COL) in ECM, develop various linear patterns. Remarkably, these patterns allow cells to self-assemble into a tubule of length ˜ 1cm and diameter ˜ 400 micron in the liquid phase (i.e., scaffold-free conditions). In contrast with conventional thought, the linear patterns arise through bi-directional transmission of traction force, but not through diffusible biochemical factors secreted by cells. In turn, the transmission of force evokes a long-range (˜ 600 micron) intercellular mechanical interaction. A feedback effect is encountered when the mechanical interaction modifies cell positioning and COL alignment. Micro-patterning experiments further reveal that such a feedback is a novel cell-number-dependent, rich-get-richer process, which allows cells to integrate mechanical interactions into long-range (> 1mm) linear coordination. Our results suggest a mechanism cells can use to form and coordinate long-range tubular patterns, independent of those controlled by diffusible biochemical factors, and provide a new strategy to engineer/regenerate epithelial organs using scaffold-free self-assembly methods.

  11. Characterization and compaction behaviour of nimesulide crystal forms.

    PubMed

    Di Martino, Piera; Censi, Roberta; Barthélémy, Christine; Gobetto, Roberto; Joiris, Etienne; Masic, Admir; Odou, Pascal; Martelli, Sante

    2007-09-01

    Nimesulide is a typical nonsteroidal anti-inflammatory drug (NSAID), widely used in solid oral formulations. By crystallizing nimesulide from an ethanol solution a crystalline form was obtained, different from the reference sample, as confirmed by X-ray powder diffraction (XRPD), Differential Scanning Calorimetry (DSC) and solid cross polarization-magic angle spinning ((13)C-CPMAS) NMR. Moreover, when crystallized from dioxane nimesulide forms a solvate. The solvate was characterized by XRPD, IR-spectrometry, DSC, thermo-gravimetric analysis (TGA) and by (13)C-CPMAS NMR. In particular, through this technique, the presence of several conformational isomers was demonstrated. In addition to the physico-chemical characterization, the technological properties of nimesulide, namely densification and tableting, were evaluated. Contrarily to the other forms that are affected by capping phenomena at increasing compression pressures, the form obtained by desolvation of dioxane solvate has positive effect on tableting properties, increasing both compressibility and tabletability of nimesulide. PMID:17583450

  12. Thermodynamics and kinetics of gas storage in porous liquids

    DOE PAGESBeta

    Zhang, Fei; Yang, Fengchang; Huang, Jingsong; Sumpter, Bobby G.; Qiao, Rui

    2016-07-05

    The recent synthesis of organic molecular liquids with permanent porosity (Giri et al., Nature, 2015, 527, 216) opens up exciting new avenues for gas capture, storage, and separation. Using molecular dynamics simulations, we study the thermodynamics and kinetics for the storage of CH4, CO2, and N2 molecules in porous liquids consisting of crown-ether substituted cage molecules in a 15-crown-5 solvent. It is found that the gas storage capacity per cage molecule follows the order of CH4 > CO2 > N2, which does not correlate simply with the size of gas molecules. Different gas molecules are stored inside the cage differently,more » e.g., CO2 molecules prefer the cage s core while CH4 molecules favor both the core and the branch regions. All gas molecules considered can enter the cage essentially without energy barriers, and their dynamics inside the cage are only slightly hindered by the nanoscale confinement. In addition, all gas molecules can leave the cage on nanosecond time scale by overcoming a modest energy penalty. The molecular mechanisms of these observations are clarified.« less

  13. Liquid/liquid metal extraction: Phase diagram topology resulting from molecular interactions between extractant, ion, oil and water

    NASA Astrophysics Data System (ADS)

    Bauer, C.; Bauduin, P.; Dufrêche, J. F.; Zemb, T.; Diat, O.

    2012-11-01

    We consider the class of surfactants called "extractants" since they specifically interact with some cations and are used in liquid-liquid separation processes. We review here features of water-poor reverse micelles in water/oil/ extractant systems as determined by combined structural studies including small angle scattering techniques on absolute scale. Origins of instabilities, liquid-liquid separation as well as emulsification failure are detected. Phase diagrams contain the same multi-phase domains as classical microemulsions, but special unusual features appear due to the high spontaneous curvature directed towards the polar cores of aggregates as well as rigidity of the film made by extracting molecules.

  14. Molecular dynamics simulation of paracetamol molecules ordering around glycogen

    NASA Astrophysics Data System (ADS)

    Lim, Wilber; Feng, Yuan Ping; Liu, X. Y.

    2005-05-01

    By the use of classical atomistic molecular dynamics simulations, we demonstrate that paracetamol molecules exist in a highly ordered phase in the presence of a glycogen substrate at 317K whereas the paracetamol fluid exists in an isotropic phase in the absence of the glycogen substrate at the same temperature. This result further validates the studies made on polysaccharide regarding its abilities to promote nucleation of paracetamol via liquid preordering. As little is known regarding liquid ordering induced by a polymeric substrate, we seek to explore the ordering mechanism from an energy perspective. This is accomplished using conformation mappings. Our analysis shows that the conformation space accessible to the paracetamol molecule at 317K in the vicinity of glycogen is smaller than the one in the absence of glycogen. An investigation on the orientation of the dipole moments of the glycogen monomers and paracetamol molecules were carried out as well. From the investigations, we show that dipolar interactions play an important role in the ordering process. These studies bear significance to the understanding of the ordering process as well as the promotion and effective control of the nucleation rate.

  15. Minimizing liquid contaminants in natural gas liquids

    SciTech Connect

    Brown, R.L.; Wines, T.H.; Williamson, K.M.

    1996-12-31

    In processing natural gas liquids, significant contamination occurs with liquid dispersions and emulsions. Natural gas liquids (NGL) and liquid petroleum gas (LPG) streams are treated with caustic to remove residual organic sulfur compounds such as mercaptans and with amines to remove hydrogen sulfide. In both cases a liquid/liquid contactor is used. Significant amounts of the caustic or amine can be carried over into the product stream in process units that are running at rates above design capacity, are treating high sulfur feed stocks, or have other operational problems. The carried over liquid results in off-spec products, excessive loses of caustic or amine, and can cause operating problems in downstream processes. In addition, water is a significant contaminant which can cause LPG and natural gasoline to be off-specification. This paper discusses a new technique for separating very stable liquid dispersions of caustic, amine, or water from natural gas liquids using liquid/liquid cartridge coalescers constructed with specially formulated polymer and fluoropolymer medium with enhanced surface properties. In addition, factors influencing the coalescer mechanism will be discussed including interfacial tension, concentration of surface active compounds, steric repulsion, and electrostatic charge affects. Results from field tests, operating data from commercial installations, and economic benefits will also be presented.

  16. Monitoring Molecules: Insights and Progress

    PubMed Central

    2015-01-01

    In August, 2014, neuroscientists and physical scientists gathered together on the campus of the University of California, Los Angeles to discuss how to monitor molecules in neuroscience. This field has seen significant growth since its inception in the 1970s. Here, the advances in this field are documented, including its advance into understanding the actions that specific neurotransmitters mediate during behavior. PMID:25514501

  17. Nucleic Acids as Information Molecules.

    ERIC Educational Resources Information Center

    McInerney, Joseph D.

    1996-01-01

    Presents an activity that aims at enabling students to recognize that DNA and RNA are information molecules whose function is to store, copy, and make available the information in biological systems, without feeling overwhelmed by the specialized vocabulary and the minutia of the central dogma. (JRH)

  18. Nanodevices for Single Molecule Studies

    NASA Astrophysics Data System (ADS)

    Craighead, H. G.; Stavis, S. M.; Samiee, K. T.

    During the last two decades, biotechnology research has resulted in progress in fields as diverse as the life sciences, agriculture and healthcare. While existing technology enables the analysis of a variety of biological systems, new tools are needed for increasing the efficiency of current methods, and for developing new ones altogether. Interest has grown in single molecule analysis for these reasons.

  19. Dialkylresorcinols as bacterial signaling molecules

    PubMed Central

    Brameyer, Sophie; Kresovic, Darko; Bode, Helge B.; Heermann, Ralf

    2015-01-01

    It is well recognized that bacteria communicate via small diffusible molecules, a process termed quorum sensing. The best understood quorum sensing systems are those that use acylated homoserine lactones (AHLs) for communication. The prototype of those systems consists of a LuxI-like AHL synthase and a cognate LuxR receptor that detects the signal. However, many proteobacteria possess LuxR receptors, yet lack any LuxI-type synthase, and thus these receptors are referred to as LuxR orphans or solos. In addition to the well-known AHLs, little is known about the signaling molecules that are sensed by LuxR solos. Here, we describe a novel cell–cell communication system in the insect and human pathogen Photorhabdus asymbiotica. We identified the LuxR homolog PauR to sense dialkylresorcinols (DARs) and cyclohexanediones (CHDs) instead of AHLs as signals. The DarABC synthesis pathway produces the molecules, and the entire system emerged as important for virulence. Moreover, we have analyzed more than 90 different Photorhabdus strains by HPLC/MS and showed that these DARs and CHDs are specific to the human pathogen P. asymbiotica. On the basis of genomic evidence, 116 other bacterial species are putative DAR producers, among them many human pathogens. Therefore, we discuss the possibility of DARs as novel and widespread bacterial signaling molecules and show that bacterial cell–cell communication goes far beyond AHL signaling in nature. PMID:25550519

  20. Engineering crystals of dendritic molecules.

    PubMed

    Lukin, Oleg; Schubert, Dirk; Müller, Claudia M; Schweizer, W Bernd; Gramlich, Volker; Schneider, Julian; Dolgonos, Grygoriy; Shivanyuk, Alexander

    2009-07-01

    A detailed single-crystal X-ray study of conformationally flexible sulfonimide-based dendritic molecules with systematically varied molecular architectures was undertaken. Thirteen crystal structures reported in this work include 9 structures of the second-generation dendritic sulfonimides decorated with different aryl groups, 2 compounds bearing branches of both second and first generation, and 2 representatives of the first generation. Analysis of the packing patterns of 9 compounds bearing second-generation branches shows that despite their lack of strong directive functional groups there is a repeatedly reproduced intermolecular interaction mode consisting in an anchor-type packing of complementary second-generation branches of neighbouring molecules. The observed interaction tolerates a wide range of substituents in meta- and para-positions of the peripheral arylsulfonyl rings. Quantum chemical calculations of the molecule-molecule interaction energies agree at the qualitative level with the packing preferences found in the crystalline state. The calculations can therefore be used as a tool to rationalize and predict molecular structures with commensurate and non-commensurate branches for programming of different packing modes in crystal. PMID:19549870

  1. Engineering crystals of dendritic molecules

    PubMed Central

    Lukin, Oleg; Schubert, Dirk; Müller, Claudia M.; Schweizer, W. Bernd; Gramlich, Volker; Schneider, Julian; Dolgonos, Grygoriy; Shivanyuk, Alexander

    2009-01-01

    A detailed single-crystal X-ray study of conformationally flexible sulfonimide-based dendritic molecules with systematically varied molecular architectures was undertaken. Thirteen crystal structures reported in this work include 9 structures of the second-generation dendritic sulfonimides decorated with different aryl groups, 2 compounds bearing branches of both second and first generation, and 2 representatives of the first generation. Analysis of the packing patterns of 9 compounds bearing second-generation branches shows that despite their lack of strong directive functional groups there is a repeatedly reproduced intermolecular interaction mode consisting in an anchor-type packing of complementary second-generation branches of neighbouring molecules. The observed interaction tolerates a wide range of substituents in meta- and para-positions of the peripheral arylsulfonyl rings. Quantum chemical calculations of the molecule-molecule interaction energies agree at the qualitative level with the packing preferences found in the crystalline state. The calculations can therefore be used as a tool to rationalize and predict molecular structures with commensurate and non-commensurate branches for programming of different packing modes in crystal. PMID:19549870

  2. Autothermal Processing of Renewable Liquids

    NASA Astrophysics Data System (ADS)

    Kruger, Jacob Scott

    The vast majority of petrochemicals are synthesized from just six building block molecules, but current feedstocks are an unsustainable resource with negative externalities. Biomass represents a potentially sustainable feedstock, but needs densification, preferably to a liquid form, to be a suitable replacement. Fermentation to butanol and pyrolysis to bio-oil are two promising liquid intermediates. Catalytic partial oxidation (CPO) of the liquid intermediates over noble metal catalysts, which converts the liquids primarily into syngas and light olefins, is a promising technique for processing densified biomass. The study of liquids at high temperatures requires consideration of a range of complex phenomena, including boiling behavior on hot surfaces, reactions of the feed molecules at high temperatures and on catalyst surfaces, and interactions of impurities in the liquid with the catalyst. Chapter 2 deals with the behavior of the transient liquid that forms when cellulose, a major constituent of biomass, is pyrolized. Fast photography experiments and numerical simulations are performed to show that the aerosols formed in the boiling of this liquid are capable of transporting nonvolatile fragments of biomass intact into the gas phase. These nonvolatile fragments have significant implications in the storage and downstream processing of bio-oil. Some of the behavior of bio-oil at high temperature may also be explained by the variety of molecules in the liquid. Many different functional groups are present, each with its own set of chemical reactions in combustion, pyrolysis, and partial oxidation on a metal catalyst. Chapters 3 and 4 investigate these reactions through a survey of two-carbon surrogates of the functional group classes found in bio-oil. Chapter 3 examines reactions occuring in the complete CPO system over Pt and Rh catalysts, and in the complete system absent O 2. The selectivity data from each molecule and the surface science literature of each

  3. Fast Method for Computing Chemical Potentials and Liquid-Liquid Phase Equilibria of Macromolecular Solutions.

    PubMed

    Qin, Sanbo; Zhou, Huan-Xiang

    2016-08-25

    Chemical potential is a fundamental property for determining thermodynamic equilibria involving exchange of molecules, such as between two phases of molecular systems. Previously, we developed the fast Fourier transform (FFT)-based method for Modeling Atomistic Protein-crowder interactions (FMAP) to calculate excess chemical potentials according to the Widom insertion. Intermolecular interaction energies were expressed as correlation functions and evaluated via FFT. Here, we extend this method to calculate liquid-liquid phase equilibria of macromolecular solutions. Chemical potentials are calculated by FMAP over a wide range of molecular densities, and the condition for coexistence of low- and high-density phases is determined by the Maxwell equal-area rule. When benchmarked on Lennard-Jones fluids, our method produces an accurate phase diagram at 18% of the computational cost of the current best method. Importantly, the gain in computational speed increases dramatically as the molecules become more complex, leading to many orders of magnitude in speed up for atomistically represented proteins. We demonstrate the power of FMAP by reporting the first results for the liquid-liquid coexistence curve of γII-crystallin represented at the all-atom level. Our method may thus open the door to accurate determination of phase equilibria for macromolecular mixtures such as protein-protein mixtures and protein-RNA mixtures, that are known to undergo liquid-liquid phase separation, both in vitro and in vivo. PMID:27327881

  4. Ionic Liquids Database- (ILThermo)

    National Institute of Standards and Technology Data Gateway

    SRD 147 Ionic Liquids Database- (ILThermo) (Web, free access)   IUPAC Ionic Liquids Database, ILThermo, is a free web research tool that allows users worldwide to access an up-to-date data collection from the publications on experimental investigations of thermodynamic, and transport properties of ionic liquids as well as binary and ternary mixtures containing ionic liquids.

  5. Liquid crystal polyester thermosets

    SciTech Connect

    Benicewicz, B.C.; Hoyt, A.E.

    1990-01-01

    The present invention relates to the field of curable liquid crystal polyester monomers and to thermoset liquid crystalline polyester compositions prepared therefrom. It is an object of this invention to provide curable liquid crystalline polyester materials. Another object of this invention is to provide a process of preparing curable liquid crystal polyester monomers. Yet another object of this invention is to provide liquid crystalline blends of polyester materials. It is a further object of this invention to provide thermoset liquid crystalline polyester compositions. It is a still further object of this invention to provide thermoset liquid crystalline polyester compositions having a high heat resistance. 1 fig.

  6. Liquid crystal polyester thermosets

    SciTech Connect

    Benicewicz, B.C.; Hoyt, A.E.

    1990-12-31

    The present invention relates to the field of curable liquid crystal polyester monomers and to thermoset liquid crystalline polyester compositions prepared therefrom. It is an object of this invention to provide curable liquid crystalline polyester materials. Another object of this invention is to provide a process of preparing curable liquid crystal polyester monomers. Yet another object of this invention is to provide liquid crystalline blends of polyester materials. It is a further object of this invention to provide thermoset liquid crystalline polyester compositions. It is a still further object of this invention to provide thermoset liquid crystalline polyester compositions having a high heat resistance. 1 fig.

  7. High Average Power Laser Gain Medium With Low Optical Distortion Using A Transverse Flowing Liquid Host

    DOEpatents

    Comaskey, Brian J.; Ault, Earl R.; Kuklo, Thomas C.

    2005-07-05

    A high average power, low optical distortion laser gain media is based on a flowing liquid media. A diode laser pumping device with tailored irradiance excites the laser active atom, ion or molecule within the liquid media. A laser active component of the liquid media exhibits energy storage times longer than or comparable to the thermal optical response time of the liquid. A circulation system that provides a closed loop for mixing and circulating the lasing liquid into and out of the optical cavity includes a pump, a diffuser, and a heat exchanger. A liquid flow gain cell includes flow straighteners and flow channel compression.

  8. [Progress in sample preparation and analytical methods for trace polar small molecules in complex samples].

    PubMed

    Zhang, Qianchun; Luo, Xialin; Li, Gongke; Xiao, Xiaohua

    2015-09-01

    Small polar molecules such as nucleosides, amines, amino acids are important analytes in biological, food, environmental, and other fields. It is necessary to develop efficient sample preparation and sensitive analytical methods for rapid analysis of these polar small molecules in complex matrices. Some typical materials in sample preparation, including silica, polymer, carbon, boric acid and so on, are introduced in this paper. Meanwhile, the applications and developments of analytical methods of polar small molecules, such as reversed-phase liquid chromatography, hydrophilic interaction chromatography, etc., are also reviewed. PMID:26753274

  9. Ultra high-throughput single molecule spectroscopy with a 1024 pixel SPAD

    PubMed Central

    Colyer, Ryan A.; Scalia, Giuseppe; Villa, Federica A.; Guerrieri, Fabrizio; Tisa, Simone; Zappa, Franco; Cova, Sergio; Weiss, Shimon; Michalet, Xavier

    2013-01-01

    Single-molecule spectroscopy is a powerful approach to measuring molecular properties such as size, brightness, conformation, and binding constants. Due to the low concentrations in the single-molecule regime, measurements with good statistical accuracy require long acquisition times. Previously we showed a factor of 8 improvement in acquisition speed using a custom-CMOS 8x1 SPAD array. Here we present preliminary results with a 64X improvement in throughput obtained using a liquid crystal on silicon spatial light modulator (LCOS-SLM) and a novel standard CMOS 1024 pixel SPAD array, opening the way to truly high-throughput single-molecule spectroscopy. PMID:24386535

  10. Towards sorting of biolibraries using single-molecule fluorescence detection techniques.

    PubMed

    Visser, Antonie J W G; Kunst, Beno H; Keller, Hans; Schots, Arjen

    2004-04-01

    The selection of specific binding molecules like peptides and proteins from biolibraries using, for instance, phage display methods can be quite time-consuming. It is therefore desirable to develop a strategy that is much faster in selection and sorting of potential binders out of a biolibrary. In this contribution we separately discuss the current achievements in generation of biolibraries, single-molecule detection techniques and microfluidic devices. A high-throughput microfluidic platform is then proposed that combines the propulsion of liquid containing fluorescent components of the biolibrary through microchannels, single-molecule fluorescence photon burst detection and real-time sorting of positive hits. PMID:15078151

  11. Formation of H-type liquid crystal dimer at air-water interface

    SciTech Connect

    Karthik, C. Gupta, Adbhut Joshi, Aditya Manjuladevi, V. Gupta, Raj Kumar; Varia, Mahesh C.; Kumar, Sandeep

    2014-04-24

    We have formed the Langmuir monolayer of H-shaped Azo linked liquid crystal dimer molecule at the air-water interface. Isocycles of the molecule showed hysteresis suggesting the ir-reversible nature of the monolayer formed. The thin film deposited on the silicon wafer was characterized using Atomic Force Microscopy (AFM) and Field Emission Scanning Electron Microscopy (FESEM). The images showed uniform domains of the dimer molecule. We propose that these molecules tend to take book shelf configuration in the liquid phase.

  12. Properties of Water Confined in Ionic Liquids

    PubMed Central

    Saihara, Koji; Yoshimura, Yukihiro; Ohta, Soichi; Shimizu, Akio

    2015-01-01

    The varying states of water confined in the nano-domain structures of typical room temperature ionic liquids (ILs) were investigated by 1H NMR and by measurements of self-diffusion coefficients while systematically varying the IL cations and anions. The NMR peaks for water in BF4-based ILs were clearly split, indicating the presence of two discrete states of confined water (H2O and HOD). Proton and/or deuterium exchange rate among the water molecules was very slowly in the water-pocket. Notably, no significant changes were observed in the chemical shifts of the ILs. Self-diffusion coefficient results showed that water molecules exhibit a similar degree of mobility, although their diffusion rate is one order of magnitude faster than that of the IL cations and anions. These findings provide information on a completely new type of confinement, that of liquid water in soft matter. PMID:26024339

  13. Adaptive lens using liquid crystal concentration redistribution

    NASA Astrophysics Data System (ADS)

    Ren, Hongwen; Lin, Yi-Hsin; Wu, Shin-Tson

    2006-05-01

    An adaptive lens using electrically induced liquid crystal (LC)/monomer concentration redistribution is demonstrated. In the absence of an electric field, the LC/monomer mixture is homogeneously distributed. Application of an inhomogeneous electric field causes the LC molecules to diffuse towards the high field region and the liquid monomer towards the low field region. On the other hand, the LC molecules tend to diffuse from high to low concentration direction in order to balance the concentration change. A gradient LC concentration is thus obtained. Using the gradient LC concentration, we demonstrate a tunable-focus lens. Compared with a conventional LC lens, our lens has advantages in small astigmatism and without light scattering, but its response time is slower.

  14. Liquid-Solid Nanofriction and Interfacial Wetting.

    PubMed

    An, Rong; Huang, Liangliang; Long, Yun; Kalanyan, Berc; Lu, Xiaohua; Gubbins, Keith E

    2016-01-26

    Using atomic force microscopy, the nanofriction coefficient was measured systematically for a series of liquids on planar graphite, silica and mica surfaces. This allows us to explore the quantitative interplay between nanofriction at liquid-solid interfaces and interfacial wetting. A corresponding states theory analysis shows that the nanofriction coefficient, μ = dF(F)/dF(N), where FF is the friction force and FN is the normal force, is a function of three dimensionless parameters that reflect the intermolecular forces involved and the structure of the solid substrate. Of these, we show that one parameter in particular, β = ρ(s)Δ(s)σ(ls)(2), where ρ(s) is the atomic density of the solid, Δ(s) is the spacing between layers of solid atoms, and σ(ls) is the molecular diameter that characterizes the liquid-substrate interaction, is very important in determining the friction coefficient. This parameter β, which we term the structure adhesion parameter, provides a measure of the intermolecular interaction between a liquid molecule and the substrate and also of the surface area of contact of the liquid molecule with the substrate. We find a linear dependence of μ on the structure adhesion parameter for the systems studied. We also find that increasing β leads to an increase in the vertical adhesion forces FA (the attractive force exerted by the solid surface on the liquid film). Our quantitative relationship between the nanofriction coefficient and the key parameter β which governs the vertical adhesive strength, opens up an opportunity for describing liquid flows on solid surfaces at the molecular level, with implications for the development of membrane and nanofluidic devices. PMID:26716469

  15. [Structural nucleic acid nanotechnology: liquid-crystalline approach].

    PubMed

    2013-01-01

    The properties of the particles of cholesteric liquid-crystalline dispersions formed by double-stranded DNA molecules obtained as a result of phase exclusion of these molecules from water-salt polymer-containing solutions are briefly described. Physicochemical properties of quasinematic layers of dispersion particles and double-stranded DNA molecules in their content are taken into account in the course of developing fundamental background of the liquid-crystalline approach to the DNA structural nanotechnology. According to different versions of this approach, which is based on intraparticle gelation of cholesteric liquid-crystalline dispersions, spatial structures (DNA nanoconstructions, "rigid" DNA particles) with unique properties, are created. By means of atomic force microscopy images of "rigid" DNA particles of different type are registered. Specific properties of metallic nanoparticles (in particular, gold nanoparticles) are considered while developing the other approach to DNA structural nanotechnology, which provides the basis for "metallized" DNA nanoconstructions. PMID:25508888

  16. [Structural nucleic acid nanotechnology: liquid-crystalline approach].

    PubMed

    Evdokimov, Iu M; Salianov, V I; Kats, E I; Skuridin, S G

    2013-01-01

    The properties of the particles of cholesteric liquid-crystalline dispersions formed by double-stranded DNA molecules obtained as a result of phase exclusion of these molecules from water-salt polymer-containing solutions are briefly described. Physicochemical properties of quasinematic layers of dispersion particles and double-stranded DNA molecules in their content are taken into account in the course of developing fundamental background of the liquid-crystalline approach to the DNA structural nanotechnology. According to different versions of this approach, which is based on intraparticle gelation of cholesteric liquid-crystalline dispersions, spatial structures (DNA nanoconstructions, "rigid" DNA particles) with unique properties, are created. By means of atomic force microscopy images of "rigid" DNA particles of different type are registered. Specific properties of metallic nanoparticles (in particular, gold nanoparticles) are considered while developing the other approach to DNA structural nanotechnology, which provides the basis for "metallized" DNA nanoconstructions. PMID:25486757

  17. Leslie thermomechanical power in diluted cholesteric liquid crystals

    NASA Astrophysics Data System (ADS)

    Oswald, P.

    2014-11-01

    I measure the Leslie thermomechnical coefficient ν in diluted cholesteric liquid crystals. The chiral molecules are R811 and cholesteryl chloride (CC) and the host nematic liquid crystals are 7CB and MBBA. I show that ν is proportional to the concentration of chiral molecules C when C\\ll1 . This allows me to define the Leslie thermomechanical power as \\textit{LTP}=ν/(2π C) by analogy with the helical twisting power, \\textit{HTP}=q/(2π C) where q denotes the equilibrium twist. I show that the LTP (dynamic in nature) and the HTP (static in nature) are independent in sign and magnitude. In addition, the same chiral molecule can rotate clockwise or counterclockwise depending on the host nematic liquid crystal used.

  18. Micro-polarimeter for high performance liquid chromatography

    DOEpatents

    Yeung, Edward E.; Steenhoek, Larry E.; Woodruff, Steven D.; Kuo, Jeng-Chung

    1985-01-01

    A micro-polarimeter interfaced with a system for high performance liquid chromatography, for quantitatively analyzing micro and trace amounts of optically active organic molecules, particularly carbohydrates. A flow cell with a narrow bore is connected to a high performance liquid chromatography system. Thin, low birefringence cell windows cover opposite ends of the bore. A focused and polarized laser beam is directed along the longitudinal axis of the bore as an eluent containing the organic molecules is pumped through the cell. The beam is modulated by air gap Faraday rotators for phase sensitive detection to enhance the signal to noise ratio. An analyzer records the beams's direction of polarization after it passes through the cell. Calibration of the liquid chromatography system allows determination of the quantity of organic molecules present from a determination of the degree to which the polarized beam is rotated when it passes through the eluent.

  19. Low Energy Ion-Molecule Reactions

    SciTech Connect

    James M. Farrar

    2004-05-01

    This objective of this project is to study the dynamics of the interactions of low energy ions important in combustion with small molecules in the gas phase and with liquid hydrocarbon surfaces. The first of these topics is a long-standing project in our laboratory devoted to probing the key features of potential energy surfaces that control chemical reactivity. The project provides detailed information on the utilization of specific forms of incident energy, the role of preferred reagent geometries, and the disposal of total reaction energy into product degrees of freedom. We employ crossed molecular beam methods under single collision conditions, at collision energies from below one eV to several eV, to probe potential surfaces over a broad range of distances and interaction energies. These studies allow us to test and validate dynamical models describing chemical reactivity. Measurements of energy and angular distributions of the reaction products with vibrational state resolution provide the key data for these studies. We employ the crossed beam low energy mass spectrometry methods that we have developed over the last several years.

  20. Cold collisions between boson or fermion molecules

    SciTech Connect

    Kajita, Masatoshi

    2004-01-01

    We theoretically investigate collisions between electrostatically trapped cold polar molecules and compare boson and fermion isotopes. Evaporative cooling seems possible for fermion molecules as the ratio of the collision loss cross section to the elastic collision cross section (R) gets smaller as the molecular temperature T lowers. With boson molecules, R gets larger as T lowers, which makes evaporative cooling difficult. The elastic collision cross section between fermion molecules can be larger than that for boson molecules with certain conditions.

  1. Dissociation energy of molecules in dense gases

    NASA Technical Reports Server (NTRS)

    Kunc, J. A.

    1992-01-01

    A general approach is presented for calculating the reduction of the dissociation energy of diatomic molecules immersed in a dense (n = less than 10 exp 22/cu cm) gas of molecules and atoms. The dissociation energy of a molecule in a dense gas differs from that of the molecule in vacuum because the intermolecular forces change the intramolecular dynamics of the molecule, and, consequently, the energy of the molecular bond.

  2. Light controlled drug delivery containers based on spiropyran doped liquid crystal micro spheres

    PubMed Central

    Petriashvili, Gia; Devadze, Lali; Zurabishvili, Tsisana; Sepashvili, Nino; Chubinidze, Ketevan

    2016-01-01

    We have developed a novel, light activated drug delivery containers, based on spiropyran doped liquid crystal micro spheres. Upon exposure to UV/violet light, the spiropyran molecules entrapped inside the nematic liquid crystal micro spheres, interconvert from the hydrophobic, oil soluble form, to the hydrophilic, water soluble merocyanine one, which stimulates the translocation of the merocyanine molecules across the nematic liquid crystal-water barrier and results their homogeneous distribution throughout in an aqueous environment. Light controllable switching property and extremely high solubility of spiropyran in the nematic liquid crystal, promise to elaborate a novel and reliable vehicles for the drug delivery systems. PMID:26977353

  3. Light controlled drug delivery containers based on spiropyran doped liquid crystal micro spheres.

    PubMed

    Petriashvili, Gia; Devadze, Lali; Zurabishvili, Tsisana; Sepashvili, Nino; Chubinidze, Ketevan

    2016-02-01

    We have developed a novel, light activated drug delivery containers, based on spiropyran doped liquid crystal micro spheres. Upon exposure to UV/violet light, the spiropyran molecules entrapped inside the nematic liquid crystal micro spheres, interconvert from the hydrophobic, oil soluble form, to the hydrophilic, water soluble merocyanine one, which stimulates the translocation of the merocyanine molecules across the nematic liquid crystal-water barrier and results their homogeneous distribution throughout in an aqueous environment. Light controllable switching property and extremely high solubility of spiropyran in the nematic liquid crystal, promise to elaborate a novel and reliable vehicles for the drug delivery systems. PMID:26977353

  4. Laser-induced separation of hydrogen isotopes in the liquid phase

    DOEpatents

    Freund, Samuel M.; Maier, II, William B.; Beattie, Willard H.; Holland, Redus F.

    1980-01-01

    Hydrogen isotope separation is achieved by either (a) dissolving a hydrogen-bearing feedstock compound in a liquid solvent, or (b) liquefying a hydrogen-bearing feedstock compound, the liquid phase thus resulting being kept at a temperature at which spectral features of the feedstock relating to a particular hydrogen isotope are resolved, i.e., a clear-cut isotope shift is delineated, irradiating the liquid phase with monochromatic radiation of a wavelength which at least preferentially excites those molecules of the feedstock containing a first hydrogen isotope, inducing photochemical reaction in the excited molecules, and separating the reaction product containing the first isotope from the liquid phase.

  5. Long DNA Molecules at Liuid-Solid Interfaces

    NASA Astrophysics Data System (ADS)

    Seo, Young-Soo; Samuilov, Vladimir; Sokolov, John; Rafailovich, Miriam; Chu, Ben

    2003-03-01

    The electrical transport of long DNA molecules was studied using a newly developed method of electrophoresis on flat surfaces [1]. We have shown that a flat silicon substrate, without any surface features, can be used to fractionate DNA on a liquid-solid interface. We determine that the ability of a flat surface to separate DNA molecules results from the local friction between the surface and the adsorbed DNA segments. The mobility of lambda- DNA molecules on this surface was found to scale as the persistent length with the ionic strength of the buffer. This experimental result indicates that at high buffer concentration the separation mechanism of solid-liquid interface electrophoresis is expected to be due to surface friction rather than biased reptation [2]. At low buffer concentrations the adsorbed DNA move in the electrical field parallel to the surface, and also due the electroosmotic convection that drags the DNA chains and they are stretched . The electric double layer is responsible for a velocity profile of the electroosmotic flow. The net electrophoretic mobility of longer DNA, being trapped closer to the surface, is higher than of the shorter ones in the electric field, oriented along the surface. [1]. N. Pernodet, V. Samuilov, K. Shin, J. Sokolov, M.H. Rafailovich, D. Gersappe, B. Chu. DNA Electrophoresis on a Flat Surface, Physical Review Letters, 85 (2000) 5651-5654. [2] Y.-S. Seo, V.A. Samuilov, J. Sokolov, M. Rafailovich, B. Tinland, J. Kim, B. Chu. DNA separation at a liquid-solid interface, Electrophoresis, 23 (2002) 2618-2625.

  6. Fluorescence imaging of single-molecule retention trajectories in reversed-phase chromatographic particles.

    PubMed

    Cooper, Justin T; Peterson, Eric M; Harris, Joel M

    2013-10-01

    Due to its high specific surface area and chemical stability, porous silica is used as a support structure in numerous applications, including heterogeneous catalysis, biomolecule immobilization, sensors, and liquid chromatography. Reversed-phase liquid chromatography (RPLC), which uses porous silica support particles, has become an indispensable separations tool in quality control, pharmaceutics, and environmental analysis requiring identification of compounds in mixtures. For complex samples, the need for higher resolution separations requires an understanding of the time scale of processes responsible for analyte retention in the stationary phase. In the present work, single-molecule fluorescence imaging is used to observe transport of individual molecules within RPLC porous silica particles. This technique allows direct measurement of intraparticle molecular residence times, intraparticle diffusion rates, and the spatial distribution of molecules within the particle. On the basis of the localization uncertainty and characteristic measured diffusion rates, statistical criteria were developed to resolve the frame-to-frame behavior of molecules into moving and stuck events. The measured diffusion coefficient of moving molecules was used in a Monte Carlo simulation of a random-walk model within the cylindrical geometry of the particle diameter and microscope depth-of-field. The simulated molecular transport is in good agreement with the experimental data, indicating transport of moving molecules in the porous particle is described by a random-walk. Histograms of stuck-molecule event times, locations, and their contributions to intraparticle residence times were also characterized. PMID:23998479

  7. High-throughput multispot single-molecule spectroscopy

    PubMed Central

    Colyer, Ryan A.; Scalia, Giuseppe; Kim, Taiho; Rech, Ivan; Resnati, Daniele; Marangoni, Stefano; Ghioni, Massimo; Cova, Sergio; Weiss, Shimon; Michalet, Xavier

    2011-01-01

    Solution-based single-molecule spectroscopy and fluorescence correlation spectroscopy (FCS) are powerful techniques to access a variety of molecular properties such as size, brightness, conformation, and binding constants. However, this is limited to low concentrations, which results in long acquisition times in order to achieve good statistical accuracy. Data can be acquired more quickly by using parallelization. We present a new approach using a multispot excitation and detection geometry made possible by the combination of three powerful new technologies: (i) a liquid crystal spatial light modulator to produce multiple diffraction-limited excitation spots; (ii) a multipixel detector array matching the excitation pattern and (iii) a low-cost reconfigurable multichannel counting board. We demonstrate the capabilities of this technique by reporting FCS measurements of various calibrated samples as well as single-molecule burst measurements. PMID:21643532

  8. Infrared frequency standard based on magnetically trapped NH molecules

    SciTech Connect

    Kajita, Masatoshi

    2006-09-15

    An infrared frequency standard based on the NH |n{sub v}=0,N{sub 0}=0,J=1,F{sub 1}=3/2,F=5/2,M{sub F}=5/2>{yields}|n{sub v}=1,N{sub 0}=0,J=1,F{sub 1}=3/2,F=5/2,M{sub F}== 5/2> transition (3 {mu}m) is proposed. There is no Zeeman shift with this transition frequency, because the Zeeman coefficient is not dependent on the vibrational state. NH molecules, precooled by collisions with liquid {sup 3}He vapor, are trapped by an inhomogeneous magnetic field. The temperature of the trapped NH molecules holds the potential to be reduced down to several {mu}K by evaporative cooling. The uncertainty of the clock transition can potentially be reduced to lower than 10{sup -17}.

  9. High sensitivity microwave characterization of organic molecule solutions of nanoliter volume

    NASA Astrophysics Data System (ADS)

    Shaforost, E. N.; Klein, N.; Vitusevich, S. A.; Barannik, A. A.; Cherpak, N. T.

    2009-03-01

    A microwave resonator composed of a sapphire cylinder and a quartz plate with a 400 nl cavity was developed for the determination of the complex permittivity of liquids at 10 GHz. This sensor was calibrated over a wide range of values for real and imaginary parts of permittivity. The measured resonator losses induced by the liquid were found to be proportional to the dipole relaxation time of the liquid molecules, as predicted by perturbation theory. Our analysis of weight concentration and temperature dependence of the measured inverse quality factor revealed a sensitivity of about 0.1% for aqueous solutions of glucose.

  10. Photorefractivity in liquid crystalline composite materials

    SciTech Connect

    Wiederrecht, G.P.; Wasielewski, M.R.

    1997-09-01

    We report recent improvements in the photorefractive of liquid crystalline thin film composites containing electron donor and acceptor molecules. The improvements primarily result from optimization of the exothermicity of the intermolecular charge transfer reaction and improvement of the diffusion characteristics of the photogenerated ions. Intramolecular charge transfer dopants produce greater photorefractivity and a 10-fold decrease in the concentration of absorbing chromophores. The mechanism for the generation of mobile ions is discussed.

  11. Molecular self-assemblies might discriminate the diffusion of chiral molecules.

    PubMed

    Galstian, Tigran; Allahverdyan, Karen

    2015-06-01

    Biological tissue has many self-aligned anisotropic molecular organizations, which are able to undergo reversible orientational deformations and spatially transfer them. At the same time, the majority of drugs and many biologically important molecules contain chiral centers. It is therefore important to understand the factors affecting the diffusion of chiral molecules in such elastic environments. We experimentally study the diffusion of chiral molecules in a nematic liquid crystal host representing the model of biological tissue. The analogy of Cano's quantization effect is observed (due to the gradient of the chiral dopant) and used to estimate the corresponding diffusion coefficients. It is shown that thanks to the collective orientational correlation of host molecules the diffusion of chiral dopants is noticeably reduced (by a factor of ≈1.6) for the case of rigid alignment of host molecules compared to the case when the same matrix is free to adjust that alignment. PMID:25902722

  12. Direct measurement of single-molecule dynamics in free solution

    SciTech Connect

    Yeung, E.S.; Xu, Xiao-Hong |

    1997-12-31

    Continuous monitoring of the solution dynamics of individual rhodamine-6G molecules and 30-base-ss-DNA tagged with rhodamine is achieved by total internal reflection fluorescence microscopy. A small observation depth is defined by exciting the molecules either through the evanescent wave at the quartz-liquid interface, or by using micron-size wires to form a thin layer of solution. A microscope thus affords diffraction-limited resolution of interconnected volume elements that are 13 aL, to 360 aL, respectively. An intensified CCD camera repeatedly records fluorescence from the same set of molecules to provide rate information on each as they diffuse and photobleach. With a special detection arrangement, time resolution down to 0.37 ms was achieved. The present technical limit is 10 ps for direct clocking of events. Statistical variations in molecular diffusion coefficients and in photobleaching rates are found. The average diffusion coefficients are smaller and the average photobleaching lifetimes are longer for the dye-DNA covalent complex compared to the molecule by itself.

  13. X(3872): charmonium or molecule?

    SciTech Connect

    Nefediev, A. V.

    2011-05-23

    A theoretical analysis of the recent experimental data from the Belle and BABAR Collaborations on the charmonium state X(3872) is performed. The analysis takes into account the proximity of an S-wave mesonic threshold and a possible presence of molecule component in the resonance wave function, finite width of the molecule constituents, and a possible interference in the final state. In particular, a model-independent approach is formulated, based on the Flatte parametrisation of near-threshold observables as well as on the Weinberg analysis of the nature of weakly bound systems generalised to the case of unstable constituents. Conclusion is made that the X(3872) is generated dynamically by a strong coupling of the bare {chi}{sub c1} charmonium to the DD-bar* hadronic channel, with a large admixture of the DD-bar* molecular component.

  14. Electrochemical detection of single molecules.

    PubMed

    Fan, F R; Bard, A J

    1995-02-10

    The electrochemical behavior of a single molecule can be observed by trapping a small volume of a dilute solution of the electroactive species between an ultramicroelectrode tip with a diameter of approximately 15 nanometers and a conductive substrate. A scanning electrochemical microscope was used to adjust the tip-substrate distance ( approximately 10 nanometers), and the oxidation of [(trimethylammonio)methyl] ferrocene (Cp(2)FeTMA(+)) to Cp(2)FeTMA(2+) was carried out. The response was stochastic, and anodic current peaks were observed as the molecule moved into and out of the electrode-substrate gap. Similar experiments were performed with a solution containing two redox species, ferrocene carboxylate (Cp(2)FeCOO(-)) and Os(bpy)(3)(2+) (bpy is 2,2'-bipyridyl). PMID:17813918

  15. Behavior of liquid hydrogen inside an ICF target

    NASA Technical Reports Server (NTRS)

    Kim, K.; Mok, L.; Bernat, T.

    1982-01-01

    The configuration of liquid hydrogen inside spherical glass shell ICF target was studied both theoretically and experimentally. Because of the zero contact angle between the .D2 liquid and glass substrate and the limited wetting surface that is continuous, the liquid hydrogen completely covers the interior of the glass shell, resulting in the formation of a void at the center. For this reason, the present problem distinguishes itself from that for a sessile drop sitting on a flat surface. A theory was formulated to calculate the liquid hydrogen configuration by including the London-dispersion force between the liquid and the substrate molecules. The net result is an augmented Bashforth-Adams equation appropriate to a spherical substrate, which is considered to be the major contribution of the present work. Preliminary calculations indicate that this equation accurately models the liquid hydrogen behavior inside a spherical microshell.

  16. Bioactive molecules from sea hares.

    PubMed

    Kamiya, H; Sakai, R; Jimbo, M

    2006-01-01

    Sea hares, belonging to the order Opisthobranchia, subclass Gastropoda, are mollusks that have attracted many researchers who are interested in the chemical defense mechanisms of these soft and "shell-less" snails. Numbers of small molecules of dietary origin have been isolated from sea hares and some have ecologically relevant activities, such as fish deterrent activity or toxicity. Recently, however, greater attention has been paid to biomedically interesting sea hare isolates such as dolastatins, a series of antitumor peptide/macrolides isolated from Dolabella auricularia. Another series of bioactive peptide/macrolides, as represented by aplyronines, have been isolated from sea hares in Japanese waters. Although earlier studies indicated the potent antitumor activity of aplyronines, their clinical development has never been conducted because of the minute amount of compound available from the natural source. Recent synthetic studies, however, have made it possible to prepare these compounds and analogs for a structure-activity relationship study, and started to uncover their unique action mechanism towards their putative targets, microfilaments. Here, recent findings of small antitumor molecules isolated from Japanese sea hares are reviewed. Sea hares are also known to produce cytotoxic and antimicrobial proteins. In contrast to the small molecules of dietary origin, proteins are the genetic products of sea hares and they are likely to have some primary physiological functions in addition to ecological roles in the sea hare. Based on the biochemical properties and phylogenetic analysis of these proteins, we propose that they belong to one family of molecule, the "Aplysianin A family," although their molecular weights are apparently divided into two groups. Interestingly, the active principles in Aplysia species and Dolabella auricularia were shown to be L-amino acid oxidase (LAAO), a flavin enzyme that oxidizes an alpha-amino group of the substrate with

  17. Simple molecules as complex systems.

    PubMed

    Furtenbacher, Tibor; Arendás, Péter; Mellau, Georg; Császár, Attila G

    2014-01-01

    For individual molecules quantum mechanics (QM) offers a simple, natural and elegant way to build large-scale complex networks: quantized energy levels are the nodes, allowed transitions among the levels are the links, and transition intensities supply the weights. QM networks are intrinsic properties of molecules and they are characterized experimentally via spectroscopy; thus, realizations of QM networks are called spectroscopic networks (SN). As demonstrated for the rovibrational states of H2(16)O, the molecule governing the greenhouse effect on earth through hundreds of millions of its spectroscopic transitions (links), both the measured and first-principles computed one-photon absorption SNs containing experimentally accessible transitions appear to have heavy-tailed degree distributions. The proposed novel view of high-resolution spectroscopy and the observed degree distributions have important implications: appearance of a core of highly interconnected hubs among the nodes, a generally disassortative connection preference, considerable robustness and error tolerance, and an "ultra-small-world" property. The network-theoretical view of spectroscopy offers a data reduction facility via a minimum-weight spanning tree approach, which can assist high-resolution spectroscopists to improve the efficiency of the assignment of their measured spectra. PMID:24722221

  18. Molecules in the early universe

    SciTech Connect

    Lepp, S.; Shull, J.M.

    1984-05-15

    We present calculations of the formation of astrophysically interesting molecules (H/sub 2/, HD, LiH, and HeH/sup +/) by gas-phase reactions during the postrecombination epoch (redshifts z = 300-30). In standard Friedmann cosmological models, H/sub 2//Hroughly-equal10/sup -6/, HD/H/sub 2/roughly-equal10/sup -4.5/, and LiH/H/sub 2/roughly-equal10/sup -6.5/. These molecules may dominate the cooling and trigger the collapse of primordial gas clouds. The dipole rotational transitions of HD and LiH are particularly important at high density and low temperature. Additional molecules form during spherical collapse of these clouds, their rotational cooling keeps the gas temperature between 400 and 1500 K over 12 decades of density increase until the H/sub 2/ lines become optically thick. The existence of molecular coolants at high redshift has significant implications for the first generation of stars and for thermal instabilities in intergalactic matter.

  19. Simple molecules as complex systems

    PubMed Central

    Furtenbacher, Tibor; Árendás, Péter; Mellau, Georg; Császár, Attila G.

    2014-01-01

    For individual molecules quantum mechanics (QM) offers a simple, natural and elegant way to build large-scale complex networks: quantized energy levels are the nodes, allowed transitions among the levels are the links, and transition intensities supply the weights. QM networks are intrinsic properties of molecules and they are characterized experimentally via spectroscopy; thus, realizations of QM networks are called spectroscopic networks (SN). As demonstrated for the rovibrational states of H216O, the molecule governing the greenhouse effect on earth through hundreds of millions of its spectroscopic transitions (links), both the measured and first-principles computed one-photon absorption SNs containing experimentally accessible transitions appear to have heavy-tailed degree distributions. The proposed novel view of high-resolution spectroscopy and the observed degree distributions have important implications: appearance of a core of highly interconnected hubs among the nodes, a generally disassortative connection preference, considerable robustness and error tolerance, and an “ultra-small-world” property. The network-theoretical view of spectroscopy offers a data reduction facility via a minimum-weight spanning tree approach, which can assist high-resolution spectroscopists to improve the efficiency of the assignment of their measured spectra. PMID:24722221

  20. A single-molecule diode

    PubMed Central

    Elbing, Mark; Ochs, Rolf; Koentopp, Max; Fischer, Matthias; von Hänisch, Carsten; Weigend, Florian; Evers, Ferdinand; Weber, Heiko B.; Mayor, Marcel

    2005-01-01

    We have designed and synthesized a molecular rod that consists of two weakly coupled electronic π -systems with mutually shifted energy levels. The asymmetry thus implied manifests itself in a current–voltage characteristic with pronounced dependence on the sign of the bias voltage, which makes the molecule a prototype for a molecular diode. The individual molecules were immobilized by sulfur–gold bonds between both electrodes of a mechanically controlled break junction, and their electronic transport properties have been investigated. The results indeed show diode-like current–voltage characteristics. In contrast to that, control experiments with symmetric molecular rods consisting of two identical π -systems did not show significant asymmetries in the transport properties. To investigate the underlying transport mechanism, phenomenological arguments are combined with calculations based on density functional theory. The theoretical analysis suggests that the bias dependence of the polarizability of the molecule feeds back into the current leading to an asymmetric shape of the current–voltage characteristics, similar to the phenomena in a semiconductor diode. PMID:15956208

  1. Functional molecules in electronic circuits.

    PubMed

    Weibel, Nicolas; Grunder, Sergio; Mayor, Marcel

    2007-08-01

    Molecular electronics is a fascinating field of research contributing to both fundamental science and future technological achievements. A promising starting point for molecular devices is to mimic existing electronic functions to investigate the potential of molecules to enrich and complement existing electronic strategies. Molecules designed and synthesized to be integrated into electronic circuits and to perform an electronic function are presented in this article. The focus is set in particular on rectification and switching based on molecular devices, since the control over these two parameters enables the assembly of memory units, likely the most interesting and economic application of molecular based electronics. Both historical and contemporary solutions to molecular rectification are discussed, although not exhaustively. Several examples of integrated molecular switches that respond to light are presented. Molecular switches responding to an electrochemical signal are also discussed. Finally, supramolecular and molecular systems with intuitive application potential as memory units due to their hysteretic switching are highlighted. Although a particularly attractive feature of molecular electronics is its close cooperation with neighbouring disciplines, this article is written from the point of view of a chemist. Although the focus here is largely on molecular considerations, innovative contributions from physics, electro engineering, nanotechnology and other scientific disciplines are equally important. However, the ability of the chemist to correlate function with structure, to design and to provide tailor-made functional molecules is central to molecular electronics. PMID:17637951

  2. Liquid membrane coated ion-exchange column solids

    DOEpatents

    Barkey, Dale P.

    1989-01-01

    This invention relates to a method for improving the performance of liquid embrane separations by coating a liquid membrane onto solid ion-exchange resin beads in a fixed bed. Ion-exchange beads fabricated from an ion-exchange resin are swelled with water and are coated with a liquid membrane material that forms a film over the beads. The beads constitute a fixed bed ion-exchange column. Fluid being treated that contains the desired ion to be trapped by the ion-exchange particle is passed through the column. A carrier molecule, contained in the liquid membrane ion-exchange material, is selected for the desired ion in the fluid. The carrier molecule forms a complex with the desired ion, transporting it through the membrane and thus separating it from the other ions. The solution is fed continuously until breakthrough occurs at which time the ion is recovered, and the bed is regenerated.

  3. Liquid membrane coated ion-exchange column solids

    DOEpatents

    Barkey, Dale P.

    1988-01-01

    This invention relates to a method for improving the performance of liquid membrane separations by coating a liquid membrane onto solid ion-exchange resin beads in a fixed bed. Ion-exchange beads fabricated from an ion-exchange resin are swelled with water and are coated with a liquid membrane material that forms a film over the beads. The beads constitute a fixed bed ion-exchange column. Fluid being treated that contains the desired ion to be trapped by the ion-exchange particle is passed through the column. A carrier molecule, contained in the liquid membrane ion-exchange material, is selective for the desired ion in the fluid. The carrier molecule forms a complex with the desired ion, transporting it through the membrane and thus separating it from the other ions. The solution is fed continuously until breakthrough occurs at which time the ion is recovered, and the bed is regenerated.

  4. Biomimetic air sampling for detection of low concentrations of molecules and bioagents : LDRD 52744 final report.

    SciTech Connect

    Hughes, Robert Clark

    2003-12-01

    Present methods of air sampling for low concentrations of chemicals like explosives and bioagents involve noisy and power hungry collectors with mechanical parts for moving large volumes of air. However there are biological systems that are capable of detecting very low concentrations of molecules with no mechanical moving parts. An example is the silkworm moth antenna which is a highly branched structure where each of 100 branches contains about 200 sensory 'hairs' which have dimensions of 2 microns wide by 100 microns long. The hairs contain about 3000 pores which is where the gas phase molecules enter the aqueous (lymph) phase for detection. Simulations of diffusion of molecules indicate that this 'forest' of hairs is 'designed' to maximize the extraction of the vapor phase molecules. Since typical molecules lose about 4 decades in diffusion constant upon entering the liquid phase, it is important to allow air diffusion to bring the molecule as close to the 'sensor' as possible. The moth acts on concentrations as low as 1000 molecules per cubic cm. (one part in 1e16). A 3-D collection system of these dimensions could be fabricated by micromachining techniques available at Sandia. This LDRD addresses the issues involved with extracting molecules from air onto micromachined structures and then delivering those molecules to microsensors for detection.

  5. Liquid crystal nanocomposites produced by mixtures of hydrogen bonded achiral liquid crystals and functionalized carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Katranchev, B.; Petrov, M.; Keskinova, E.; Naradikian, H.; Rafailov, P. M.; Dettlaff-Weglikowska, U.; Spassov, T.

    2014-12-01

    The liquid crystalline (LC) nature of alkyloxybenzoic acids is preserved after adding of any mesogenic or non-mesogenic compound through hydrogen bonding. However, this noncovalent interaction provokes a sizable effect on the physical properties as, e. g. melting point and mesomorphic states. In the present work we investigate nanocomposites, prepared by mixture of the eighth homologue of p-n-alkyloxybenzoic acids (8OBA) with single-walled carbon nanotubes (SWCNT) with the purpose to modify the optical properties of the liquid crystal. We exercise optical control on the LC system by inserting SWCNT specially functionalized by carboxylic groups. Since the liquid crystalline state combines order and mobility at the molecular (nanoscale) level, molecular modification can lead to different macroscopical nanocomposite symmetry. The thermal properties of the functionalized nanocomposite are confirmed by DSC analyses. The mechanism of the interaction between surface-treated nanoparticles (functionalized nanotubes) and the liquid crystal 8OBA bent- dimer molecules is briefly discussed.

  6. Homophilic Adhesion Mechanism of Neurofascin, a Member of the L1 Family of Neural Cell Adhesion Molecules

    SciTech Connect

    Liu, Heli; Focia, Pamela J.; He, Xiaolin

    2012-02-13

    The L1 family neural cell adhesion molecules play key roles in specifying the formation and remodeling of the neural network, but their homophilic interaction that mediates adhesion is not well understood. We report two crystal structures of a dimeric form of the headpiece of neurofascin, an L1 family member. The four N-terminal Ig-like domains of neurofascin form a horseshoe shape, akin to several other immunoglobulin superfamily cell adhesion molecules such as hemolin, axonin, and Dscam. The neurofascin dimer, captured in two crystal forms with independent packing patterns, reveals a pair of horseshoes in trans-synaptic adhesion mode. The adhesion interaction is mediated mostly by the second Ig-like domain, which features an intermolecular {beta}-sheet formed by the joining of two individual GFC {beta}-sheets and a large but loosely packed hydrophobic cluster. Mutagenesis combined with gel filtration assays suggested that the side chain hydrogen bonds at the intermolecular {beta}-sheet are essential for the homophilic interaction and that the residues at the hydrophobic cluster play supplementary roles. Our structures reveal a conserved homophilic adhesion mode for the L1 family and also shed light on how the pathological mutations of L1 affect its structure and function.

  7. Molecular Models of Liquid Crystal Elastomers

    NASA Astrophysics Data System (ADS)

    Rajshekhar

    Liquid crystal elastomers combine the elastic properties of conventional rubbers with the optical properties of liquid crystals. This dual nature gives rise to unusual physical properties, including the stress induced transition from a polydomain state, consisting of multiple nematic regions with independent orientations, to a monodomain state consisting of a single nematic region with a uniform director. We propose several molecular-scale coarse-grained models of liquid crystal elastomers with varying degrees of resolution. The models employ the Gay-Berne soft potential, and exhibit the chain connectivity of a diamond network. Simulation results show that these models are able to capture the polydomain state exhibited by liquid crystal elastomers in the absence of any external stress. When subjected to uniaxial stress, our models exhibit a polydomain to monodomain transition. We explain that the polydomain state occurs through the aggregation of liquid crystal molecules assisted by crosslinking sites, and conclude that the transition mechanism to the monodomain state is based on the reorientation of nematic domains along the direction of applied stress. Our modeling efforts are primarily focused on three models. The first two models consider the effects of rigid and flexible crosslinkers in liquid crystal elastomers with a diamond topology for chain connectivity. The third model deviates from the diamond network topology and adopts a random network topology.

  8. Small molecule-assisted fabrication of black phosphorus quantum dots with a broadband nonlinear optical response.

    PubMed

    Gao, Lin-Feng; Xu, Jing-Yin; Zhu, Zhi-Yuan; Hu, Chen-Xia; Zhang, Lei; Wang, Qiang; Zhang, Hao-Li

    2016-08-18

    Ultrathin BP QDs with a uniform size of ∼3.4 nm were prepared via small molecule-assisted liquid phase exfoliation and they exhibited superior broadband nonlinear saturable absorption promising for nonlinear optical applications. Laser photolysis measurement implied that the nonlinear response origin was related to the long-lived electron-hole pairs delocalized within the BP QDs. PMID:27491959

  9. Liquid level detector

    DOEpatents

    Grasso, A.P.

    1984-02-21

    A liquid level detector for low pressure boilers. A boiler tank, from which vapor, such as steam, normally exits via a main vent, is provided with a vertical side tube connected to the tank at the desired low liquid level. When the liquid level falls to the level of the side tube vapor escapes therethrough causing heating of a temperature sensitive device located in the side tube, which, for example, may activate a liquid supply means for adding liquid to the boiler tank. High liquid level in the boiler tank blocks entry of vapor into the side tube, allowing the temperature sensitive device to cool, for example, to ambient temperature.

  10. Liquid level detector

    DOEpatents

    Grasso, Albert P.

    1986-01-01

    A liquid level detector for low pressure boilers. A boiler tank, from which apor, such as steam, normally exits via a main vent, is provided with a vertical side tube connected to the tank at the desired low liquid level. When the liquid level falls to the level of the side tube vapor escapes therethrough causing heating of a temperature sensitive device located in the side tube, which, for example, may activate a liquid supply means for adding liquid to the boiler tank. High liquid level in the boiler tank blocks entry of vapor into the side tube, allowing the temperature sensitive device to cool, for example, to ambient temperature.

  11. The relationship between local liquid density and force applied on a tip of atomic force microscope: A theoretical analysis for simple liquids

    SciTech Connect

    Amano, Ken-ichi Takahashi, Ohgi; Suzuki, Kazuhiro; Fukuma, Takeshi; Onishi, Hiroshi

    2013-12-14

    The density of a liquid is not uniform when placed on a solid. The structured liquid pushes or pulls a probe employed in atomic force microscopy, as demonstrated in a number of experimental studies. In the present study, the relation between the force on a probe and the local density of a liquid is derived based on the statistical mechanics of simple liquids. When the probe is identical to a solvent molecule, the strength of the force is shown to be proportional to the vertical gradient of ln(ρ{sub DS}) with the local liquid's density on a solid surface being ρ{sub DS}. The intrinsic liquid's density on a solid is numerically calculated and compared with the density reconstructed from the force on a probe that is identical or not identical to the solvent molecule.

  12. Doped ionic liquid crystals as effective weakly alignment media for polar solutes

    NASA Astrophysics Data System (ADS)

    Di Pietro, Maria Enrica; Celebre, Giorgio; De Luca, Giuseppina

    2016-06-01

    The ionic liquid crystal 1-dodecyl-3-methylimidazolium tetrafluoroborate slightly doped with water is presented as a promising NMR alignment medium for the measurement of residual dipolar couplings for polar molecules dissolved therein.

  13. Doped ionic liquid crystals as effective weakly alignment media for polar solutes.

    PubMed

    Di Pietro, Maria Enrica; Celebre, Giorgio; De Luca, Giuseppina

    2016-06-01

    The ionic liquid crystal 1-dodecyl-3-methylimidazolium tetrafluoroborate slightly doped with water is presented as a promising NMR alignment medium for the measurement of residual dipolar couplings for polar molecules dissolved therein. PMID:27128198

  14. Detecting single DNA molecule interactions with optical microcavities (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Vollmer, Frank

    2015-09-01

    circular optical path, similar to an acoustic wave guided along the wall of St. Paul's Cathedral. These so called whispering gallery modes (WGM) propagate with little loss, so that even a whisper can be heard on the other side of the gallery. In the optical case, the light beam can travel many thousand times around the inside of the microsphere before being scattered or absorbed, thereby making numerous interactions with an analyte molecule, bound to microsphere from surrounding sample solution. The most part of the light intensity, however, remains inside the microsphere, just below the reflecting glass surface, resulting in a relatively weak interaction between the light and the bound molecule. To enhance this interaction further, we attach tiny 42 nm x 12 nm gold nanorods to the glass surface. When passing a nanorod, the lightwave induces oscillations of conduction electrons, resulting in so called plasmon resonance. These nanorod plasmons greatly enhance the light intensity on the nanorod, so that the interaction of the light with a molecule attached to the nanorod is also enhanced[4-6]. This enhanced interaction results in an increase in sensitivity by more than a factor of one thousand, putting our experiments of single DNA molecule detection within reach. For the specific detection of nucleic acids, we attach single-stranded DNA to the nanorod and immerse our device in a liquid solution. When a matching, i.e. complementary DNA fragment binds from solution to the "bait" on the nanorod, the enhanced interaction with the light results in an observable shift of the WGM wavelength. Since light propagates in a WGM only for a very precise resonance wavelength or frequency, this shift can be detected with great accuracy[3]. On our current biosensor platform, we detect wavelength shifts with an accuracy of less than one femtometer, resulting in an extremely high sensitivity for biosensing, which we leverage for the specific detection of single 8 mer oligonucleotides as well

  15. Light Propagation in Liquid Crystals with a Chiral Dopant

    NASA Astrophysics Data System (ADS)

    Lawson, Justin; Saunders, Karl; Gantner, Logan

    2009-11-01

    This project will investigate the design and feasibility of a novel liquid crystal sensor that could be used to detect the presence and amount of foreign biological and/or chemical airborne agents. Such a sensor would have the advantage of being very portable. As such could have particular value in detecting biological or chemical weapons in the field of military operations. It would also be of use in a rapid response to a chemical or biological terrorist attack. The device would operate on the basic principal that when certain types of molecules bind to a liquid crystal molecule, the conformation of the liquid crystal molecule changes. This would in turn lead to a change in the overall arrangement of the liquid crystal, which could be detected using polarized light. In the absence of a contaminant the average molecular direction (optical axis, n ) is constant throughout the liquid crystal. The dopant adds a chirality or twist so that n precesses as a function of depth. We first solve for the reflected and transmitted light off of the air-liquid crystal boundary in the simplified case where there is linear chirality or a spiral configuration which repeats itself over some fixed interval (or pitch). We then generalize for cases in which this repeat distance varies with crystal depth. Finally we will obtain an expression for the contaminated crystal configuration which should depend on time and a diffusion constant and examine how the light properties change with respect to intensity and duration of exposure to the contaminant.

  16. Computer simulations of liquid crystals

    NASA Astrophysics Data System (ADS)

    Smondyrev, Alexander M.

    Liquid crystal physics is an exciting interdisciplinary field of research with important practical applications. Their complexity and the presence of strong translational and orientational fluctuations require a computational approach, especially in the studies of nonequlibrium phenomena. In this dissertation we present the results of computer simulation studies of liquid crystals using the molecular dynamics technique. We employed the Gay-Berne phenomenological model of liquid crystals to describe the interaction between the molecules. Both equilibrium and non-equilibrium phenomena were studied. In the first case we studied the flow properties of the liquid crystal system in equilibrium as well as the dynamics of the director. We measured the viscosities of the Gay-Berne model in the nematic and isotropic phases. The temperature-dependence of the rotational and shear viscosities, including the nonmonotonic behavior of one shear viscosity, are in good agreement with experimental data. The bulk viscosities are significantly larger than the shear viscosities, again in agreement with experiment. The director motion was found to be ballistic at short times and diffusive at longer times. The second class of problems we focused on is the properties of the system which was rapidly quenched to very low temperatures from the nematic phase. We find a glass transition to a metastable phase with nematic order and frozen translational and orientational degrees of freedom. For fast quench rates the local structure is nematic-like, while for slower quench rates smectic order is present as well. Finally, we considered a system in the isotropic phase which is then cooled to temperatures below the isotropic-nematic transition temperature. We expect topological defects to play a central role in the subsequent equilibration of the system. To identify and study these defects we require a simulation of a system with several thousand particles. We present the results of large

  17. Quantum theory of chiral interactions in cholesteric liquid crystals

    NASA Astrophysics Data System (ADS)

    Issaenko, S. A.; Harris, A. B.; Lubensky, T. C.

    1999-07-01

    The effective chiral interaction between molecules arising from long-range quantum interactions between fluctuating charge moments is analyzed in terms of a simple model of chiral molecules. This model is based on the approximations that (a) the dominant excited states of a molecule form a band whose width is small compared to the average energy of excitation above the ground state and (b) biaxial orientational correlation between adjacent molecules can be neglected. Previous treatments of quantum chiral interactions have been based on a multipole expansion of the effective interaction energy within second-order perturbation theory. We consider a system consisting of elongated molecules and, although we invoke the expansion in terms of coordinates transverse to the long axis of constituent molecules, we treat the longitudinal coordinate exactly. Such an approximation is plausible for molecules in real liquid crystals. The macroscopic cholesteric wave vector Q (Q=2π/P, where P is the pitch) is obtained via Q=h/K2, where K2 is the Frank elastic constant for twist and h is the torque field which we calculate from the effective chiral interaction κIJaI×aJ.RIJ, where the unit vector aI specifies the orientation of molecule I and RIJ is the displacement of molecule I relative to molecule J. We identify two distinct physical limits depending on whether one or both of the interacting molecules are excited in the virtual state. When both molecules are excited, we regain the R-8IJ dependence of κIJ on intermolecular separation found previously by Van der Meer et al. [J. Chem. Phys. 65, 3935 (1976)]. The two-molecule, unlike the one-molecule term, can be interpreted in terms of a superposition of pairwise interactions between individual atoms (or local chiral centers) on the two molecules. Contributions to κIJ when one molecule is excited in the virtual state are of order R-7IJ for helical molecules which are assumed not to have a global dipole moment, but whose atoms

  18. DUO: Spectra of diatomic molecules

    NASA Astrophysics Data System (ADS)

    Yurchenko, Sergei N.; Lodi, Lorenzo; Tennyson, Jonathan; Stolyarov, Andrey V.

    2016-05-01

    Duo computes rotational, rovibrational and rovibronic spectra of diatomic molecules. The software, written in Fortran 2003, solves the Schrödinger equation for the motion of the nuclei for the simple case of uncoupled, isolated electronic states and also for the general case of an arbitrary number and type of couplings between electronic states. Possible couplings include spin–orbit, angular momenta, spin-rotational and spin–spin. Introducing the relevant couplings using so-called Born–Oppenheimer breakdown curves can correct non-adiabatic effects.

  19. XUV ionization of aligned molecules

    SciTech Connect

    Kelkensberg, F.; Siu, W.; Gademann, G.; Rouzee, A.; Vrakking, M. J. J.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.

    2011-11-15

    New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

  20. Nanoelectronics of a DNA molecule

    NASA Astrophysics Data System (ADS)

    Albuquerque, E. L.; Fulco, U. L.; Caetano, E. W. S.; Freire, V. N.; Lyra, M. L.; Moura, F. A. B. F.

    2014-03-01

    We investigate the nanoelectronic properties of a double-strand quasiperiodic DNA molecule, modeled by a tight-binding effective Hamiltonian, which includes contributions from the nucleobasis system as well as the sugar-phosphate backbone. Our theoretical approach makes use of Dyson's equation together with a transfer-matrix treatment, to investigate the electronic density of states, the electronic transmissivity, and the current-voltage characteristic curves of sequences of a DNA finite segment.We compared the electronic transport found for the quasiperiodic structure to those using a sequence of natural DNA, as part of the human chromosome Ch22.