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Sample records for aggregated gas molecules

  1. Aggregated Gas Molecules: Toxic to Protein?

    PubMed Central

    Zhang, Meng; Zuo, Guanghong; Chen, Jixiu; Gao, Yi; Fang, Haiping

    2013-01-01

    The biological toxicity of high levels of breathing gases has been known for centuries, but the mechanism remains elusive. Earlier work mainly focused on the influences of dispersed gas molecules dissolved in water on biomolecules. However, recent studies confirmed the existence of aggregated gas molecules at the water-solid interface. In this paper, we have investigated the binding preference of aggregated gas molecules on proteins with molecular dynamics simulations, using nitrogen (N2) gas and the Src-homology 3 (SH3) domain as the model system. Aggregated N2 molecules were strongly bound by the active sites of the SH3 domain, which could impair the activity of the protein. In contrast, dispersed N2 molecules did not specifically interact with the SH3 domain. These observations extend our understanding of the possible toxicity of aggregates of gas molecules in the function of proteins. PMID:23588597

  2. Single molecule force spectroscopy of asphaltene aggregates.

    PubMed

    Long, Jun; Xu, Zhenghe; Masliyah, Jacob H

    2007-05-22

    Asphaltene aggregation and deposition cause severe problems in nearly all phases of petroleum processing. To resolve those problems, understanding the aggregation mechanisms is a prerequisite and has attracted the interest of a great number of investigators. However, to date, the nature and extent of asphaltene aggregation remain widely debated. In the present study, we attempt to investigate asphaltene aggregation from a completely new perspective. The technique of single molecule force spectroscopy (SMFS) was used to investigate the response of single asphaltene aggregates under an external pulling force. Force curves representing the stretching of single asphaltene aggregates were obtained in simple electrolyte solutions (KCl and calcium) and organic solvents (toluene and heptane). These force curves were well-fitted by the modified worm-like chain model, indicating that those asphaltene aggregates acted like long-chain polymers under pulling by an external force. It was found that lower solution pH values and the presence of divalent cations resulted in a lower bending rigidity of the formed aggregates. The information retrieved from the force curves suggests that asphaltene molecules with a structure featuring small aromatic clusters connected by aliphatic chains do exist and that asphaltene aggregation could occur through a linear polymerization mechanism. The current study extends the application scope of SMFS.

  3. Oligomeric baroeffect and gas aggregation states

    NASA Technical Reports Server (NTRS)

    Noever, David A.

    1992-01-01

    The baroeffect is analyzed to include a gas that aggregates into higher-order polymers or oligomers. The resulting pressure change is found to vary independently of the molecular weight of the gas components and to depend only on the aggregation or oligomeric order of the gas. With increasing aggregation, diffusive slip velocities are found to increase. The calculations are extended to include general counterdiffusion of two distinct aggregation states (k-, j-mer) for the gas, and the pressure change is derived as a function that is independent of both molecular weight and the absolute aggregation. The only parameter that determines the baroeffect is the ratio of aggregated states, beta = k/j. For gases that reversibly aggregate, possible oscillatory behavior and complex dynamics for pressure are discussed. Gas aggregation may play a role for low-temperature crystal-growth conditions in which vapor concentrations of one (or more) species are high.

  4. Aggregation and folding phase transitions of RNA molecules

    NASA Astrophysics Data System (ADS)

    Bundschuh, Ralf

    2007-03-01

    RNA is a biomolecule that is involved in nearly all aspects of cellular functions. In order to perform many of these functions, RNA molecules have to fold into specific secondary structures. This folding is driven by the tendency of the bases to form Watson-Crick base pairs. Beyond the biological importance of RNA, the relatively simple rules for structure formation of RNA make it a very interesting system from the statistical physics point of view. We will present examples of phase transitions in RNA secondary structure formation that are amenable to analytical descriptions. A special focus will be on aggregation between several RNA molecules which is important for some regulatory circuits based on RNA structure, triplet repeat diseases like Huntington's, and as a model for prion diseases. We show that depending on the relative strength of the intramolecular and the intermolecular base pairing, RNA molecules undergo a transition into an aggregated phase and quantitatively characterize this transition.

  5. A quantum gas of polar molecules

    NASA Astrophysics Data System (ADS)

    Ni, Kang-Kuen

    Ultracold polar molecular gases promise new directions and exciting applications in precision measurements, ultracold chemistry, electric-field controlled collisions, dipolar quantum gases, and quantum information sciences. This thesis presents experimental realization of a near quantum degenerate gas of polar molecules, where the phase-space density of the gas achieved is more than 10 orders of magnitude higher than previous results. The near quantum degenerate gas of polar molecules is created using two coherent steps. First, atoms in an ultracold gas mixture are converted into extremely weakly bound molecules near a Fano-Feshbach resonance. Second, the weakly bound molecules are transferred to the ro-vibronic ground state using a coherent two-photon Raman technique. The fact that these ground-state molecules are polar is confirmed with a spectroscopic measurement of the permanent electric dipole moment. Finally, manipulation of the molecular hyperfine state is demonstrated; this allows molecules to be populated in a single quantum state, in particular, the lowest energy state. With an ultracold gas of molecules, full control of molecular internal state, and electric field as a new handle, ultracold molecular collisions, including ultracold chemical reactions and dipolar collisions, are studied.

  6. Detecting gas molecules via atomic magnetization.

    PubMed

    Choi, Heechae; Lee, Minho; Kim, Seungchul; Lee, Kwang-Ryeol; Chung, Yong-Chae

    2014-09-14

    Adsorptions of gas molecules were found to alter the directions and magnitudes of magnetic moments of transition metal (Co, Fe) atoms adsorbed on graphene. Using first-principles calculations, we demonstrated that magnetism of surface atoms can be used to identify the kind of existing gas molecules via spin-reorientation and/or demagnetizations caused by the reconfigurations of 3d electron energy levels of Co and Fe. We suggest for the first time that magnetic properties of transition metal-embedded nanostructures can be used in highly selective gas-sensing applications.

  7. Identification of small molecule aggregators from large compound libraries by support vector machines.

    PubMed

    Rao, Hanbing; Li, Zerong; Li, Xiangyuan; Ma, Xiaohua; Ung, Choongyong; Li, Hu; Liu, Xianghui; Chen, Yuzong

    2010-03-01

    Small molecule aggregators non-specifically inhibit multiple unrelated proteins, rendering them therapeutically useless. They frequently appear as false hits and thus need to be eliminated in high-throughput screening campaigns. Computational methods have been explored for identifying aggregators, which have not been tested in screening large compound libraries. We used 1319 aggregators and 128,325 non-aggregators to develop a support vector machines (SVM) aggregator identification model, which was tested by four methods. The first is five fold cross-validation, which showed comparable aggregator and significantly improved non-aggregator identification rates against earlier studies. The second is the independent test of 17 aggregators discovered independently from the training aggregators, 71% of which were correctly identified. The third is retrospective screening of 13M PUBCHEM and 168K MDDR compounds, which predicted 97.9% and 98.7% of the PUBCHEM and MDDR compounds as non-aggregators. The fourth is retrospective screening of 5527 MDDR compounds similar to the known aggregators, 1.14% of which were predicted as aggregators. SVM showed slightly better overall performance against two other machine learning methods based on five fold cross-validation studies of the same settings. Molecular features of aggregation, extracted by a feature selection method, are consistent with published profiles. SVM showed substantial capability in identifying aggregators from large libraries at low false-hit rates. (c) 2009 Wiley Periodicals, Inc.

  8. A Mechanofluorochromic Push-Pull Small Molecule with Aggregation-Controlled Linear and Nonlinear Optical Properties.

    PubMed

    Jiang, Yue; Gindre, Denis; Allain, Magali; Liu, Ping; Cabanetos, Clément; Roncali, Jean

    2015-08-05

    A small push-pull molecule involving a diphenylamine substituted by an oligo-oxyethylene chain is described. The compound exhibits aggregation-induced emission with solvent-dependent emission wavelength. Spin-cast deep-red amorphous films rapidly self-reorganize into colorless crystalline films which exhibit mechanofluorochromism and aggregation-induced second-harmonic generation.

  9. Harnessing Chaperones to Generate Small-Molecule Inhibitors of Amyloid β Aggregation

    NASA Astrophysics Data System (ADS)

    Gestwicki, Jason E.; Crabtree, Gerald R.; Graef, Isabella A.

    2004-10-01

    Protein aggregation is involved in the pathogenesis of neurodegenerative diseases and hence is considered an attractive target for therapeutic intervention. However, protein-protein interactions are exceedingly difficult to inhibit. Small molecules lack sufficient steric bulk to prevent interactions between large peptide surfaces. To yield potent inhibitors of β-amyloid (Aβ) aggregation, we synthesized small molecules that increase their steric bulk by binding to chaperones but also have a moiety available for interaction with Aβ. This strategy yields potent inhibitors of Aβ aggregation and could lead to therapeutics for Alzheimer's disease and other forms of neurodegeneration.

  10. Single-Molecule Imaging of Individual Amyloid Protein Aggregates in Human Biofluids.

    PubMed

    Horrocks, Mathew H; Lee, Steven F; Gandhi, Sonia; Magdalinou, Nadia K; Chen, Serene W; Devine, Michael J; Tosatto, Laura; Kjaergaard, Magnus; Beckwith, Joseph S; Zetterberg, Henrik; Iljina, Marija; Cremades, Nunilo; Dobson, Christopher M; Wood, Nicholas W; Klenerman, David

    2016-03-16

    The misfolding and aggregation of proteins into amyloid fibrils characterizes many neurodegenerative disorders such as Parkinson's and Alzheimer's diseases. We report here a method, termed SAVE (single aggregate visualization by enhancement) imaging, for the ultrasensitive detection of individual amyloid fibrils and oligomers using single-molecule fluorescence microscopy. We demonstrate that this method is able to detect the presence of amyloid aggregates of α-synuclein, tau, and amyloid-β. In addition, we show that aggregates can also be identified in human cerebrospinal fluid (CSF). Significantly, we see a twofold increase in the average aggregate concentration in CSF from Parkinson's disease patients compared to age-matched controls. Taken together, we conclude that this method provides an opportunity to characterize the structural nature of amyloid aggregates in a key biofluid, and therefore has the potential to study disease progression in both animal models and humans to enhance our understanding of neurodegenerative disorders.

  11. Single-Molecule Imaging of Individual Amyloid Protein Aggregates in Human Biofluids

    PubMed Central

    2016-01-01

    The misfolding and aggregation of proteins into amyloid fibrils characterizes many neurodegenerative disorders such as Parkinson’s and Alzheimer’s diseases. We report here a method, termed SAVE (single aggregate visualization by enhancement) imaging, for the ultrasensitive detection of individual amyloid fibrils and oligomers using single-molecule fluorescence microscopy. We demonstrate that this method is able to detect the presence of amyloid aggregates of α-synuclein, tau, and amyloid-β. In addition, we show that aggregates can also be identified in human cerebrospinal fluid (CSF). Significantly, we see a twofold increase in the average aggregate concentration in CSF from Parkinson’s disease patients compared to age-matched controls. Taken together, we conclude that this method provides an opportunity to characterize the structural nature of amyloid aggregates in a key biofluid, and therefore has the potential to study disease progression in both animal models and humans to enhance our understanding of neurodegenerative disorders. PMID:26800462

  12. Stability of Soil Carbon Fractions - from molecules to aggregates

    NASA Astrophysics Data System (ADS)

    Mueller, C. W.; Mueller, K. E.; Freeman, K. H.; Eissenstat, D.; Kögel-Knabner, I.

    2009-12-01

    The turnover of soil organic matter (SOM) is controlled both by its chemical composition, its spatial bioavailability and the association with the mineral phase. Separation by physical fractionation of bulk soils and subsequent chemical analysis of these fractions should give insights to how compositional differences in SOM drive turnover rates of different size-defined carbon pools. The main objective of the study was to elucidate the relative abundance and recalcitrance of lignin and plant lipids (e.g. cutin and suberin) in the course of SOM decomposition within aggregated bulk soils and SOM fractions. By the parallel incubation of physically-separated size fractions and bulk soils of the Ah horizon from a forested soil (Picea abies L.Karst) over a period of 400 days, a unique set of samples was created to study SOM dynamics. We used solid-state 13C-CPMAS NMR spectroscopy and GC-MS (after copper oxide oxidation and solvent extraction) to analyze the composition of the incubated samples. The abundance and isotopic composition (including 13C and 14C) of respired CO2 further enabled us to monitor the dynamics of SOM mineralization. This approach allowed for differentiating between C stabilization of soil fractions due to accessibility/aggregation and to recalcitrance at different scales of resolution (GC-MS, NMR). A relative enrichment of alkyl C and decreasing lignin contents in the order of sand < silt < clay were observed by 13C-NMR and GC-MS within soils and fractions before the incubation, resulting in increased lipid to lignin ratios with decreasing particle size. A relative enrichment of lignin in the incubated fractions compared to the incubated bulk soils clearly indicated the preferential mineralization of less recalcitrant C compounds that were spatially inaccessible in aggregates of the bulk soil. Differences in the abundance of various lignin, cutin, and suberin monomers measured by GC-MS before and after the incubation indicate selective degradation

  13. Single Molecule Characterization of α-Synuclein in Aggregation-Prone States

    PubMed Central

    Trexler, Adam J.; Rhoades, Elizabeth

    2010-01-01

    α-Synuclein (αS) is an intrinsically disordered protein whose aggregation into ordered, fibrillar structures underlies the pathogenesis of Parkinson's disease. A full understanding of the factors that cause its conversion from soluble protein to insoluble aggregate requires characterization of the conformations of the monomer protein under conditions that favor aggregation. Here we use single molecule Förster resonance energy transfer to probe the structure of several aggregation-prone states of αS. Both low pH and charged molecules have been shown to accelerate the aggregation of αS and induce conformational changes in the protein. We find that at low pH, the C-terminus of αS undergoes substantial collapse, with minimal effect on the N-terminus and central region. The proximity of the N- and C-termini and the global dimensions of the protein are relatively unaffected by the C-terminal collapse. Moreover, although compact at low pH, with restricted chain motion, the structure of the C-terminus appears to be random. Low pH has a dramatically different effect on αS structure than the molecular aggregation inducers spermine and heparin. Binding of these molecules gives rise to only minor conformational changes in αS, suggesting that their mechanism of aggregation enhancement is fundamentally different from that of low pH. PMID:21044603

  14. Electron scattering from molecules and molecular aggregates of biological relevance

    NASA Astrophysics Data System (ADS)

    Gorfinkiel, Jimena D.; Ptasinska, Sylwia

    2017-09-01

    In this Topical Review we survey the current state of the art in the study of low energy electron collisions with biologically relevant molecules and molecular clusters. We briefly describe the methods and techniques used in the investigation of these processes and summarise the results obtained so far for DNA constituents and their model compounds, amino acids, peptides and other biomolecules. The applications of the data obtained is briefly described as well as future required developments.

  15. β-sheet interfering molecules acting against β-amyloid aggregation and fibrillogenesis.

    PubMed

    Francioso, Antonio; Punzi, Pasqualina; Boffi, Alberto; Lori, Clorinda; Martire, Sara; Giordano, Cesare; D'Erme, Maria; Mosca, Luciana

    2015-04-15

    β-Sheet aggregates and amyloid fibrils rising from conformational changes of proteins are observed in several pathological human conditions. These structures are organized in β-strands that can reciprocally interact by hydrophobic and π-π interactions. The amyloid aggregates can give rise to pathological conditions through complex biochemical mechanisms whose physico-chemical nature has been understood in recent times. This review focuses on the various classes of natural and synthetic small molecules able to act against β-amyloid fibrillogenesis and toxicity that may represent new pharmacological tools in Alzheimer's diseases. Some peptides, named 'β-sheet breaker peptides', are able to hamper amyloid aggregation and fibrillogenesis by interfering with and destabilizing the non native β-sheet structures. Other natural compounds, like polyphenols or indolic molecules such as melatonin, can interfere with β-amyloid peptide pathogenicity by inhibiting aggregation and counteracting oxidative stress that is a key hallmark in Alzheimer's disease.

  16. Gas molecule-molecule interaction and the gas-surface scattering effect on the rarefied gas flow through a slit into a vacuum

    NASA Astrophysics Data System (ADS)

    Sazhin, O.

    2009-05-01

    The effect of the gas molecule-molecule interaction and the gas-surface scattering on the gas flow through a slit into a vacuum are investigated in a wide range of the gas rarefaction using the direct simulation Monte Carlo method. To study the gas molecule-molecule interaction influence, we used the variable hard sphere and variable soft sphere models defined for an inverse-power-law potential and the generalized hard sphere model defined for the 12-6 Lennard-Jones potential. The Maxwell, Cercignani-Lampis, and Epstein models were used to simulate the gas-surface scattering. This study demonstrates that the gas molecule-molecule interaction can have a significant influence on the rarefied gas flow through a slit, while the influence of the gas-surface scattering is negligibly small. The presented numerical results are in agreement with the corresponding experimental ones.

  17. Gas molecule-molecule interaction and the gas-surface scattering effect on the rarefied gas flow through a slit into a vacuum

    SciTech Connect

    Sazhin, O.

    2009-05-15

    The effect of the gas molecule-molecule interaction and the gas-surface scattering on the gas flow through a slit into a vacuum are investigated in a wide range of the gas rarefaction using the direct simulation Monte Carlo method. To study the gas molecule-molecule interaction influence, we used the variable hard sphere and variable soft sphere models defined for an inverse-power-law potential and the generalized hard sphere model defined for the 12-6 Lennard-Jones potential. The Maxwell, Cercignani-Lampis, and Epstein models were used to simulate the gas-surface scattering. This study demonstrates that the gas molecule-molecule interaction can have a significant influence on the rarefied gas flow through a slit, while the influence of the gas-surface scattering is negligibly small. The presented numerical results are in agreement with the corresponding experimental ones.

  18. Changes in aggregation behavior of collagen molecules in solution with varying concentrations of acetic acid.

    PubMed

    Yang, Huan; Xu, Songcheng; Shen, Lirui; Liu, Wentao; Li, Guoying

    2016-11-01

    A critical aggregation concentration of 0.30-0.50mg/mL was previously obtained for type I collagen at 0.1M acetic acid (AA). In the present study, the aggregation behavior of collagen in solution (0.5mg/mL) in the presence of 0.1-2.0M AA was investigated. Circular dichroism showed that the three helix structure was maintained across the whole AA concentration range. However, the ratio of positive peak intensity over negative peak intensity varied depending on the conformational state of collagen aggregates. Ultra-sensitive differential scanning calorimetry revealed that transition temperatures Tm1 and Tm2 decreased by 8.35°C and 7.80°C, respectively, between 0.1M and 2.0M, indicating a possible relationship between the aggregation state and the thermal effect. The surrounding polarity of collagen molecules in solution containing pyrene was investigated by fluorescence spectroscopy, which demonstrated that disaggregation of collagen aggregates was enhanced with increasing AA concentration. This observation was correlated with changes in collagen fiber size observed by atomic force microscopy. Furthermore, collagen tyrosine residues were blue-shifted in an intrinsic fluorescence spectra, further indicating changes in aggregation behavior with increasing AA concentration. Finally, the dynamic response of collagen molecules to AA was analyzed by two-dimensional correlation fluorescence spectra. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Small molecule proteostasis regulators that reprogram the ER to reduce extracellular protein aggregation

    PubMed Central

    Plate, Lars; Cooley, Christina B; Chen, John J; Paxman, Ryan J; Gallagher, Ciara M; Madoux, Franck; Genereux, Joseph C; Dobbs, Wesley; Garza, Dan; Spicer, Timothy P; Scampavia, Louis; Brown, Steven J; Rosen, Hugh; Powers, Evan T; Walter, Peter; Hodder, Peter; Wiseman, R Luke; Kelly, Jeffery W

    2016-01-01

    Imbalances in endoplasmic reticulum (ER) proteostasis are associated with etiologically-diverse degenerative diseases linked to excessive extracellular protein misfolding and aggregation. Reprogramming of the ER proteostasis environment through genetic activation of the Unfolded Protein Response (UPR)-associated transcription factor ATF6 attenuates secretion and extracellular aggregation of amyloidogenic proteins. Here, we employed a screening approach that included complementary arm-specific UPR reporters and medium-throughput transcriptional profiling to identify non-toxic small molecules that phenocopy the ATF6-mediated reprogramming of the ER proteostasis environment. The ER reprogramming afforded by our molecules requires activation of endogenous ATF6 and occurs independent of global ER stress. Furthermore, our molecules phenocopy the ability of genetic ATF6 activation to selectively reduce secretion and extracellular aggregation of amyloidogenic proteins. These results show that small molecule-dependent ER reprogramming, achieved through preferential activation of the ATF6 transcriptional program, is a promising strategy to ameliorate imbalances in ER function associated with degenerative protein aggregation diseases. DOI: http://dx.doi.org/10.7554/eLife.15550.001 PMID:27435961

  20. Scattering Properties of Gas Molecules on a Water Adsorbed Surface

    NASA Astrophysics Data System (ADS)

    Takeuchi, Hideki; Yamamoto, Kyoji; Hyakutake, Toru

    2011-05-01

    The thermal problem of a rarefied argon (Ar) gas between two parallel walls is considered to investigate the characteristics of the reflected gas molecule at a platinum (Pt) wall surface which physically adsorbs water (H2O) molecules. The analysis is based on the molecular dynamics (MD) method for the interaction of gas molecules with the water adsorbed wall surface together with the direct simulation Monte-Carlo (DSMC) method for the motion of gas molecule. The accommodation coefficients of energy and normal momentum are obtained. The temperature distribution between two walls and the velocity distribution function of the reflected molecule are also obtained. It is found that the accommodation coefficients for the water adsorbed surface decrease with increasing the adsorption rate.

  1. Comparative studies on the structure and aggregative properties of the myosin molecule. III. The in vitro aggregative properties of the lobster myosin molecule.

    PubMed

    Siemankowski, R F; Zobel, C R

    1976-02-20

    The solubility of rabbit skeletal and lobster abdominal muscle myosin has been studied in monovalent salt solutions as a function of pH (over the range 4.75 to 8.5) and ionic strength (50-500 mM). Rabbit skeletal muscle myosin was found to precipitate over a narrower pH range than the lobster abdominal muscle myosin but at equivalent pH values and ionic strengths the former exhibited greater solubility. Comparison of the solubility of rabbit myosin, per se with that of light meromyosin and lobster myosin with its equivalent proteolytically produced fragment (fraction B1) showed that both rod fragments were more soluble than their parent molecules. Under conditions of low solubility (low ionic strength and pH) the quantitiy of protein in solution remained essentially constant with increasing total protein, thus suggesting that the aggregation phenomenon is of a phase transition type. Examination of the aggregates by electron microscopy revealed that rabbit myosin formed classical, elongate, spindle-shaped filaments similar to those previously observed by others. In contrast lobster myosin only formed short, dumbbell-shaped filaments 0.2-0.3 mum long. Consideration of the pH ranges over which aggregation occurred suggests that protonation of histidine residues may be involved in rabbit myosin filament formation while for lobster myosin, aggregation may involve protonation of epsilon-amino or guanidino groups. The possible relationship between the distribution of these groups along the rod portion of the myosin molecule and the formation of elongate filaments has been explored.

  2. Quasi-one-dimensional cyano-phenylene aggregates: Uniform molecule alignment contrasts varying electrostatic surface potential

    NASA Astrophysics Data System (ADS)

    Balzer, Frank; Resel, Roland; Lützen, Arne; Schiek, Manuela

    2017-04-01

    The epitaxial growth of the mono-functionalized para-quaterphenylene molecule CNHP4 on muscovite mica is investigated. The vacuum deposited molecules aggregate into nanofibers of varying morphology. Due to muscovite's cm symmetry, almost mutually parallel fibers grow. Polarized light microscopy together with X-ray diffraction resolves the projected orientation of the molecules on the substrate surface and within the fibers. Several different contact planes with the substrate are detected. For all of them, the molecules orient with their long molecule axis approximately perpendicular to the grooved muscovite direction, so that the alignment of the molecules on the substrate is uniform. Kelvin probe force microscopy finds vastly different electrostatic properties of different fiber types and facets.

  3. Tandem repeating modular proteins avoid aggregation in single molecule force spectroscopy experiments.

    PubMed

    Dougan, Lorna; Fernandez, Julio M

    2007-12-13

    We have used single molecule force spectroscopy to explore the unfolding and refolding behavior of the immunoglobulin-like I27 protein in aqueous 2,2,2-trifluoroethanol (TFE). In bulk solution experiments, a 28% v/v TFE solution has previously been observed to enhance intermolecular attractions and lead to misfolding and aggregation of tandem modular proteins of high sequence identity. In our single molecule experiments, however, we measure successful refolding of the polyprotein I27(8) in all TFE solutions up to 35% v/v. Using a single molecule micromanipulation technique, we have shown that refolding of a polyprotein with identical repeats is not hindered by the presence of this cosolvent. These experimental results provide new insight into the properties of tandem repeating proteins and raise interesting questions as to the evolutionary success of such proteins in avoiding misfolding and aggregation.

  4. Novel Applications of Buffer-gas Cooling to Cold Atoms, Diatomic Molecules, and Large Molecules

    NASA Astrophysics Data System (ADS)

    Drayna, Garrett Korda

    Cold gases of atoms and molecules provide a system for the exploration of a diverse set of physical phenomena. For example, cold gasses of magnetically and electrically polar atoms and molecules are ideal systems for quantum simulation and quantum computation experiments, and cold gasses of large polar molecules allow for novel spectroscopic techniques. Buffer-gas cooling is a robust and widely applicable method for cooling atoms and molecules to temperatures of approximately 1 Kelvin. In this thesis, I present novel applications of buffer-gas cooling to obtaining gases of trapped, ultracold atoms and diatomic molecules, as well as the study of the cooling of large organic molecules. In the first experiment of this thesis, a buffer-gas beam source of atoms is used to directly load a magneto-optical trap. Due to the versatility of the buffer-gas beam source, we obtain trapped, sub-milliKelvin gases of four different lanthanide species using the same experimental apparatus. In the second experiment of this thesis, a buffer-gas beam is used as the initial stage of an experiment to directly laser cool and magneto-optically trap the diatomic molecule CaF. In the third experiment of this thesis, buffer-gas cooling is used to study the cooling of the conformational state of large organic molecules. We directly observe conformational relaxation of gas-phase 1,2-propanediol due to cold collisions with helium gas. Lastly, I present preliminary results on a variety of novel applications of buffer-gas cooling, such as mixture analysis, separation of chiral mixtures, the measurement of parity-violation in chiral molecules, and the cooling and spectroscopy of highly unstable reaction intermediates.

  5. Tunneling properties of nonplanar molecules in a gas medium

    SciTech Connect

    Bahrami, Mohammad; Bassi, Angelo

    2011-12-15

    We propose a simple, general, and accurate formula for analyzing the tunneling between classical configurations of a nonplanar molecule in a gas medium, as a function of the thermodynamic parameters of the gas. We apply it to two interesting cases: (i) the shift to zero frequency of the inversion line of ammonia, upon an increase in the pressure of the gas; and (ii) the destruction of the coherent tunneling of D{sub 2}S{sub 2} molecules in a He gas. In both cases, we compare our analysis with previous theoretical and experimental results.

  6. Kinetics of aggregation of an anisotropic model of self-assembling molecules.

    PubMed

    Khan, Siddique; Haaga, Jason; Gunton, J D

    2015-07-14

    We study the kinetics of aggregation of a two site model of interacting spherical molecules. A given site on one molecule can interact with one or more sites on other neighboring molecules. The sites represent the result of a simple coarse graining of putative amino acid residues or two specifically designed sites on a colloidal particle. We study the kinetics and equilibrium morphology for a fixed angle between the two sites, for several angles between 30° and 150°. In the model, the sites interact via an attractive Asakura-Oosawa potential and the molecules have the usual hard sphere repulsion interaction. We find a transition from a micelle-like morphology at small angles to a rod-like morphology at intermediate angles and to a gel-like structure at values of the angle greater than about ninety degrees. However, at 150 degrees, after a long induction time during which there is no aggregation, we observe a nucleation and growth process that leads to a final spherical-like aggregate. Our results show that this angle is a control parameter for the kinetics and equilibrium properties of the system.

  7. Ultraviolet absorption spectra of metalorganic molecules diluted in hydrogen gas

    NASA Astrophysics Data System (ADS)

    Itoh, Hideo; Watanabe, Masanobu; Mukai, Seiji; Yajima, Hiroyoshi

    1988-12-01

    Ultraviolet absorption spectra of trimethyl gallium, triethyl gallium, and trimethyl aluminum diluted in hydrogen gas were measured as a function of the wavelength (185-350 nm) and the concentration of the molecules (4.8×10 -6 -1.6×10 -4 mol/liter). Their absorbances changed linearly with the concentration of the molecules, which allowed us to calculate the molar absorption coefficients of the molecules on the basis of the Beer-Lambert law.

  8. Aggregation of dipolar molecules in SiO2 hybrid organic-inorganic films: use of silver nanoparticles as inhibitors of molecular aggregation

    NASA Astrophysics Data System (ADS)

    Franco, Alfredo; García-Macedo, Jorge; Brusatin, Giovanna; Guglielmi, Massimo

    2013-04-01

    The technological implementation of hybrid organic-inorganic materials in second order nonlinear optical photonic devices depends strongly on the ability of the host matrixes to contain high loads of dipolar molecules without aggregation. Some organic molecules are often used to diminish the attracting interactions between dipolar molecules in such kind of materials, but their efficiency as inhibitors of molecular aggregation is limited by their polarizability. In this work, we report the use of silver nanoparticles as inhibitors of molecular aggregation in hybrid organic-inorganic films doped with dipolar molecules. The large polarizability of the silver nanoparticles makes them ideal moieties for the inhibition of the electrostatic interactions between dipolar nonlinear optical molecules. The average size of the silver nanoparticles in this work was 70.5 nm in diameter, they were synthesized using silver nitrate (AgNO3) as precursor and aminoethylaminopropyltrimethoxysilane as reducing agent. These nanoparticles were immersed in SiO2 hybrid organic-inorganic sol-gel films doped with dipolar chromophores to study their effect as inhibitors of dipolar chromophores aggregation. The presence of the silver nanoparticles in the solid films was confirmed by transmission electronic microscopy and UV-Visible spectroscopy. UV-Visible spectroscopy was also used to monitor the dipolar chromophores aggregation in the SiO2 films. We found that, at room temperature, silver nanoparticles are good inhibiting chromophores aggregation in comparison with the performance of organic inhibitors.

  9. Heme binding site in apomyoglobin may be effectively targeted with small molecules to control aggregation.

    PubMed

    Azami-Movahed, Mehrnaz; Shariatizi, Sajad; Sabbaghian, Marjan; Ghasemi, Atiyeh; Ebrahim-Habibi, Azadeh; Nemat-Gorgani, Mohsen

    2013-02-01

    A number of ligands with affinities for the heme binding site of apomyoglobin were tested to control amorphous and fibrillar aggregation in the protein. Several techniques, including fluorescence, dynamic light scattering, transmission electron microscopy, dot blot analysis combined with viability studies were employed for structural characterization and cytotoxicity assessment of the intermediate and final protein structures formed during the aggregation process. Of the small molecules investigated, chrysin and Nile red with high structural similarities to heme were chosen for further studies. Only fibril formation was found to be prevented by Nile red, while chrysin, with a greater structural flexibility, was able to prevent both types of aggregate formation. The two ligands were found to influence aggregation at different stages of intermediate structure formation, an ability determined by their degrees of similarities with heme. Based on structural characterization and toxicity studies, it is concluded that ligands similar in structure to heme may be effective in influencing various stages of aggregate formation and toxicity potencies of the protein structures. Since metalloproteins constitute more than thirty percent of all known proteins, it is concluded that the present strategy may be of general significance.

  10. Influence of organic molecules on the aggregation of TiO2 nanoparticles in acidic conditions

    NASA Astrophysics Data System (ADS)

    Danielsson, Karin; Gallego-Urrea, Julián A.; Hassellov, Martin; Gustafsson, Stefan; Jonsson, Caroline M.

    2017-04-01

    Engineered nanoparticles released into the environment may interact with natural organic matter (NOM). Surface complexation affects the surface potential, which in turn may lead to aggregation of the particles. Aggregation of synthetic TiO2 (anatase) nanoparticles in aqueous suspension was investigated at pH 2.8 as a function of time in the presence of various organic molecules and Suwannee River fulvic acid (SRFA), using dynamic light scattering (DLS) and high-resolution transmission electron microscopy (TEM). Results showed that the average hydrodynamic diameter and ζ-potential were dependent on both concentration and molecular structure of the organic molecule. Results were also compared with those of quantitative batch adsorption experiments. Further, a time study of the aggregation of TiO2 nanoparticles in the presence of 2,3-dihydroxybenzoic acid (2,3-DHBA) and SRFA, respectively, was performed in order to observe changes in ζ-potential and particle size over a time period of 9 months. In the 2,3-DHBA-TiO2 system, ζ-potentials decreased with time resulting in charge neutralization and/or inversion depending on ligand concentration. Aggregate sizes increased initially to the micrometer size range, followed by disaggregation after several months. No or very little interaction between SRFA and TiO2 occurred at the lowest concentrations tested. However, at the higher concentrations of SRFA, there was an increase in both aggregate size and the amount of SRFA adsorbed to the TiO2 surface. This was in correlation with the ζ-potential that decreased with increased SRFA concentration, leading to destabilization of the system. These results stress the importance of performing studies over both short and long time periods to better understand and predict the long-term effects of nanoparticles in the environment.

  11. Small Molecule Catalysts for Harvesting Methane Gas

    SciTech Connect

    Baker, S. E.; Ceron-Hernandez, M.; Oakdale, J.; Lau, E. Y.

    2016-12-06

    As the average temperature of the earth increases the impact of these changes are becoming apparent. One of the most dramatic changes to the environment is the melting of arctic permafrost. The disappearance of the permafrost has resulted in release of streams of methane that was trapped in remote areas as gas hydrates in ice. Additionally, the use of fracking has also increased emission of methane. Currently, the methane is either lost to the atmosphere or flared. If these streams of methane could be brought to market, this would be an abundant source of revenue. A cheap conversion of gaseous methane to a more convenient form for transport would be necessary to economical. Conversion of methane is a difficult reaction since the C-H bond is very stable (104 kcal/mole). At the industrial scale, the Fischer-Tropsch reaction can be used to convert gaseous methane to liquid methanol but is this method is impractical for these streams that have low pressures and are located in remote areas. Additionally, the Fischer-Tropsch reaction results in over oxidation of the methane leading to many products that would need to be separated.

  12. Creation of ultracold molecules from a Fermi gas of atoms.

    PubMed

    Regal, Cindy A; Ticknor, Christopher; Bohn, John L; Jin, Deborah S

    2003-07-03

    Following the realization of Bose-Einstein condensates in atomic gases, an experimental challenge is the production of molecular gases in the quantum regime. A promising approach is to create the molecular gas directly from an ultracold atomic gas; for example, bosonic atoms in a Bose-Einstein condensate have been coupled to electronic ground-state molecules through photoassociation or a magnetic field Feshbach resonance. The availability of atomic Fermi gases offers the prospect of coupling fermionic atoms to bosonic molecules, thus altering the quantum statistics of the system. Such a coupling would be closely related to the pairing mechanism in a fermionic superfluid, predicted to occur near a Feshbach resonance. Here we report the creation and quantitative characterization of ultracold 40K2 molecules. Starting with a quantum degenerate Fermi gas of atoms at a temperature of less than 150 nK, we scan the system over a Feshbach resonance to create adiabatically more than 250,000 trapped molecules; these can be converted back to atoms by reversing the scan. The small binding energy of the molecules is controlled by detuning the magnetic field away from the Feshbach resonance, and can be varied over a wide range. We directly detect these weakly bound molecules through their radio-frequency photodissociation spectra; these probe the molecular wavefunction, and yield binding energies that are consistent with theory.

  13. Systematic development of small molecules to inhibit specific microscopic steps of Aβ42 aggregation in Alzheimer’s disease

    PubMed Central

    Habchi, Johnny; Chia, Sean; Limbocker, Ryan; Mannini, Benedetta; Ahn, Minkoo; Perni, Michele; Hansson, Oskar; Arosio, Paolo; Kumita, Janet R.; Challa, Pavan Kumar; Cohen, Samuel I. A.; Dobson, Christopher M.; Knowles, Tuomas P. J.; Vendruscolo, Michele

    2017-01-01

    The aggregation of the 42-residue form of the amyloid-β peptide (Aβ42) is a pivotal event in Alzheimer’s disease (AD). The use of chemical kinetics has recently enabled highly accurate quantifications of the effects of small molecules on specific microscopic steps in Aβ42 aggregation. Here, we exploit this approach to develop a rational drug discovery strategy against Aβ42 aggregation that uses as a read-out the changes in the nucleation and elongation rate constants caused by candidate small molecules. We thus identify a pool of compounds that target specific microscopic steps in Aβ42 aggregation. We then test further these small molecules in human cerebrospinal fluid and in a Caenorhabditis elegans model of AD. Our results show that this strategy represents a powerful approach to identify systematically small molecule lead compounds, thus offering an appealing opportunity to reduce the attrition problem in drug discovery. PMID:28011763

  14. Small stress molecules inhibit aggregation and neurotoxicity of prion peptide 106-126

    SciTech Connect

    Kanapathipillai, Mathumai; Ku, Sook Hee; Girigoswami, Koyeli; Park, Chan Beum

    2008-01-25

    In prion diseases, the posttranslational modification of host-encoded prion protein PrP{sup c} yields a high {beta}-sheet content modified protein PrP{sup sc}, which further polymerizes into amyloid fibrils. PrP106-126 initiates the conformational changes leading to the conversion of PrP{sup c} to PrP{sup sc}. Molecules that can defunctionalize such peptides can serve as a potential tool in combating prion diseases. In microorganisms during stressed conditions, small stress molecules (SSMs) are formed to prevent protein denaturation and maintain protein stability and function. The effect of such SSMs on PrP106-126 amyloid formation is explored in the present study using turbidity, atomic force microscopy (AFM), and cellular toxicity assay. Turbidity and AFM studies clearly depict that the SSMs-ectoine and mannosylglyceramide (MGA) inhibit the PrP106-126 aggregation. Our study also connotes that ectoine and MGA offer strong resistance to prion peptide-induced toxicity in human neuroblastoma cells, concluding that such molecules can be potential inhibitors of prion aggregation and toxicity.

  15. Supramolecular aggregation of inorganic molecules at Au(111) electrodes under a strong ionic atmosphere.

    PubMed

    Fu, Yong-Chun; Su, Yu-Zhuan; Wu, De-Yin; Yan, Jia-Wei; Xie, Zhao-Xiong; Mao, Bing-Wei

    2009-10-21

    Neutral inorganic molecules are generally weak in surface adsorption and intermolecular interactions. Self-assembly of such types of molecule would provide valuable information about various interactions. At electrochemical interfaces, the relative strength of these interactions may be modified through control of electrode potential and electrolyte, which may lead to the discovery of new structures and new phenomena. However, studies of this nature are as yet lacking. In this work, we consider the covalent-bound semimetal compound molecules, XCl(3) (X = Sb, Bi), as model systems of neutral inorganic molecules to investigate their self-assembly at electrochemical interfaces under a high ionic atmosphere. To fulfill such investigations, in situ STM and cyclic voltammetry are employed, and comparative experiments are performed on Au(111) in ionic liquids as well as aqueous solutions with high ionic strength. In the room temperature ionic liquid of 1-butyl-3-methylimidazolium tetrafluoroborate (BMIBF(4)), potential-dependent partial charge transfer between the Au surface and XCl(3) molecules creates a molecule-surface interaction and provides the driving force for adsorption of the molecules. Supramolecular aggregations of adsorbed XCl(3) are promoted through chlorine-based short-range intermolecular correlation under crystallographic constraint, while repulsive Coulombic interactions created between the partially charged aggregations facilitate their long-range ordering. For SbCl(3) molecules, hexagonally arranged 6- or 7-member clusters are formed at 0.08 to -0.2 V (vs Pt), which assemble into a secondary ( radical31 x radical31)R8.9 degrees structure. For BiCl(3) molecules, both the 6-membered hexagonal and 3-membered trigonal clusters are formed in the narrow potential range -0.3 to -0.35 V, and are also arranged into an ordered secondary structure. Comparative studies were performed with SbCl(3) in concentrated aqueous solutions containing 2 M HCl to simulate the

  16. Ion-Molecule Reactions in Gas Phase Radiation Chemistry.

    ERIC Educational Resources Information Center

    Willis, Clive

    1981-01-01

    Discusses some aspects of the radiation chemistry of gases, focusing on the ion-molecule and charge neutralization reactions which set study of the gas phase apart. Uses three examples that illustrate radiolysis, describing the radiolysis of (1) oxygen, (2) carbon dioxide, and (3) acetylene. (CS)

  17. Ion-Molecule Reactions in Gas Phase Radiation Chemistry.

    ERIC Educational Resources Information Center

    Willis, Clive

    1981-01-01

    Discusses some aspects of the radiation chemistry of gases, focusing on the ion-molecule and charge neutralization reactions which set study of the gas phase apart. Uses three examples that illustrate radiolysis, describing the radiolysis of (1) oxygen, (2) carbon dioxide, and (3) acetylene. (CS)

  18. Interaction of gas molecules with Ti-benzene complexes.

    PubMed

    Chen, G; Jena, P; Kawazoe, Y

    2008-08-21

    Using first-principles calculations based on gradient corrected density functional theory, we have studied the interaction of NH(3), H(2), and O(2) with Ti-benzene complexes [Ti(Bz)(2) and Ti(2)(Bz)(2)]. The energy barriers as the gas molecules approach the Ti-benzene complexes as well as the geometries of the ground state of these interacting complexes were obtained by starting with several initial configurations. While NH(3) and H(2) were found to physisorb on the Ti(Bz)(2) complex, the O(2) reacts with it strongly leading to dissociative chemisorption of the oxygen molecule. In contrast all the gas molecules react with the Ti(2)(Bz)(2) complex. These studies indicate that the reaction of certain, but not all, gas molecules can be used to probe the equilibrium geometries of organometallic complexes. Under special conditions, such as high pressure, the Ti atom intercalated between benzene molecules in Ti(Bz)(2) and the Ti(2)(Bz)(2) complexes could store hydrogen in chemisorbed states. The results are compared to available experimental data.

  19. The prebiotic molecules observed in the interstellar gas

    PubMed Central

    Thaddeus, P

    2006-01-01

    Over 130 molecules have been identified in the interstellar gas and circumstellar shells, the largest among them is a carbon chain with 13 atoms and molecular weight of 147 (twice that of the simplest amino acid glycine). The high reliability of astronomical identifications, as well as the fairly accurate quantitative analysis which can often be achieved, is emphasized. Glycine itself has been claimed, but a recent analysis indicates that few, if any, of the astronomical radio lines attributed to glycine are actually from that molecule. Polycyclic aromatic hydrocarbons (PAHs) have long been proposed as the source of the unidentified infrared bands between 3 and 16 μm, but no single PAH has been identified in space, partly because PAHs generally have weak or non-existent radio spectra. A remarkable exception is the non-planar corannulene molecule (C20H10) that has a strong radio spectrum; in the rich molecular cloud TMC-1, it is found that less than 10−5 of the carbon is contained in this molecule, suggesting that PAHs are not the dominant large molecules in the interstellar gas, as has been claimed. Owing to inherent spectroscopic limitations, determining the structures of the large molecules in space may require capture of the dust grains, which are continually entering the outer Solar System. PMID:17008209

  20. Fluorescence study on the aggregation of collagen molecules in acid solution influenced by hydroxypropyl methylcellulose.

    PubMed

    Ding, Cuicui; Zhang, Min; Li, Guoying

    2016-01-20

    The effect of hydroxypropyl methylcellulose (HPMC) on the aggregation of collagen molecules with collagen concentrations of 0.25, 0.5 and 1.0mg/mL was studied by fluorescence techniques. On one hand, both the synchronous fluorescence spectra and fluorescence emission spectra showed that there was no change in the fluorescence intensity of collagen intrinsic fluorescence when 30% HPMC was added, while it decreased obviously when HPMC content ≥ 50%. From the two-dimensional fluorescence correlation analysis, it was indicated that collagen molecules in 0.25 and 0.5mg/mL collagen solutions were more sensitive to HPMC than those in 1.0mg/mL collagen solution. On the other hand, the pyrene fluorescence and the fluorescence anisotropy measurements indicated that HPMC inhibited the collagen aggregation for 0.25 and 0.5mg/mL collagen, but promoted it for 1.0mg/mL collagen. The atomic force microscopy images further confirmed the effect of HPMC on collagen with different initial states.

  1. Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model.

    PubMed

    Ebrahimi, Ali; Or, Dani

    2016-09-01

    Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Recent mechanistic models of microbial processes in unsaturated aggregate-like pore networks revealed a highly dynamic interplay between oxic and anoxic microsites jointly shaped by hydration conditions and by aerobic and anaerobic microbial community abundance and self-organization. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support substantial anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3D angular pore networks. Model aggregates of different sizes were subjected to variable water, carbon and oxygen contents that varied with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain estimates of biogeochemical fluxes from the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2 O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of practical interest for hydrological and climate models. © 2016 John Wiley & Sons Ltd.

  2. Deposition and aggregation of aspirin molecules on a phospholipid bilayer pattern.

    PubMed

    Mao, Guangzhao; Chen, Dongzhong; Handa, Hitesh; Dong, Wenfei; Kurth, Dirk G; Möhwald, Helmuth

    2005-01-18

    Aspirin and 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine (DMPE) are deposited from their alcoholic mixed solution onto highly oriented pyrolytic graphite (HOPG) by spin coating. The film structure and morphology are characterized by atomic force microscopy (AFM). The barely soluble DMPE forms a highly oriented stripe phase as a result of its one-dimensional epitaxy with the HOPG lattice. The bilayer stripe pattern exposes the cross section of the lipid bilayer lamellae and enables the direct visualization of the molecular interactions of drug or biological molecules with either the hydrophobic or the hydrophilic part of the phospholipid bilayer. The bilayer pattern affects the aspirin molecular deposition and aggregation. AFM shows that the aspirin molecules prefer to deposit and aggregate along the aliphatic interior part of the bilayer pattern, giving rise to parallel dimer rods in registry with the underlying pattern. The nonpolar interactions between aspirin and the phospholipid bilayer are consistent with the lipophilic nature of aspirin. The bilayer pattern not only stabilizes the rodlike aggregate structure of aspirin at low aspirin concentration but also inhibits crystallization of aspirin at high aspirin concentration. Molecular models show that the width of the DMPE aliphatic chain interior can accommodate no more than two aspirin dimers. The bilayer confinement may prevent aspirin from reaching its critical nucleus size. This study illustrates a general method to induce a metastable or amorphous form of an active pharmaceutical ingredient (API) by chemical confinement under high undercooling conditions. Metastable and amorphous solids often display better solubility and bioavailability than the stable crystalline form of the API.

  3. Interactions and aggregation of apoferritin molecules in solution: effects of added electrolytes.

    PubMed Central

    Petsev, D N; Thomas, B R; Yau, S; Vekilov, P G

    2000-01-01

    We have studied the structure of the protein species and the protein-protein interactions in solutions containing two apoferritin molecular forms, monomers and dimers, in the presence of Na(+) and Cd(2+) ions. We used chromatographic, and static and dynamic light scattering techniques, and atomic force microscopy (AFM). Size-exclusion chromatography was used to isolate these two protein fractions. The sizes and shapes of the monomers and dimers were determined by dynamic light scattering and AFM. Although the monomer is an apparent sphere with a diameter corresponding to previous x-ray crystallography determinations, the dimer shape corresponds to two, bound monomer spheres. Static light scattering was applied to characterize the interactions between solute molecules of monomers and dimers in terms of the second osmotic virial coefficients. The results for the monomers indicate that Na(+) ions cause strong intermolecular repulsion even at concentrations higher than 0.15 M, contrary to the predictions of the commonly applied Derjaguin-Landau-Verwey-Overbeek theory. We argue that the reason for such behavior is hydration force due to the formation of a water shell around the protein molecules with the help of the sodium ions. The addition of even small amounts of Cd(2+) changes the repulsive interactions to attractive but does not lead to oligomer formation, at least at the protein concentrations used. Thus, the two ions provide examples of strong specificity of their interactions with the protein molecules. In solutions of the apoferritin dimer, the molecules attract even in the presence of Na(+) only, indicating a change in the surface of the apoferritin molecule. In view of the strong repulsion between the monomers, this indicates that the dimers and higher oligomers form only after partial denaturation of some of the apoferritin monomers. These observations suggest that aggregation and self-assembly of protein molecules or molecular subunits may be driven by

  4. Line broadening of confined CO gas: from molecule-wall to molecule-molecule collisions with pressure.

    PubMed

    Hartmann, J-M; Boulet, C; Auwera, J Vander; El Hamzaoui, H; Capoen, B; Bouazaoui, M

    2014-02-14

    The infrared absorption in the fundamental band of CO gas confined in porous silica xerogel has been recorded at room temperature for pressures between about 5 and 920 hPa using a high resolution Fourier transform spectrometer. The widths of individual lines are determined from fits of measured spectra and compared with ab initio predictions obtained from requantized classical molecular dynamics simulations. Good agreement is obtained from the low pressure regime where the line shapes are governed by molecule-wall collisions to high pressures where the influence of molecule-molecule interactions dominates. These results, together with those obtained with a simple analytical model, indicate that both mechanisms contribute in a practically additive way to the observed linewidths. They also confirm that a single collision of a molecule with a wall changes its rotational state. These results are of interest for the determination of some characteristics of the opened porosity of porous materials through optical soundings.

  5. PRODUCTION OF CONSTRUCTION AGGREGATES FROM FLUE GAS DESULFURIZATION SLUDGE

    SciTech Connect

    M.M. Wu; D.C. McCoy; R.O. Scandrol; M.L. Fenger; J.A. Withum; R.M. Statnick

    2000-05-01

    The three main conclusions of this report are: (1) The pilot plant successfully demonstrated the continuous, fully-integrated, long-term process operation, including the mixing, pelletizing, and curing steps for aggregate production. The curing vessel, which was designed for the pilot plant test, was operated in a mass flow mode and performed well during pilot plant operation. (2) The pilot plant test demonstrated process flexibility. The same equipment was used to produce lightweight, medium-weight, and road aggregates. The only change was the mix formulation. Aggregates were produced from a variety of mix designs and from FGD sludge with solids concentrations between 45.0% and 56.7% and moisture contents between 55.0% and 43.3%. (3) The pilot plant provided operating data and experience to design and cost a commercial plant, which was not part of the cooperative agreement.

  6. Production of manufactured aggregates from flue gas desulfurization by-products

    SciTech Connect

    Wu, M.M.; McCoy, D.C.; Fenger, M.L.; Scandrol, R.O.; Winschel, R.A.; Withum, J.A.; Statnick, R.M.

    1999-07-01

    CONSOL R and D has developed a disk pelletization process to produce manufactured aggregates from the by-products of various technologies designed to reduce sulfur emissions produced from coal utilization. Aggregates have been produced from the by-products of the Coolside and LIMB sorbent injection, the fluidized-bed combustion (FBC), spray dryer absorption (SDA), and lime and limestone wet flue gas desulfurization (FGD) processes. The aggregates produced meet the general specifications for use as road aggregate in road construction and for use as lightweight aggregate in concrete masonry units. Small field demonstrations with 1200 lb to 5000 lb of manufactured aggregates were conducted using aggregates produced from FBC ash and lime wet FGD sludge in road construction and using aggregates made from SDA ash and lime wet FGD sludge to manufacture concrete blocks. The aggregates for this work were produced with a bench-scale (200--400 lb batch) unit. In 1999, CONSOL R and D constructed and operated a 500 lb/hr integrated, continuous pilot plant. A variety of aggregate products were produced from lime wet FGD sludge. The pilot plant test successfully demonstrated the continuous, integrated operation of the process. The pilot plant demonstration was a major step toward commercialization of manufactured aggregate production from FGD by-products. In this paper, progress made in the production of aggregates from dry FGD (Coolside, LIMB, SDA) and FBC by-products, and lime wet FGD sludge is discussed. The discussion covers bench-scale and pilot plant aggregate production and aggregate field demonstrations.

  7. Using Coupled Harmonic Oscillators to Model Some Greenhouse Gas Molecules

    SciTech Connect

    Go, Clark Kendrick C.; Maquiling, Joel T.

    2010-07-28

    Common greenhouse gas molecules SF{sub 6}, NO{sub 2}, CH{sub 4}, and CO{sub 2} are modeled as harmonic oscillators whose potential and kinetic energies are derived. Using the Euler-Lagrange equation, their equations of motion are derived and their phase portraits are plotted. The authors use these data to attempt to explain the lifespan of these gases in the atmosphere.

  8. Detection of individual gas molecules adsorbed on graphene.

    PubMed

    Schedin, F; Geim, A K; Morozov, S V; Hill, E W; Blake, P; Katsnelson, M I; Novoselov, K S

    2007-09-01

    The ultimate aim of any detection method is to achieve such a level of sensitivity that individual quanta of a measured entity can be resolved. In the case of chemical sensors, the quantum is one atom or molecule. Such resolution has so far been beyond the reach of any detection technique, including solid-state gas sensors hailed for their exceptional sensitivity. The fundamental reason limiting the resolution of such sensors is fluctuations due to thermal motion of charges and defects, which lead to intrinsic noise exceeding the sought-after signal from individual molecules, usually by many orders of magnitude. Here, we show that micrometre-size sensors made from graphene are capable of detecting individual events when a gas molecule attaches to or detaches from graphene's surface. The adsorbed molecules change the local carrier concentration in graphene one by one electron, which leads to step-like changes in resistance. The achieved sensitivity is due to the fact that graphene is an exceptionally low-noise material electronically, which makes it a promising candidate not only for chemical detectors but also for other applications where local probes sensitive to external charge, magnetic field or mechanical strain are required.

  9. Initial partition and aggregation of uncharged polyaromatic molecules at the oil-water interface: a molecular dynamics simulation study.

    PubMed

    Teklebrhan, Robel B; Ge, Lingling; Bhattacharjee, Subir; Xu, Zhenghe; Sjöblom, Johan

    2014-01-30

    Initial partitioning and aggregation of several uncharged polyaromatic (PA) molecules with the same polyaromatic core but different terminal moieties at oil-water interfaces from the bulk oil phase were studied by molecular dynamics simulation. The partition of the PA molecules between the bulk organic phase and oil-water interface was highly dependent on the terminal moiety structure of the PA molecules and aromaticity of the organic phase. The polarity ratio between the oil and water phases showed a significant influence on adsorption of the PA molecules at the oil-water interface. The presence of hydrophobic aromatic moieties in PA molecules hindered the adsorption process. Larger aromatic rings in PA molecules lowered the interfacial activity due to strong intermolecular π-π interactions and molecular aggregation in the bulk oil phase. The presence of a terminal carboxylic functional group on the side chain enhanced the adsorption of the PA molecules at the oil-water interface. The fused ring plane of the uncharged PA molecules was found to preferentially adsorb at the oil-water interface in a head-on or side-on orientation with the polyaromatic core staying in the nonaqueous phase (i.e., the principal plane of the molecule perpendicular to the oil-water interface). The results obtained from this study could provide a scientific direction for the design of proper chemical demulsifiers for PA molecule-mediated emulsions formed under specific process conditions of temperature, pressure, and pH.

  10. Cool Mist Scavenging of Gas-Phase Molecules.

    PubMed

    Wu, Pei-Chi; Dutkiewicz, Ewelina P; Urban, Pawel L

    2017-01-01

    The purpose of analytical extractions is to simplify sample matrix without losing analyte molecules. Here we present a technique of extracting volatile compounds by scavenging gas-phase molecules with tiny liquid droplets (<10 μm). A cool mist of the extracting solvent is generated by an ultrasonic transducer, transferred to the headspace of the sample chamber under atmospheric conditions, and pushed by a small pressure difference toward a condenser. By slowly passing over the sample, the microdroplets extract volatile species present in the sample headspace, and they coalesce in a cooled zone. The condensed liquid is collected for analysis by direct infusion mass spectrometry or chromatography coupled with mass spectrometry. Due to the high surface-to-volume ratio of the microdroplets, the mist depletes a great share of the volatile organics present in the headspace. Other advantages of cool mist scavenging include: selective extraction of gas-phase molecules, the extracting solvent can be miscible with the sample solvent, simplicity, high speed, and no requirement for heating that could potentially decompose the sample. In this study, cool mist scavenging was first tested on artificial samples containing esters. The relationship between the sample concentration and the extract concentration was verified theoretically and experimentally. Some of the possible confounding effects were tested and discussed. The technique was subsequently applied to qualitative analysis of selected complex samples in liquid and solid phase as well as an esterification reaction.

  11. Aggregation induced enhanced and exclusively highly Stokes shifted emission from an excited state intramolecular proton transfer exhibiting molecule.

    PubMed

    Behera, Santosh Kumar; Murkherjee, Anwesha; Sadhuragiri, G; Elumalai, Palani; Sathiyendiran, M; Kumar, Manishekhar; Mandal, Biman B; Krishnamoorthy, G

    2017-02-01

    The inner filter effect due to self-quenching dominates the normal emission of dyes at higher concentrations, which would limit their applications. Since normal emission was also observed with aggregation induced emission enhancement (AIEE) active excited state intramolecular proton transfer (ESIPT) exhibiting molecules, two new molecules are synthesized and studied to obtain normal emission free AIEE. The molecules are 4-(3-(benzo[d]thiazol-2-yl)-5-tert-butyl-4-hydroxybenzyl)-2-(benzo[d]thiazol-2-yl)-6-tert-butyl phenol (bis-HPBT) and its oxazole analogue (bis-HPBO). Of these molecules, bis-HPBT, which is weakly fluorescent in tetrahydrofuran solution, shows a sudden high enhancement in fluorescence upon addition of 70% water due to the formation of aggregates. Though the normal emission is also observed in tetrahydrofuran, it is completely eliminated in the aggregates, and the aggregates display exclusive tautomer emission. However, bis-HPBO does not emit such an exclusive tautomer emission in the water/tetrahydrofuran mixture. The enhancement in the fluorescence quantum yield of bis-HPBT in 70% water is ∼300 times higher than that in tetrahydrofuran. The modulated molecular structure of bis-HPBT is the cause of this outstanding AIEE. The observation of almost exclusive tautomer emission is a new additional advantage of AIEE from bis-HPBT over other ESIPT molecules. Since the tautomer emission is highly Stokes shifted, no overlap with the absorption spectrum occurs and therefore, the inner filter effect is averted. The aggregated structure acts as a good fluorescence chemosensor for metal ions as well as anions. The aggregated structure is cell permeable and can be used for cell imaging.

  12. Molecule formation in quasar broad-line cloud gas

    NASA Technical Reports Server (NTRS)

    Kallman, T.; Lepp, S.; Giovannoni, P.

    1987-01-01

    Models for the broad-line emitting clouds of quasars typically assume that the clouds have column densities of at most 10 to the 23rd/sq cm. The consequences of relaxing this assumption are examined, and it is shown that: (1) at slightly larger column densities the gas may cool to about 1000 K as a result of molecule formation; (2) in much of the molecule-forming region the temperature may have either of two values, about 1000 K or 6000-8000 K; (3) the strengths of most observable optical lines, including C II semiforbidden 2326-A lines and Fe II lines, are unaffected by such large column densities; and (4) lines from low-ionization species such as Na I are readily formed at large column densities. Observations of such lines provide evidence for large cloud column densities.

  13. The diffusion of individual molecules within a gas

    NASA Technical Reports Server (NTRS)

    Bird, G. A.

    1986-01-01

    The Direct Simulation Monte Carlo method is used to study the positional history of the individual molecules in a gas that is homogeneous at the macroscopic level and is in Maxwellian equilibrium at the microscopic level. The behavior at small times is characterized by 'persistence of velocity' effects, and a 'random walk' type of dispersal occurs over a longer timescale. It is shown that the rate of dispersal can be directly related to the self-diffusion coefficient. In addition, the diffusion coefficients are obtained directly from one-dimensional calculations, and the local Knudsen number at which the Chapman-Enskog theory breaks down is determined. Results are presented for both simple gases and gas mixtures.

  14. Monitoring of conditions inside gas aggregation cluster source during production of Ti/TiOx nanoparticles

    NASA Astrophysics Data System (ADS)

    Kousal, J.; Kolpaková, A.; Shelemin, A.; Kudrna, P.; Tichý, M.; Kylián, O.; Hanuš, J.; Choukourov, A.; Biederman, H.

    2017-10-01

    Gas aggregation sources are nowadays rather widely used in the research community for producing nanoparticles. However, the direct diagnostics of conditions inside the source are relatively scarce. In this work, we focused on monitoring the plasma parameters and the composition of the gas during the production of the TiOx nanoparticles. We studied the role of oxygen in the aggregation process and the influence of the presence of the particles on the plasma. The construction of the source allowed us to make a 2D map of the plasma parameters inside the source.

  15. High-Resolution Single-Molecule Fluorescence Imaging of Zeolite Aggregates within Real-Life Fluid Catalytic Cracking Particles**

    PubMed Central

    Ristanović, Zoran; Kerssens, Marleen M; Kubarev, Alexey V; Hendriks, Frank C; Dedecker, Peter; Hofkens, Johan; Roeffaers, Maarten B J; Weckhuysen, Bert M

    2015-01-01

    Fluid catalytic cracking (FCC) is a major process in oil refineries to produce gasoline and base chemicals from crude oil fractions. The spatial distribution and acidity of zeolite aggregates embedded within the 50–150 μm-sized FCC spheres heavily influence their catalytic performance. Single-molecule fluorescence-based imaging methods, namely nanometer accuracy by stochastic chemical reactions (NASCA) and super-resolution optical fluctuation imaging (SOFI) were used to study the catalytic activity of sub-micrometer zeolite ZSM-5 domains within real-life FCC catalyst particles. The formation of fluorescent product molecules taking place at Brønsted acid sites was monitored with single turnover sensitivity and high spatiotemporal resolution, providing detailed insight in dispersion and catalytic activity of zeolite ZSM-5 aggregates. The results point towards substantial differences in turnover frequencies between the zeolite aggregates, revealing significant intraparticle heterogeneities in Brønsted reactivity. PMID:25504139

  16. Molecular Dynamics Simulation of Reflected Gas Molecules on Water Adsorbed Surface

    NASA Astrophysics Data System (ADS)

    Takeuchi, Hideki; Yamamoto, Kyoji; Hyakutake, Toru

    2008-12-01

    The Couette flow of a rarefied argon gas between two platinum walls is considered to investigate the characteristics of the reflected gas molecule at a physically adsorbed surface by H2O molecules. The analysis is based on the molecular dynamics (MD) method for the interaction of gas molecules with the wall surface together with the direct simulation Monte-Carlo (DSMC) method for the motion of gas molecule. The accommodation coefficients are obtained. The flow velocity distribution between two walls and the velocity distribution function of the reflected molecule are also obtained. It is found that the Maxwell type reflection condition describes the distribution function of the reflected molecules well.

  17. Inhibition of polyglutamine aggregation by SIMILAR huntingtin N-terminal sequences: Prospective molecules for preclinical evaluation in Huntington's disease.

    PubMed

    Burra, Gunasekhar; Thakur, Ashwani Kumar

    2017-04-12

    The mutant huntingtin protein (mHtt) fragments with expanded polyglutamine sequence forms microscopically visible aggregates in neurons, a hallmark of Huntington's disease (HD). The aggregation process and aggregates are possible targets of therapeutic intervention in HD. Due to lack of treatment and cure, the patients die within 15-20 years after the disease onset. Therefore, discovering therapeutic molecules that may either inhibit the aggregation mechanism or downregulate the toxic effects of mhtt are highly needed. The present study demonstrates the design and use of peptide inhibitors based on the role played by the N-terminal seventeen amino acid sequence (NT17 ) of huntingtin fragment in its aggregation. Fug-NT17 (Fugu), Xen-NT17 (Xenopus), Dro-NT17 (Drosophila), Aib-NT17 , and Pro-NT17 sequences were tested for their ability to inhibit aggregation. Among them, the first three are the sequence variants of human NT17 from evolutionarily distant organisms and the latter two are the analogs of human NT17 containing aminoisobutyric acid (Aib) and proline (Pro). Four out of five inhibited the aggregation of huntingtin fragment, NT17 Q35 P10 K2 polypeptide. Data indicates that the physicochemical properties of the inhibitors play a crucial role in exhibiting the inhibitory effect. These inhibitors can be tested in cell and animal models for the preclinical evaluation in the treating of HD. This article is protected by copyright. All rights reserved.

  18. Bacteriochlorophyll aggregates self-assembled on functionalized gold nanorod cores as mimics of photosynthetic chlorosomal antennae: a single molecule study.

    PubMed

    Furumaki, Shu; Vacha, Frantisek; Hirata, Shuzo; Vacha, Martin

    2014-03-25

    We prepare artificial aggregates that mimic the structure and function of natural chlorosomal light harvesting complexes of green photosynthetic bacteria. Gold nanorods functionalized with hydroxyl groups and immobilized on a substrate serve as cores for the growth of bacteriochlorophyll (BChl) aggregates from a buffer solution. The BChl pigments form large self-assembled aggregate particles with sizes more than twice that of natural chlorosomes. The size is controllable by the aggregation time. The aggregates are characterized on a single-particle level by atomic force microscopy, electron microscopy, and single-molecule spectroscopy. The absorption and fluorescence spectral properties which reflect the molecular level arrangement of the BChl aggregates closely resemble those of the natural chlorosomes of the photosynthetic bacterium Chlorobaculum tepidum. On the other hand, the results of linear dichroism and circular dichroism are different from those of the chlorosomes and indicate a different mesoscopic structure for the artificial aggregates. These results emphasize the structural role played by the baseplate pigment-protein complex in natural chlorosomes.

  19. Complex organic molecules in strongly UV-irradiated gas

    NASA Astrophysics Data System (ADS)

    Cuadrado, S.; Goicoechea, J. R.; Cernicharo, J.; Fuente, A.; Pety, J.; Tercero, B.

    2017-07-01

    We investigate the presence of complex organic molecules (COMs) in strongly UV-irradiated interstellar molecular gas. We have carried out a complete millimetre (mm) line survey using the IRAM 30 m telescope towards the edge of the Orion Bar photodissociation region (PDR), close to the H2 dissociation front, a position irradiated by a very intense far-UV (FUV) radiation field. These observations have been complemented with 8.5'' resolution maps of the H2CO JKa,Kc = 51,5 → 41,4 and C18O J = 3 → 2 emission at 0.9 mm. Despite being a harsh environment, we detect more than 250 lines from COMs and related precursors: H2CO, CH3OH, HCO, H2CCO, CH3CHO, H2CS, HCOOH, CH3CN, CH2NH, HNCO, H213CO, and HC3N (in decreasing order of abundance). For each species, the large number of detected lines allowed us to accurately constrain their rotational temperatures (Trot) and column densities (N). Owing to subthermal excitation and intricate spectroscopy of some COMs (symmetric- and asymmetric-top molecules such as CH3CN and H2CO, respectively), a correct determination of N and Trot requires building rotational population diagrams of their rotational ladders separately. The inferred column densities are in the 1011-1013 cm-2 range. We also provide accurate upper limit abundances for chemically related molecules that might have been expected, but are not conclusively detected at the edge of the PDR (HDCO, CH3O, CH3NC, CH3CCH, CH3OCH3, HCOOCH3, CH3CH2OH, CH3CH2CN, and CH2CHCN). A non-thermodynamic equilibrium excitation analysis for molecules with known collisional rate coefficients suggests that some COMs arise from different PDR layers but we cannot resolve them spatially. In particular, H2CO and CH3CN survive in the extended gas directly exposed to the strong FUV flux (Tk = 150-250 K and Td≳ 60 K), whereas CH3OH only arises from denser and cooler gas clumps in the more shielded PDR interior (Tk = 40-50 K). The non-detection of HDCO towards the PDR edge is consistent with the

  20. Smart-aggregation imaging for single molecule localisation with SPAD cameras

    NASA Astrophysics Data System (ADS)

    Gyongy, Istvan; Davies, Amy; Dutton, Neale A. W.; Duncan, Rory R.; Rickman, Colin; Henderson, Robert K.; Dalgarno, Paul A.

    2016-11-01

    Single molecule localisation microscopy (SMLM) has become an essential part of the super-resolution toolbox for probing cellular structure and function. The rapid evolution of these techniques has outstripped detector development and faster, more sensitive cameras are required to further improve localisation certainty. Single-photon avalanche photodiode (SPAD) array cameras offer single-photon sensitivity, very high frame rates and zero readout noise, making them a potentially ideal detector for ultra-fast imaging and SMLM experiments. However, performance traditionally falls behind that of emCCD and sCMOS devices due to lower photon detection efficiency. Here we demonstrate, both experimentally and through simulations, that the sensitivity of a binary SPAD camera in SMLM experiments can be improved significantly by aggregating only frames containing signal, and that this leads to smaller datasets and competitive performance with that of existing detectors. The simulations also indicate that with predicted future advances in SPAD camera technology, SPAD devices will outperform existing scientific cameras when capturing fast temporal dynamics.

  1. Smart-aggregation imaging for single molecule localisation with SPAD cameras.

    PubMed

    Gyongy, Istvan; Davies, Amy; Dutton, Neale A W; Duncan, Rory R; Rickman, Colin; Henderson, Robert K; Dalgarno, Paul A

    2016-11-23

    Single molecule localisation microscopy (SMLM) has become an essential part of the super-resolution toolbox for probing cellular structure and function. The rapid evolution of these techniques has outstripped detector development and faster, more sensitive cameras are required to further improve localisation certainty. Single-photon avalanche photodiode (SPAD) array cameras offer single-photon sensitivity, very high frame rates and zero readout noise, making them a potentially ideal detector for ultra-fast imaging and SMLM experiments. However, performance traditionally falls behind that of emCCD and sCMOS devices due to lower photon detection efficiency. Here we demonstrate, both experimentally and through simulations, that the sensitivity of a binary SPAD camera in SMLM experiments can be improved significantly by aggregating only frames containing signal, and that this leads to smaller datasets and competitive performance with that of existing detectors. The simulations also indicate that with predicted future advances in SPAD camera technology, SPAD devices will outperform existing scientific cameras when capturing fast temporal dynamics.

  2. Smart-aggregation imaging for single molecule localisation with SPAD cameras

    PubMed Central

    Gyongy, Istvan; Davies, Amy; Dutton, Neale A. W.; Duncan, Rory R.; Rickman, Colin; Henderson, Robert K.; Dalgarno, Paul A.

    2016-01-01

    Single molecule localisation microscopy (SMLM) has become an essential part of the super-resolution toolbox for probing cellular structure and function. The rapid evolution of these techniques has outstripped detector development and faster, more sensitive cameras are required to further improve localisation certainty. Single-photon avalanche photodiode (SPAD) array cameras offer single-photon sensitivity, very high frame rates and zero readout noise, making them a potentially ideal detector for ultra-fast imaging and SMLM experiments. However, performance traditionally falls behind that of emCCD and sCMOS devices due to lower photon detection efficiency. Here we demonstrate, both experimentally and through simulations, that the sensitivity of a binary SPAD camera in SMLM experiments can be improved significantly by aggregating only frames containing signal, and that this leads to smaller datasets and competitive performance with that of existing detectors. The simulations also indicate that with predicted future advances in SPAD camera technology, SPAD devices will outperform existing scientific cameras when capturing fast temporal dynamics. PMID:27876857

  3. Aggregation and sedimentation in gas-fluidized beds of cohesive powders.

    PubMed

    Castellanos, A; Valverde, J M; Quintanilla, M A

    2001-10-01

    We present measurements on the settling velocity of gas-fluidized beds of fine cohesive powders. In the solidlike regime (solid volume fraction straight phi>straight phi(c)) particles are static, sustained by enduring contacts. The settling is hindered by interparticle contacts and is a very slow process. In the fluidlike regime (straight phiaggregates, and for this reason the sedimentation velocity exceeds the predicted value by empirical or theoretical laws on the settling of individual particles. We use an extension of the Richardson-Zaki empirical law for the settling of aggregates in the fluidlike regime to fit the experimental data. Aggregates are characterized by the number of aggregated particles N and by an effective radius R. The trend followed by these parameters with particle size is confirmed by direct visualization of the aggregates, and shows that cohesive effects become important when the adhesion force between particles is above particle weight. Results show that aggregates form open structures with a fractal dimension close to the predicted one in the diffusion-limited-aggregation model (D=2.5).

  4. Thermodynamic properties of small aggregates of rare-gas atoms

    NASA Technical Reports Server (NTRS)

    Etters, R. D.; Kaelberer, J.

    1975-01-01

    The present work reports on the equilibrium thermodynamic properties of small clusters of xenon, krypton, and argon atoms, determined from a biased random-walk Monte Carlo procedure. Cluster sizes ranged from 3 to 13 atoms. Each cluster was found to have an abrupt liquid-gas phase transition at a temperature much less than for the bulk material. An abrupt solid-liquid transition is observed for thirteen- and eleven-particle clusters. For cluster sizes smaller than 11, a gradual transition from solid to liquid occurred over a fairly broad range of temperatures. Distribution of number of bond lengths as a function of bond length was calculated for several systems at various temperatures. The effects of box boundary conditions are discussed. Results show the importance of a correct description of boundary conditions. A surprising result is the slow rate at which system properties approach bulk behavior as cluster size is increased.

  5. A lattice-gas model for amyloid fibril aggregation

    PubMed Central

    Hong, Liu; Qi, Xianghong; Zhang, Yang

    2012-01-01

    A simple lattice-gas model, with two fundamental energy terms —elongation and nucleation effects, is proposed for understanding the mechanisms of amyloid fibril formation. Based on the analytical solution and Monte Carlo simulation of 1D system, we have thoroughly explored the dependence of mass concentration, number concentration of amyloid filaments and the lag-time on the initial protein concentration, the critical nucleus size, the strengths of nucleation and elongation effects, respectively. We also found that thickening process (self-association of filaments into multi-strand fibrils) is not essential for the modeling of amyloid filaments through simulations on 2D lattice. Compared with the kinetic model recently proposed by Knowles et al., highly quantitative consistency of two models in the calculation of mass fraction of filaments is found. Moreover our model can generate a better prediction on the number fraction, which is closer to experimental values when the elongation strength gets stronger. PMID:23275684

  6. A Fragment-Based Method of Creating Small-Molecule Libraries to Target the Aggregation of Intrinsically Disordered Proteins.

    PubMed

    Joshi, Priyanka; Chia, Sean; Habchi, Johnny; Knowles, Tuomas P J; Dobson, Christopher M; Vendruscolo, Michele

    2016-03-14

    The aggregation process of intrinsically disordered proteins (IDPs) has been associated with a wide range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Currently, however, no drug in clinical use targets IDP aggregation. To facilitate drug discovery programs in this important and challenging area, we describe a fragment-based approach of generating small-molecule libraries that target specific IDPs. The method is based on the use of molecular fragments extracted from compounds reported in the literature to inhibit of the aggregation of IDPs. These fragments are used to screen existing large generic libraries of small molecules to form smaller libraries specific for given IDPs. We illustrate this approach by describing three distinct small-molecule libraries to target, Aβ, tau, and α-synuclein, which are three IDPs implicated in Alzheimer's and Parkinson's diseases. The strategy described here offers novel opportunities for the identification of effective molecular scaffolds for drug discovery for neurodegenerative disorders and to provide insights into the mechanism of small-molecule binding to IDPs.

  7. Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles

    NASA Astrophysics Data System (ADS)

    Ebrahimi, Ali; Or, Dani

    2016-04-01

    Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Mechanistic models of microbial processes in unsaturated aggregate pore networks revealed dynamic interplay between oxic and anoxic microsites that are jointly shaped by hydration and by aerobic and anaerobic microbial communities. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support significant anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3-D angular pore networks with profiles of water, carbon, and oxygen that vary with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain biogeochemical fluxes over the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of interest for hydrological and climate models.

  8. Adsorption of two gas molecules at a single metal site in a metal–organic framework

    SciTech Connect

    Runčevski, Tomče; Kapelewski, Matthew T.; Torres-Gavosto, Rodolfo M.; Tarver, Jacob D.; Brown, Craig M.; Long, Jeffrey R.

    2016-01-01

    One strategy to markedly increase the gas storage capacity of metal-organic frameworks is to introduce coordinatively-unsaturated metal centers capable of binding multiple gas molecules. Herein, we provide an initial demonstration that a single metal site within a framework can support the terminal coordination of two gas molecules--specifically hydrogen, methane, or carbon dioxide.

  9. Buffer Gas Cooled Molecule Source for Cpmmw Spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhou, Yan; Grimes, David; Barnum, Timothy J.; Klein, Ethan; Field, Robert W.

    2014-06-01

    We have built a new molecular beam source that implements 20 K Neon buffer gas cooling for the study of the spectra of small molecules. In particular, laser ablation of BaF2 pellets has been optimized to produce a molecular beam of BaF with a number density more than 100 times greater than what we have previously obtained from a typical Smalley-type photoablation supersonic beam source. Moreover, the forward beam velocity of 150 m/s in our apparatus represents an approximate 10-fold reduction, improving spectroscopic resolution from 500 kHz to better than 50 kHz at 100 GHz in a chirped-pulse millimeter-wave experiment in which resolution is limited by Doppler broadening. Novel improvements in our buffer gas source and advantages for CPmmW spectroscopy studies will be discussed. We thank David Patterson, John Barry, John Doyle, and David DeMille for help in the design of our source.

  10. Method of monitoring photoactive organic molecules in-situ during gas-phase deposition of the photoactive organic molecules

    DOEpatents

    Forrest, Stephen R.; Vartanian, Garen; Rolin, Cedric

    2015-06-23

    A method for in-situ monitoring of gas-phase photoactive organic molecules in real time while depositing a film of the photoactive organic molecules on a substrate in a processing chamber for depositing the film includes irradiating the gas-phase photoactive organic molecules in the processing chamber with a radiation from a radiation source in-situ while depositing the film of the one or more organic materials and measuring the intensity of the resulting photoluminescence emission from the organic material. One or more processing parameters associated with the deposition process can be determined from the photoluminescence intensity data in real time providing useful feedback on the deposition process.

  11. Detection of Mutant Huntingtin Aggregation Conformers and Modulation of SDS-Soluble Fibrillar Oligomers by Small Molecules

    PubMed Central

    Sontag, Emily Mitchell; Lotz, Gregor P.; Yang, Guocheng; Sontag, Christopher J.; Cummings, Brian J.; Glabe, Charles G.; Muchowski, Paul J.; Thompson, Leslie Michels

    2012-01-01

    The Huntington’s disease (HD) mutation leads to a complex process of Huntingtin (Htt) aggregation into multimeric species that eventually form visible inclusions in cytoplasm, nuclei and neuronal processes. One hypothesis is that smaller, soluble forms of amyloid proteins confer toxic effects and contribute to early cell dysfunction. However, analysis of mutant Htt aggregation intermediates to identify conformers that may represent toxic forms of the protein and represent potential drug targets remains difficult. We performed a detailed analysis of aggregation conformers in multiple in vitro, cell and ex vivo models of HD. Conformation-specific antibodies were used to identify and characterize aggregation species, allowing assessment of multiple conformers present during the aggregation process. Using a series of assays together with these antibodies, several forms could be identified. Fibrillar oligomers, defined as having a β-sheet rich conformation, are observed in vitro using recombinant protein and in protein extracts from cells in culture or mouse brain and shown to be globular, soluble and non-sedimentable structures. Compounds previously described to modulate visible inclusion body formation and reduce toxicity in HD models were also tested and consistently found to alter the formation of fibrillar oligomers. Interestingly, these compounds did not alter the rate of visible inclusion formation, indicating that fibrillar oligomers are not necessarily the rate limiting step of inclusion body formation. Taken together, we provide insights into the structure and formation of mutant Htt fibrillar oligomers that are modulated by small molecules with protective potential in HD models. PMID:24086178

  12. A Theoretical Study of some Rheological Properties of the Aggregation of the Molecules Deoxy- Hemoglobin S

    NASA Astrophysics Data System (ADS)

    Mensah, Francis; Grant, Julius; Thorpe, Arthur

    2010-02-01

    Sickle cell disease is a serious public health problem that affects many people worldwide. In this paper, the Langevin equation is used for hemoglobin's aggregation in sickle cell anemia. Several parameters are explored such as the time-dependent deformation of the aggregates whose plot gives a sigmoid, the time-dependent expressions obtained for the coefficient of viscosity and the elastic modulus which characterize the aggregation of the sickle hemoglobin. Other properties such as the viscoelastic and the elasto-thixotropic properties of the sickle hemoglobin polymer are also described. An attempt is made to approach the polymerization process in terms of a dynamical system. )

  13. The Effect of Thermal Convection on Earth-Atmosphere CO2 Gas Exchange in Aggregated Soil

    NASA Astrophysics Data System (ADS)

    Ganot, Y.; Weisbrod, N.; Dragila, M. I.

    2011-12-01

    Gas transport in soils and surface-atmosphere gas exchange are important processes that affect different aspects of soil science such as soil aeration, nutrient bio-availability, sorption kinetics, soil and groundwater pollution and soil remediation. Diffusion and convection are the two main mechanisms that affect gas transport, fate and emissions in the soils and in the upper vadose zone. In this work we studied CO2 soil-atmosphere gas exchange under both day-time and night-time conditions, focusing on the impact of thermal convection (TCV) during the night. Experiments were performed in a climate-controlled laboratory. One meter long columns were packed with matrix of different grain size (sand, gravel and soil aggregates). Air with 2000 ppm CO2 was injected into the bottom of the columns and CO2 concentration within the columns was continuously monitored by an Infra Red Gas Analyzer. Two scenarios were compared for each soil: (1) isothermal conditions, representing day time conditions; and (2) thermal gradient conditions, i.e., atmosphere colder than the soil, representing night time conditions. Our results show that under isothermal conditions, diffusion is the major mechanism for surface-atmosphere gas exchange for all grain sizes; while under night time conditions the prevailing mechanism is dependent on the air permeability of the matrix: for sand and gravel it is diffusion, and for soil aggregates it is TCV. Calculated CO2 flux for the soil aggregates column shows that the TCV flux was three orders of magnitude higher than the diffusive flux.

  14. A gas aggregation source for the production of heterogeneous molecular clusters

    NASA Astrophysics Data System (ADS)

    Braud, I.; Zamith, S.; L'Hermite, J.-M.

    2017-04-01

    We present the design of a versatile gas aggregation source that allows producing molecular beams of charged clusters containing a controlled amount of chosen impurities. Several examples of clusters production using this source characterized by time of flight mass spectrometry are presented here. We demonstrate the source ability to produce homogeneous clusters, such as pure protonated water and alcohol clusters, as well as inhomogeneous ones such as water clusters containing a few units of uracil, glycine, sulfuric acid, or pyrene.

  15. High-resolution single-molecule fluorescence imaging of zeolite aggregates within real-life fluid catalytic cracking particles.

    PubMed

    Ristanović, Zoran; Kerssens, Marleen M; Kubarev, Alexey V; Hendriks, Frank C; Dedecker, Peter; Hofkens, Johan; Roeffaers, Maarten B J; Weckhuysen, Bert M

    2015-02-02

    Fluid catalytic cracking (FCC) is a major process in oil refineries to produce gasoline and base chemicals from crude oil fractions. The spatial distribution and acidity of zeolite aggregates embedded within the 50-150 μm-sized FCC spheres heavily influence their catalytic performance. Single-molecule fluorescence-based imaging methods, namely nanometer accuracy by stochastic chemical reactions (NASCA) and super-resolution optical fluctuation imaging (SOFI) were used to study the catalytic activity of sub-micrometer zeolite ZSM-5 domains within real-life FCC catalyst particles. The formation of fluorescent product molecules taking place at Brønsted acid sites was monitored with single turnover sensitivity and high spatiotemporal resolution, providing detailed insight in dispersion and catalytic activity of zeolite ZSM-5 aggregates. The results point towards substantial differences in turnover frequencies between the zeolite aggregates, revealing significant intraparticle heterogeneities in Brønsted reactivity. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Nanomolar oligomerization and selective co-aggregation of α-synuclein pathogenic mutants revealed by single-molecule fluorescence

    PubMed Central

    Sierecki, Emma; Giles, Nichole; Bowden, Quill; Polinkovsky, Mark E.; Steinbeck, Janina; Arrioti, Nicholas; Rahman, Diya; Bhumkar, Akshay; Nicovich, Philip R.; Ross, Ian; Parton, Robert G.; Böcking, Till; Gambin, Yann

    2016-01-01

    Protein aggregation is a hallmark of many neurodegenerative diseases, notably Alzheimer’s and Parkinson’s disease. Parkinson’s disease is characterized by the presence of Lewy bodies, abnormal aggregates mainly composed of α-synuclein. Moreover, cases of familial Parkinson’s disease have been linked to mutations in α-synuclein. In this study, we compared the behavior of wild-type (WT) α-synuclein and five of its pathological mutants (A30P, E46K, H50Q, G51D and A53T). To this end, single-molecule fluorescence detection was coupled to cell-free protein expression to measure precisely the oligomerization of proteins without purification, denaturation or labelling steps. In these conditions, we could detect the formation of oligomeric and pre-fibrillar species at very short time scale and low micromolar concentrations. The pathogenic mutants surprisingly segregated into two classes: one group forming large aggregates and fibrils while the other tending to form mostly oligomers. Strikingly, co-expression experiments reveal that members from the different groups do not generally interact with each other, both at the fibril and monomer levels. Together, this data paints a completely different picture of α-synuclein aggregation, with two possible pathways leading to the development of fibrils. PMID:27892477

  17. Nanomolar oligomerization and selective co-aggregation of α-synuclein pathogenic mutants revealed by single-molecule fluorescence.

    PubMed

    Sierecki, Emma; Giles, Nichole; Bowden, Quill; Polinkovsky, Mark E; Steinbeck, Janina; Arrioti, Nicholas; Rahman, Diya; Bhumkar, Akshay; Nicovich, Philip R; Ross, Ian; Parton, Robert G; Böcking, Till; Gambin, Yann

    2016-11-28

    Protein aggregation is a hallmark of many neurodegenerative diseases, notably Alzheimer's and Parkinson's disease. Parkinson's disease is characterized by the presence of Lewy bodies, abnormal aggregates mainly composed of α-synuclein. Moreover, cases of familial Parkinson's disease have been linked to mutations in α-synuclein. In this study, we compared the behavior of wild-type (WT) α-synuclein and five of its pathological mutants (A30P, E46K, H50Q, G51D and A53T). To this end, single-molecule fluorescence detection was coupled to cell-free protein expression to measure precisely the oligomerization of proteins without purification, denaturation or labelling steps. In these conditions, we could detect the formation of oligomeric and pre-fibrillar species at very short time scale and low micromolar concentrations. The pathogenic mutants surprisingly segregated into two classes: one group forming large aggregates and fibrils while the other tending to form mostly oligomers. Strikingly, co-expression experiments reveal that members from the different groups do not generally interact with each other, both at the fibril and monomer levels. Together, this data paints a completely different picture of α-synuclein aggregation, with two possible pathways leading to the development of fibrils.

  18. Analysis of the Molecules Structure and Vertical Electron Affinity of Organic Gas Impact on Electric Strength

    NASA Astrophysics Data System (ADS)

    Jiao, Juntao; Xiao, Dengming; Zhao, Xiaoling; Deng, Yunkun

    2016-05-01

    It is necessary to find an efficient selection method to pre-analyze the gas electric strength from the perspective of molecule structure and the properties for finding the alternative gases to sulphur hexafluoride (SF6). As the properties of gas are determined by the gas molecule structure, the research on the relationship between the gas molecule structure and the electric strength can contribute to the gas pre-screening and new gas development. In this paper, we calculated the vertical electron affinity, molecule orbits distribution and orbits energy of gas molecules by the means of density functional theory (DFT) for the typical structures of organic gases and compared their electric strengths. By this method, we find part of the key properties of the molecule which are related to the electric strength, including the vertical electron affinity, the lowest unoccupied molecule orbit (LUMO) energy, molecule orbits distribution and negative-ion system energy. We also listed some molecule groups such as unsaturated carbons double bonds (C=C) and carbonitrile bonds (C≡N) which have high electric strength theoretically by this method. supported by National Natural Science Foundation of China (Nos. 51177101 and 51337006)

  19. Tuning morphology and fluorescence of aggregated nanostructures of derived perylene diimide molecules.

    PubMed

    He, Xiaorong; Zhou, Weidong; Li, Yuliang; Liu, Xiaofeng; Li, Cuihong; Liu, Huibiao; Zhu, Daoben

    2008-04-01

    In this paper, we report on the self-assembly of water-soluble N,N'-di(N,N'-dimethyl-dodecane-1, 12-diamide)-perylene-3,4,9,10-tetracarboxylic diimide (PDDoAM) in formic acid and chloride salts for producing varied nano-aggregates with different optical properties. Interestingly, the self-assembly can lead to nanocubic, microsheet and "tower-like" nanostructures respectively, as demonstrated by Scanning Electron Microscopy (SEM) images. The optical properties of molecular aggregates were investigated by means of Confocal Raman Microscopy, indicating the morphologies and fluorescence of these nanomaterials are dependent on acids, acid concentrations and casting methods.

  20. Collision cross section calculations for polyatomic ions considering rotating diatomic/linear gas molecules

    SciTech Connect

    Larriba-Andaluz, Carlos Hogan, Christopher J.

    2014-11-21

    Structural characterization of ions in the gas phase is facilitated by measurement of ion collision cross sections (CCS) using techniques such as ion mobility spectrometry. Further information is gained from CCS measurement when comparison is made between measurements and accurately predicted CCSs for model ion structures and the gas in which measurements are made. While diatomic gases, namely molecular nitrogen and air, are being used in CCS measurement with increasingly prevalency, the majority of studies in which measurements are compared to predictions use models in which gas molecules are spherical or non-rotating, which is not necessarily appropriate for diatomic gases. Here, we adapt a momentum transfer based CCS calculation approach to consider rotating, diatomic gas molecule collisions with polyatomic ions, and compare CCS predictions with a diatomic gas molecule to those made with a spherical gas molecular for model spherical ions, tetra-alkylammonium ions, and multiply charged polyethylene glycol ions. CCS calculations are performed using both specular-elastic and diffuse-inelastic collisions rules, which mimic negligible internal energy exchange and complete thermal accommodation, respectively, between gas molecule and ion. The influence of the long range ion-induced dipole potential on calculations is also examined with both gas molecule models. In large part we find that CCSs calculated with specular-elastic collision rules decrease, while they increase with diffuse-inelastic collision rules when using diatomic gas molecules. Results clearly show the structural model of both the ion and gas molecule, the potential energy field between ion and gas molecule, and finally the modeled degree of kinetic energy exchange between ion and gas molecule internal energy are coupled to one another in CCS calculations, and must be considered carefully to obtain results which agree with measurements.

  1. Collision cross section calculations for polyatomic ions considering rotating diatomic/linear gas molecules.

    PubMed

    Larriba-Andaluz, Carlos; Hogan, Christopher J

    2014-11-21

    Structural characterization of ions in the gas phase is facilitated by measurement of ion collision cross sections (CCS) using techniques such as ion mobility spectrometry. Further information is gained from CCS measurement when comparison is made between measurements and accurately predicted CCSs for model ion structures and the gas in which measurements are made. While diatomic gases, namely molecular nitrogen and air, are being used in CCS measurement with increasingly prevalency, the majority of studies in which measurements are compared to predictions use models in which gas molecules are spherical or non-rotating, which is not necessarily appropriate for diatomic gases. Here, we adapt a momentum transfer based CCS calculation approach to consider rotating, diatomic gas molecule collisions with polyatomic ions, and compare CCS predictions with a diatomic gas molecule to those made with a spherical gas molecular for model spherical ions, tetra-alkylammonium ions, and multiply charged polyethylene glycol ions. CCS calculations are performed using both specular-elastic and diffuse-inelastic collisions rules, which mimic negligible internal energy exchange and complete thermal accommodation, respectively, between gas molecule and ion. The influence of the long range ion-induced dipole potential on calculations is also examined with both gas molecule models. In large part we find that CCSs calculated with specular-elastic collision rules decrease, while they increase with diffuse-inelastic collision rules when using diatomic gas molecules. Results clearly show the structural model of both the ion and gas molecule, the potential energy field between ion and gas molecule, and finally the modeled degree of kinetic energy exchange between ion and gas molecule internal energy are coupled to one another in CCS calculations, and must be considered carefully to obtain results which agree with measurements.

  2. Scattering properties of gas molecules on self-assembled monolayers using molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Takeuchi, Hideki

    2016-11-01

    The scattering properties of argon gas molecules on the SAM (self-assembled monolayer) surface which consists of 1-propanethiol molecules chemically adsorbed on a gold surface have been investigated by using the molecular dynamics method. The trapping probability, the angular distribution and the angular scattering distribution for the gas molecule have been obtained for various incident energies and angles. It is shown that the trapping probability decreases with increasing the incident energy. The angular distribution for small incident angle is almost close to the cosine distribution. In addition, the partial accommodation coefficients of tangential momentum and energy for gas molecules are discussed.

  3. Trehalose impairs aggregation of PrPSc molecules and protects prion-infected cells against oxidative damage.

    PubMed

    Béranger, Florence; Crozet, Carole; Goldsborough, Andrew; Lehmann, Sylvain

    2008-09-12

    Neurodegenerative disorders such as Alzheimer's, Huntington's, and prion diseases are characterized by abnormal protein deposits in the brain of affected patients. In prion diseases, a key event in the pathogenesis is the conversion of the normal prion protein (PrP(c)) into abnormal protease resistant PrP(Sc) deposits, a phenomenon associated with a higher sensitivity to oxidative stress in vitro. In cellular models of Alzheimer and Huntington diseases, the disaccharide trehalose has been shown to be effective in inhibiting huntingtin and Abeta peptide aggregates and reducing their associated toxicity. We show in this study that trehalose treatment of prion-infected cells decreases the size of de novo produced PrP(Sc) aggregates and modify their subcellular localization. Despite the fact that trehalose does not modify the protease resistance properties of PrP(Sc) molecules, it significantly protects prion-infected cells from induced oxidative damage, suggesting that this compound is of therapeutic interest.

  4. Co-CoO nanoparticles prepared by reactive gas-phase aggregation

    NASA Astrophysics Data System (ADS)

    González, J. A.; Andrés, J. P.; De Toro, J. A.; Muñiz, P.; Muñoz, T.; Crisan, O.; Binns, C.; Riveiro, J. M.

    2009-11-01

    The technique of gas-phase aggregation has been used to prepare partially oxidized Co nanoparticles films by allowing a controlled flow of oxygen gas into the aggregation zone. This method differs from those previously reported, that is, the passivation of a beam of preformed particles in a secondary chamber and the conventional (low Ar pressure) reactive sputtering of Co to produce Co-CoO composite films. Transmission electron microscopy shows that the mean size of the particles is about 6 nm. For sufficiently high oxygen pressures, the nanoparticles films become super-paramagnetic at room temperature. X-ray diffraction patterns display reflections corresponding to fcc Co and fcc CoO phases, with an increasing dominance of the latter upon increasing the oxygen pressure in the aggregation zone, which is consistent with the observed reduction in saturation magnetization. The cluster films assembled with particles grown under oxygen in the condensation zone exhibit exchange-bias fields (about 8 kOe at 20 K) systematically higher than those measured for Co-CoO core-shell nanoparticles prepared by oxidizing preformed particles in the deposition chamber, which we attribute, in the light of results from annealing experiments, to a higher ferromagnetic-antiferromagnetic (Co-CoO) interface density.

  5. Investigation of the bistability in J aggregates upon resonant optical excitation with inclusion of pair correlations between molecules

    NASA Astrophysics Data System (ADS)

    Nesterov, L. A.; Rosanov, N. N.

    2016-09-01

    A theory of resonant interaction with radiation of J aggregates based on chains of two-level molecules coupled by the retarded dipole‒dipole interaction has been developed. The effect of pair correlations between the chain molecules on the bistable response of this system under the influence of external resonant radiation has been investigated within the homogeneous chain model. Traditionally, these systems have been described using single-particle density matrices corresponding to each molecule. In this description, twoparticle interactions are represented in the factorized form and do not include correlations between the interacting molecules. In this study, the correlation corrections have been estimated taking into account the influence of only the nearest neighbors, while their values have found to be of the same order of magnitude as the factorized two-particle expectation values for which these corrections have been calculated. As a result, the dipole‒dipole interaction of a particular molecule with the nearest neighbors is so strong that the description of this interaction in the factorized form becomes inappropriate and can be used only for a qualitative analysis of the response of the chain. In order to obtain correct quantitative characteristics, it is necessary to abandon the factorization of the two-particle expectation values, at least for nearest neighbors.

  6. A Piezochromic Dysprosium(III) Single-Molecule Magnet Based on an Aggregation-Induced-Emission-Active Tetraphenylethene Derivative Ligand.

    PubMed

    Chen, Wen-Bin; Chen, Yan-Cong; Liu, Jun-Liang; Jia, Jian-Hua; Wang, Long-Fei; Li, Quan-Wen; Tong, Ming-Liang

    2017-08-07

    A bifunctional dysprosium(III) dimer, [Dy2(HTPEIP(OMe))2(OAc)4(NO3)2] (1), comprising an AIE-active (AIE = aggregation-induced emission) ligand of 2-methoxy-6-[[[4-(1,2,2-triphenylvinyl)phenyl]imino]methyl]phenol (HTPEIP(OMe)), was successfully synthesized. It not only behaves as a single-molecule magnet (SMM) with an energy barrier of 168(15) K at zero field but also exhibits piezochromism during the pressing-fuming cycle with switchable color, photoluminescence, and magnetic response.

  7. High density flux of Co nanoparticles produced by a simple gas aggregation apparatus

    SciTech Connect

    Landi, G. T.; Romero, S. A.; Santos, A. D.

    2010-03-15

    Gas aggregation is a well known method used to produce clusters of different materials with good size control, reduced dispersion, and precise stoichiometry. The cost of these systems is relatively high and they are generally dedicated apparatuses. Furthermore, the usual sample production speed of these systems is not as fast as physical vapor deposition devices posing a problem when thick samples are needed. In this paper we describe the development of a multipurpose gas aggregation system constructed as an adaptation to a magnetron sputtering system. The cost of this adaptation is negligible and its installation and operation are both remarkably simple. The gas flow for flux in the range of 60-130 SCCM (SCCM denotes cubic centimeter per minute at STP) is able to completely collimate all the sputtered material, producing spherical nanoparticles. Co nanoparticles were produced and characterized using electron microscopy techniques and Rutherford back-scattering analysis. The size of the particles is around 10 nm with around 75 nm/min of deposition rate at the center of a Gaussian profile nanoparticle beam.

  8. High density flux of Co nanoparticles produced by a simple gas aggregation apparatus.

    PubMed

    Landi, G T; Romero, S A; Santos, A D

    2010-03-01

    Gas aggregation is a well known method used to produce clusters of different materials with good size control, reduced dispersion, and precise stoichiometry. The cost of these systems is relatively high and they are generally dedicated apparatuses. Furthermore, the usual sample production speed of these systems is not as fast as physical vapor deposition devices posing a problem when thick samples are needed. In this paper we describe the development of a multipurpose gas aggregation system constructed as an adaptation to a magnetron sputtering system. The cost of this adaptation is negligible and its installation and operation are both remarkably simple. The gas flow for flux in the range of 60-130 SCCM (SCCM denotes cubic centimeter per minute at STP) is able to completely collimate all the sputtered material, producing spherical nanoparticles. Co nanoparticles were produced and characterized using electron microscopy techniques and Rutherford back-scattering analysis. The size of the particles is around 10 nm with around 75 nm/min of deposition rate at the center of a Gaussian profile nanoparticle beam.

  9. Adsorption of two gas molecules at a single metal site in a metal–organic framework

    SciTech Connect

    Runčevski, Tomče; Kapelewski, Matthew T.; Torres-Gavosto, Rodolfo M.; Tarver, Jacob D.; Brown, Craig M.; Long, Jeffrey R.

    2016-11-21

    One strategy to markedly increase the gas storage capacity of metal–organic frameworks is to introduce coordinatively-unsaturated metal centers capable of binding multiple gas molecules. Herein, we provide an initial demonstration that a single metal site within a framework can support the terminal coordination of two gas molecules—specifically hydrogen, methane, or carbon dioxide.

  10. Detecting ordered small molecule drug aggregates in live macrophages: a multi-parameter microscope image data acquisition and analysis strategy

    PubMed Central

    Rzeczycki, Phillip; Yoon, Gi Sang; Keswani, Rahul K.; Sud, Sudha; Stringer, Kathleen A.; Rosania, Gus R.

    2017-01-01

    Following prolonged administration, certain orally bioavailable but poorly soluble small molecule drugs are prone to precipitate out and form crystal-like drug inclusions (CLDIs) within the cells of living organisms. In this research, we present a quantitative multi-parameter imaging platform for measuring the fluorescence and polarization diattenuation signals of cells harboring intracellular CLDIs. To validate the imaging system, the FDA-approved drug clofazimine (CFZ) was used as a model compound. Our results demonstrated that a quantitative multi-parameter microscopy image analysis platform can be used to study drug sequestering macrophages, and to detect the formation of ordered molecular aggregates formed by poorly soluble small molecule drugs in animals. PMID:28270989

  11. Mn12 single-molecule magnet aggregates as magnetic resonance imaging contrast agents.

    PubMed

    Wang, Yinglin; Li, Wen; Zhou, Shengyan; Kong, Daliang; Yang, Haishan; Wu, Lixin

    2011-03-28

    Mn(12) single-molecule magnets have been dispersed in water through an emulsion-assisted self-assembly method with an improved stability in water, in order to investigate the use of Mn(12) as MRI contrast agents.

  12. Sodium glycodeoxycholate and glycocholate mixed aggregates in gas and solution phases.

    PubMed

    de Petris, Giulia; Festa, Maria Rosa; Galantini, Luciano; Giglio, Edoardo; Leggio, Claudia; Pavel, Nicolae Viorel; Troiani, Anna

    2009-05-21

    This paper deals with electrospray ionization mass spectrometry (ESIMS), small-angle X-ray scattering (SAXS), and dynamic light scattering (DLS) measurements in order to provide information on the existence, aggregation, composition, and structure of the two-component aggregates of sodium glycocholate (NaGC) and sodium glycodeoxycholate (NaGDC) in the gas and solution phases. Five samples, containing 100% NaGC and 100% NaGDC, and NaGDC/NaGC molar ratios of 3 (75D), 1 (50D), and 1/3 (25D), have been analyzed by ESIMS in positive-ion detection mode starting from 10(-3) and 10(-2) M total bile salt concentration in aqueous solutions. Generally, dimers or trimers prevail in the 100% NaGC or NaGDC samples, respectively, as observed in the preceding one-component ESIMS measurements and in agreement with the proposed micellar aggregate structures in aqueous solution. Moreover, it is observed that the composition of multimers in the samples 75D, 50D, and 25D deviates from the one expected on the basis of a random association of the monomers, the NaGDC contribution generally prevailing on the NaGC one. It happens also under the same percentage condition (50D sample), in agreement with a greater aggregation ability of NaGDC with respect to NaGC. SAXS and DLS data were recorded on six samples containing a NaGC+NaGDC 40 mM total concentration, one bile salt having 40, 32, 24, 16, 8, and 0 mM concentration and the other the complementary one, keeping constant the NaCl concentration (0.6 M). The NaGDC 40 mM sample presents SAXS curves in agreement with a cylindrical shape of the aggregates as shown in a previous paper. For the bile salt mixtures, the progressive decrease of the sizes and change of the aggregate morphology, toward a globular-like geometry, are observed by increasing the NaGC fraction, thus confirming the hypothesis about the ability of trihydroxy salts to inhibit the growth of dihydroxy salt aggregates. Fits on the basis of cylindrical model can be accomplished

  13. Self-assembled aggregates of amphiphilic perylene diimide-based semiconductor molecules: effect of morphology on conductivity.

    PubMed

    Chen, Yanli; Feng, Yajuan; Gao, Jian; Bouvet, Marcel

    2012-02-15

    Two amphiphilic perylenetetracarboxylic diimide derivatives modified with different side chains at imide nitrogen, N-n-hexyl-N'-(2-hydroxyethyl)-1,7-di(4'-t-butyl)phenoxy-perylene-3,4:9,10-tetracarboxylic diimide (PDI 1) and N,N'-di(2-hydroxyethyl)-1,7-di(4'-t-butyl)phenoxy-perylene-3,4:9,10-tetracarboxylic diimide (PDI 2), were fabricated into organic nanostructures via solution-phase self-assembly. Their self-assembling properties in methanol and n-hexane have been comparatively studied by electronic absorption, fluorescence, and Fourier transform infrared spectroscopy (FT-IR). The morphologies and structures of the self-assemblies were examined by scanning electronic microscopy (SEM), atomic force microscopy (AFM), as well as X-ray diffraction (XRD) techniques. The conducting properties were evaluated by current-voltage (I-V) measurements. Due to the presence of different number of hydroxyethyl groups in the molecule of PDI 1 and PDI 2, the self-assembly of the two molecules in methanol and n-hexane results in nanostructures with distinctly different morphology as follows: nanobelts and nanoleaves for PDI 1 and nanobelt dendrites and nanosheets for PDI 2, respectively. Analysis of the spectral change for the aggregates relative to that of monomeric PDI in solution revealed that in polar and apolar solvents, both nanobelts and nanoleaves precipitated from PDI 1 adopt the H aggregation mode, whereas nanobelt dendrites and nanosheets from PDI 2 adopt H and J aggregation mode, respectively, implying the effect of both side-chain substituent and solvent on tuning the intermolecular stacking. Furthermore, the conductivity of the aggregates of either PDI 1 or PDI 2 from methanol is more than ca. 1 order of magnitude higher than those from n-hexane. In particular, the well-defined, one-dimensional (1D) nanobelts of PDI 1 show excellent semiconducting property with the electrical conductivity as high as 3.3×10(-3) S cm(-1), which might serve as promising candidates for

  14. Two-Photon Optical Properties of AIE-active D-TPE-A Molecules: Aggregation Enhancement and Structure-Property Relationships

    NASA Astrophysics Data System (ADS)

    Zhang, Yilin; Li, Jie; Tang, Ben Zhong; Wong, Kam Sing

    We present an aggregation enhancement in two-photon-excited fluorescence (TPEF) of about two orders of magnitude in a series of novel non-centrosymmetric D- π-A molecules. Aggregation-induced emission characteristics are introduced into these D- π-A molecules via tetraphenylethylene (TPE), which is used as their π-bridge. Detailed analysis shows that the TPEF of these molecules are enhanced in aggregation environment with both fluorescence quantum efficiency and two-photon absorptivity concomitantly. The two-photon absorption (TPA) transition bands of these branched- or butterfly-configured molecules are similar to those in their linear absorption. The molecular TPA cross sections in aggregation environment reach around 50-130 GM, and peak within the available wavelength ranges of a Ti:Sapphire femtosecond oscillator. We also observe that two-photon absorptivity increases progressively with the addition of donor/acceptor moieties on the TPE backbone. This phenomenon is presumably attributed to the improved conjugation length and enhanced intramolecular charge transfer, hence better delocalization of π-electrons. For each compound, the aggregation enhancement in TPA may also offers clues of aggregation effect on the molecular electronic structure.

  15. Production of Long-Lived Ultracold LI2 Molecules from a Fermi Gas

    NASA Astrophysics Data System (ADS)

    Cubizolles, J.; Bourdel, T.; Kokkelmans, S. J. J. M. F.; Salomon, C.; Shlyapnikov, G. V.

    2004-12-01

    We create weakly-bound Li2 molecules from a degenerate two-component Fermi gas by sweeping a magnetic field across a Feshbach resonance. The atom-molecule transfer efficiency can reach 85 % and is studied as a function of magnetic field and initial temperature. The bosonic molecules remain trapped for 0.5s and their temperature is within a factor of two of the Bose-Einstein condensation temperature. A thermodynamical model reproduces qualitatively the experimental findings.

  16. Coupled plasmon-exciton hybrid excitations in colloidal gold nanorods coated with J-aggregated dye molecules (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Simon, Thomas; Melnikau, Dimitry; Sanchez-Iglesia, Ana; Grzelczak, Marek; Liz-Marzán, Luis M.; Rakovich, Yury P.; Feldmann, Jochen; Urban, Alexander S.

    2016-09-01

    Strong coupling of plasmons and excitons can form hybrid states, the so called "plexcitons". Especially with molecular J-aggregated dye molecules strong interaction becomes observable even under ambient conditions. In our work we investigate the nature of plexcitonic states formed in gold nanorods coated with a cyanine dye by transient absorption spectroscopy. We demonstrate that plexcitons show tunable plasmonic and excitonic non-linear optical behaviour. Our experimental data can be explained on the basis of a simple Lorentz oscillator model. We find that both the quality factor and the coupling strength between plasmons and excitons can be optically manipulated on an ultrashort time scale. T. Simon, D. Melnikau, A. Sánchez-Iglesias, M. Grzelczak, L. Liz-Marzán, Y. Rakovich, J. Feldmann and A. Urban, Exploring the optical non-linearities of plasmon-exciton hybrid resonances in coupled colloidal nanostructures, submitted (2016)

  17. Molecules, magic and forgetful fruit flies: the supernatural science of medical gas research.

    PubMed

    Mychaskiw, George

    2011-09-06

    Medical gas research often involves the study of molecules under extraphysiologic conditions, that is, conditions that do not exist in nature. This "supernatural" nature of medical gas research sometimes produces results that appear to be almost "magic" to those schooled in traditional physiology"Any sufficiently advanced technology is indistinguishable from magic".-Arthur C. Clarke.

  18. Molecules, magic and forgetful fruit flies: the supernatural science of medical gas research

    PubMed Central

    2011-01-01

    Medical gas research often involves the study of molecules under extraphysiologic conditions, that is, conditions that do not exist in nature. This "supernatural" nature of medical gas research sometimes produces results that appear to be almost "magic" to those schooled in traditional physiology "Any sufficiently advanced technology is indistinguishable from magic". -Arthur C. Clarke PMID:22146602

  19. Characterization of Sizes of Aggregates of Insulin Analogs and the Conformations of the Constituent Protein Molecules: A Concomitant Dynamic Light Scattering and Raman Spectroscopy Study.

    PubMed

    Zhou, Chen; Qi, Wei; Lewis, E Neil; Carpenter, John F

    2016-02-01

    To generate aggregates, 3 insulin analogs, lispro, aspart, and glulisine, were incubated without phenolic preservatives for 30 days at 37 °C. As a function of incubation time, aggregation was quantified with size exclusion chromatography, and the sizes of aggregates and the conformations of the constituent molecules were characterized with concomitant dynamic light scattering and Raman spectroscopy. During incubation, lispro was progressively converted into soluble aggregates with hydrodynamic diameters of circa 15 nm, and 95% of the native protein had aggregated at day 30. Raman spectroscopy documented that aggregation resulted in conversion of a large fraction of native alpha helix into nonnative beta sheet structure and a distortion of disulfide bonds. In contrast, for aspart and glulisine only 20% of the native proteins aggregated after 30 days, and minimal structural perturbations were detected. In addition, consistent with the relative aggregation rates during isothermal incubation, Raman spectroscopy showed that during heating the onset temperature for secondary structural perturbations of lispro occurred 7 °C-10 °C lower than those for aspart or glulisine. Overall the results of this study demonstrated that-as in the case during formation of amyloid fibrils from insulin-formation of soluble aggregates of lispro resulted in a high level of conversion of alpha helix into beta sheet.

  20. Interactions of gas molecules with monolayer MoSe2: A first principle study

    NASA Astrophysics Data System (ADS)

    Sharma, Munish; Jamdagni, Pooja; Kumar, Ashok; Ahluwalia, P. K.

    2016-05-01

    We present a first principle study of interaction of toxic gas molecules (NO, NO2 and SO2) with monolayer MoSe2. The predicted order of sensitivity of gas molecule is NO2 > SO2 > NO. Adsorbed molecules strongly influence the electronic behaviour of monolayer MoSe2 by inducing impurity levels in the vicinity of Fermi energy. NO and SO2 is found to induce p-type doping effect while semiconductor to metallic transitions occur on NO2 adsorption. Our findings may guide the experimentalist for fabricating sensor devices based on MoSe2 monolayer.

  1. Lattice gas cellular automation model for rippling and aggregation in myxobacteria

    NASA Astrophysics Data System (ADS)

    Alber, Mark S.; Jiang, Yi; Kiskowski, Maria A.

    2004-05-01

    A lattice gas cellular automation (LGCA) model is used to simulate rippling and aggregation in myxobacteria. An efficient way of representing cells of different cell size, shape and orientation is presented that may be easily extended to model later stages of fruiting body formation. This LGCA model is designed to investigate whether a refractory period, a minimum response time, a maximum oscillation period and non-linear dependence of reversals of cells on C-factor are necessary assumptions for rippling. It is shown that a refractory period of 2-3 min, a minimum response time of up to 1 min and no maximum oscillation period best reproduce rippling in the experiments of Myxococcus xanthus. Non-linear dependence of reversals on C-factor is critical at high cell density. Quantitative simulations demonstrate that the increase in wavelength of ripples when a culture is diluted with non-signaling cells can be explained entirely by the decreased density of C-signaling cells. This result further supports the hypothesis that levels of C-signaling quantitatively depend on and modulate cell density. Analysis of the interpenetrating high density waves shows the presence of a phase shift analogous to the phase shift of interpenetrating solitons. Finally, a model for swarming, aggregation and early fruiting body formation is presented.

  2. Gas-phase laser synthesis of aggregation-free, size-controlled hydroxyapatite nanoparticles

    NASA Astrophysics Data System (ADS)

    Bapat, Parimal V.; Kraft, Rebecca; Camata, Renato P.

    2012-10-01

    Nanophase hydroxyapatite (HA) is finding applications in many areas of biomedical research, including bone tissue engineering, drug delivery, and intracellular imaging. Details in chemical composition, crystal phase makeup, size, and shape of HA nanoparticles play important roles in achieving the favorable biological responses required in these applications. Most of the nanophase HA synthesis techniques involve solution-based methods that exhibit substantial aggregation of particles upon precipitation. Typically these methods also have limited control over the particle size and crystal phase composition. In this study, we describe the gas-phase synthesis of aggregation-free, size-controlled HA nanoparticles with mean size in the 20-70 nm range using laser ablation followed by aerosol electrical mobility classification. Nanoparticle deposits with adjustable number concentration were obtained on solid substrates. Particles were characterized by transmission electron microscopy, atomic force microscopy, and X-ray diffraction. Samples are well represented by log-normal size distributions with geometric standard deviation σ g ≈ 1.2. The most suitable conditions for HA nanoparticle formation at a laser fluence of 5 J/cm2 were found to be a temperature of 800 °C and a partial pressure of water of 160 mbar.

  3. Cooling, Collisions and non-Sticking of Polyatomic Molecules in a Cryogenic Buffer Gas Cell

    NASA Astrophysics Data System (ADS)

    Piskorski, Julia Hege

    We cool and study trans-Stilbene, Nile Red and Benzonitrile in a cryogenic (7K) cell filled with low density helium buffer gas. No molecule-helium cluster formation is observed, indicating limited atom-molecule sticking in this system. We place an upper limit of 5% on the population of clustered He-trans-Stilbene, consistent with a measured He-molecule collisional residence time of less than 1 mus. With several low energy torsional modes, trans-Stilbene is less rigid than any molecule previously buffer gas cooled into the Kelvin regime. We report cooling and gas phase visible spectroscopy of Nile Red, a much larger molecule. Our data suggest that buffer gas cooling will be feasible for a variety of small biological molecules. The same cell is also ideal for studying collisional relaxation cross sections. Measurements of Benzonitrile vibrational state decay results in determination of the vibrational relaxation cross sections of sigma22 = 8x10-15 cm2 and sigma 21 = 6x10-15 cm2 for the 22 (v=1) and 21 (v=1) states. For the first time, we directly observe formation of cold molecular dimers in a cryogenic buffer gas cell and determine the dimer formation cross section to be ˜10-13 cm2.

  4. Effects of gas molecules on an ultraviolet photodetector with a single-layer titania nanosheet

    NASA Astrophysics Data System (ADS)

    Matsuzaki, Koji; Taniguchi, Takaaki; Matsumoto, Yasumichi; Hara, Masahiro

    2015-01-01

    We have demonstrated an ultraviolet photodetector fabricated from a chemically exfoliated single-layer titania nanosheet. The photocurrent showed a clear on/off switching with a short time response under periodic pulsed illuminations. Suppressions of the photocurrent due to environmental gas molecules were observed under medium vacuum region (1.0-300 Pa). The observation even in inert nitrogen gas implies an enhancement of annihilations of photo-excited carriers due to collisions of inert gas molecules on the surface-sensitive titania nanosheet.

  5. High-resolution mid-infrared spectroscopy of buffer-gas-cooled methyltrioxorhenium molecules

    NASA Astrophysics Data System (ADS)

    Tokunaga, S. K.; Hendricks, R. J.; Tarbutt, M. R.; Darquié, B.

    2017-05-01

    We demonstrate cryogenic buffer-gas cooling of gas-phase methyltrioxorhenium (MTO). This molecule is closely related to chiral organometallic molecules where the parity-violating energy differences between enantiomers is measurable. The molecules are produced with a rotational temperature of approximately 6 K by laser ablation of an MTO pellet inside a cryogenic helium buffer gas cell. Facilitated by the low temperature, we demonstrate absorption spectroscopy of the 10.2 μm antisymmetric Re=O stretching mode of MTO with a resolution of 8 MHz and a frequency accuracy of 30 MHz. We partially resolve the hyperfine structure and measure the nuclear quadrupole coupling of the excited vibrational state. Our ability to produce dense samples of complex molecules of this type at low temperatures represents a key step towards a precision measurement of parity violation in a chiral species.

  6. Research on Sources of Gas Phase Metastable Atoms and Molecules

    DTIC Science & Technology

    1982-05-01

    PAGI(Whi DeE# WA..teod) -systems of interest to such diverse areas as gas discharge physics, chemical physics, flame chemistry and plasma physics. "A...second task involved a literature review of prior basic research meta- stable sources followed by the development and experimental testing of appro...appropriate for this phase of the program. The operation of this type of metastable source wab investigated and tested for the production of metastable argon

  7. Preferable binding site of gas molecules on graphene nanoribbon with Stone–Wales defect

    NASA Astrophysics Data System (ADS)

    Auzar, Zuriana; Johari, Zaharah; Sakina, S. H.; Alias, N. E.; Abidin, M. S. Z.

    2017-02-01

    The issue of sensitivity of sensing device has focused on the development of sensing devices by using new materials, such as graphene. The gas molecules in different positions such as on, near and far from the defect are placed in the same binding site in two graphene configurations for fair comparison. The interaction between two different graphene configurations such as (pristine armchair graphene nanoribbon (P-AGNR) and Stone–Wales defect on graphene surface (SW-AGNR)) with gas molecules (e.g. O2, N2 and NH3) have been investigated to observe the preferential position site of adsorbate gas molecules. The preferable position sites are investigated by using Extended-Huckel Theory. It is found that, the electronic properties of each configuration are strongly depends on the position of gas molecules and graphene system. Meanwhile, the binding site of the gas molecules on the defective site of graphene surface is a significant factor in determining the sensing behavior of graphene based gas defection device.

  8. Aggregation of mononuclear and red blood cells through an {alpha}4{beta}1-Lu/basal cell adhesion molecule interaction in sickle cell disease.

    PubMed

    Chaar, Vicky; Picot, Julien; Renaud, Olivier; Bartolucci, Pablo; Nzouakou, Ruben; Bachir, Dora; Galactéros, Frédéric; Colin, Yves; Le Van Kim, Caroline; El Nemer, Wassim

    2010-11-01

    Abnormal interactions between red blood cells, leukocytes and endothelial cells play a critical role in the occurrence of the painful vaso-occlusive crises associated with sickle cell disease. We investigated the interaction between circulating leukocytes and red blood cells which could lead to aggregate formation, enhancing the incidence of vaso-occlusive crises. Blood samples from patients with sickle cell disease (n=25) and healthy subjects (n=5) were analyzed by imaging and classical flow cytometry after density gradient separation. The identity of the cells in the peripheral blood mononuclear cell layer was determined using antibodies directed specifically against white (anti-CD45) or red (anti-glycophorin A) blood cells. Aggregates between red blood cells and peripheral blood mononuclear cells were visualized in whole blood from patients with sickle cell disease. The aggregation rate was 10-fold higher in these patients than in control subjects. Both mature red blood cells and reticulocytes were involved in these aggregates through their interaction with mononuclear cells, mainly with monocytes. The size of the aggregates was variable, with one mononuclear cell binding to one, two or several red blood cells. Erythroid Lu/basal cell adhesion molecule and α(4)β(1) integrin were involved in aggregate formation. The aggregation rate was lower in patients treated with hydroxycarbamide than in untreated patients. Our study gives visual evidence of the existence of circulating red blood cell-peripheral blood mononuclear cell aggregates in patients with sickle cell disease and shows that these aggregates are decreased during hydroxycarbamide treatment. Our results strongly suggest that erythroid Lu/basal cell adhesion molecule proteins are implicated in these aggregates through their interaction with α(4)β(1) integrin on peripheral blood mononuclear cells.

  9. ESI-IMS-MS: A method for rapid analysis of protein aggregation and its inhibition by small molecules.

    PubMed

    Young, Lydia M; Saunders, Janet C; Mahood, Rachel A; Revill, Charlotte H; Foster, Richard J; Ashcroft, Alison E; Radford, Sheena E

    2016-02-15

    Electrospray ionisation-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is a powerful method for the study of conformational changes in protein complexes, including oligomeric species populated during protein self-aggregation into amyloid fibrils. Information on the mass, stability, cross-sectional area and ligand binding capability of each transiently populated intermediate, present in the heterogeneous mixture of assembling species, can be determined individually in a single experiment in real-time. Determining the structural characterisation of oligomeric species and alterations in self-assembly pathways observed in the presence of small molecule inhibitors is of great importance, given the urgent demand for effective therapeutics. Recent studies have demonstrated the capability of ESI-IMS-MS to identify small molecule modulators of amyloid assembly and to determine the mechanism by which they interact (positive, negative, non-specific binding, or colloidal) in a high-throughput format. Here, we demonstrate these advances using self-assembly of Aβ40 as an example, and reveal two new inhibitors of Aβ40 fibrillation. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  10. Adsorption and Gas Separation of Molecules by Carbon Nanohorns.

    PubMed

    Gatica, Silvina M; Nekhai, Anton; Scrivener, Adam

    2016-05-19

    In this paper, we report the results of Monte Carlo simulations of the adsorption of neon, argon, methane and carbon dioxide in carbon nanohorns. We model the nanohorns as an array of carbon cones and obtained adsorption isotherms and isosteric heats. The main sites of adsorption are inside the cones and in the interstices between three cones. We also calculated the selectivity of carbon dioxide/methane, finding that nanohorns are a suitable substrate for gas separation. Our simulations are compared to available experimental data.

  11. Control of water molecule aggregations in copper 1,4-cyclohexanedicarboxylate coordination polymers containing pyridyl-piperazine type ligands

    NASA Astrophysics Data System (ADS)

    Qiblawi, Sultan H.; LaDuca, Robert L.

    2014-01-01

    A series of layered divalent copper coordination polymers containing 1,4-cyclohexanedicarboxylate and long-spanning pyridyl-piperazine type ligands exhibits greatly different co-crystallized water molecule aggregations depending on the specific ligands used. Both [Cu(t-14cdc)(4-bpmp)]n (1, t-14cdc = trans-1,4-cyclohexanedicarboxylate, 4-bpmp = bis(4-pyridylmethyl)piperazine) and {[Cu(t-14cdc)(4-bpfp)(H2O)2]·6H2O}n (2, 4-bpfp = bis(4-pyridylformyl)piperazine) possess 2D (4,4) coordination polymer grids. However 1 lacks any co-crystallized water and has pinched grid apertures, while 2 manifests infinite water tapes with T6(2)4(2) classification and rectangular grid apertures. {[Cu2(c-14cdc)2(4-bpmp)]·2H2O}n (3, c-14cdc = cis-1,4-cyclohexanedicarboxylate) has [Cu2(c-14cdc)]2 ribbons with paddlewheel dimeric units linked into 2D slabs by 4-bpmp tethers, along with isolated water molecule pairs. In contrast, {[Cu2(c-14cdc)2(4-bpfp)]·10H2O}n (4) shows a very similar underlying coordination polymer topology but entrains unique decameric water molecule clusters. The minor product {[Cu2(c-14cdcH)2(t-1,4-cdc)(4-bpfp)2(H2O)2]·2H2O}n (5) was isolated along with 4; this compound underwent some in situ cis to trans cyclohexane-dicarboxylate ligand isomerization and exhibits a ladder polymer motif.

  12. GAS-PHASE MOLECULAR DYNAMICS: VIBRATIONAL DYNAMICS OF POLYATOMIC MOLECULES

    SciTech Connect

    MUCKERMAN,J.T.

    1999-06-09

    The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high-temperature, flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wavepacket calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics.

  13. Small molecule inhibitors block Gas6-inducible TAM activation and tumorigenicity

    PubMed Central

    Kimani, Stanley G.; Kumar, Sushil; Bansal, Nitu; Singh, Kamalendra; Kholodovych, Vladyslav; Comollo, Thomas; Peng, Youyi; Kotenko, Sergei V.; Sarafianos, Stefan G.; Bertino, Joseph R.; Welsh, William J.; Birge, Raymond B.

    2017-01-01

    TAM receptors (Tyro-3, Axl, and Mertk) are a family of three homologous type I receptor tyrosine kinases that are implicated in several human malignancies. Overexpression of TAMs and their major ligand Growth arrest-specific factor 6 (Gas6) is associated with more aggressive staging of cancers, poorer predicted patient survival, acquired drug resistance and metastasis. Here we describe small molecule inhibitors (RU-301 and RU-302) that target the extracellular domain of Axl at the interface of the Ig-1 ectodomain of Axl and the Lg-1 of Gas6. These inhibitors effectively block Gas6-inducible Axl receptor activation with low micromolar IC50s in cell-based reporter assays, inhibit Gas6-inducible motility in Axl-expressing cell lines, and suppress H1299 lung cancer tumor growth in a mouse xenograft NOD-SCIDγ model. Furthermore, using homology models and biochemical verifications, we show that RU301 and 302 also inhibit Gas6 inducible activation of Mertk and Tyro3 suggesting they can act as pan-TAM inhibitors that block the interface between the TAM Ig1 ectodomain and the Gas6 Lg domain. Together, these observations establish that small molecules that bind to the interface between TAM Ig1 domain and Gas6 Lg1 domain can inhibit TAM activation, and support the further development of small molecule Gas6-TAM interaction inhibitors as a novel class of cancer therapeutics. PMID:28272423

  14. Single target sputter deposition of alloy nanoparticles with adjustable composition via a gas aggregation cluster source

    NASA Astrophysics Data System (ADS)

    Vahl, Alexander; Strobel, Julian; Reichstein, Wiebke; Polonskyi, Oleksandr; Strunskus, Thomas; Kienle, Lorenz; Faupel, Franz

    2017-04-01

    Alloy nanoparticles with variable compositions add a new dimension to nanoscience and have many applications. Here we suggest a novel approach for the fabrication of variable composition alloy nanoparticles that is based on a Haberland type gas aggregation cluster source with a custom-made multicomponent target for magnetron sputtering. The approach, which was demonstrated here for gold-rich AgAu nanoparticles, combines a narrow nanoparticle size distribution with in operando variation of composition via the gas pressure as well as highly efficient usage of target material. The latter is particularly attractive for precious metals. Varying argon pressure during deposition, we achieved in operando changes of AgAu alloy nanoparticle composition of more than 13 at%. The alloy nanoparticles were characterized by x-ray photoelectron spectroscopy and energy dispersive x-ray spectroscopy. The characteristic plasmon resonances of multilayer nanoparticle composites were analyzed by UV-vis spectroscopy. Tuning of the number of particles per unit area (particle densities) within individual layers showed an additional degree of freedom to tailor the optical properties of multilayer nanocomposites. By extension of this technique to more complex systems, the presented results are expected to encourage and simplify further research based on plasmonic multi-element nanoparticles. The present method is by no means restricted to plasmonics or nanoparticle based applications, but is also highly relevant for conventional magnetron sputtering of alloys and can be extended to in operando control of alloy concentration by magnetic field.

  15. Single target sputter deposition of alloy nanoparticles with adjustable composition via a gas aggregation cluster source.

    PubMed

    Vahl, Alexander; Strobel, Julian; Reichstein, Wiebke; Polonskyi, Oleksandr; Strunskus, Thomas; Kienle, Lorenz; Faupel, Franz

    2017-04-28

    Alloy nanoparticles with variable compositions add a new dimension to nanoscience and have many applications. Here we suggest a novel approach for the fabrication of variable composition alloy nanoparticles that is based on a Haberland type gas aggregation cluster source with a custom-made multicomponent target for magnetron sputtering. The approach, which was demonstrated here for gold-rich AgAu nanoparticles, combines a narrow nanoparticle size distribution with in operando variation of composition via the gas pressure as well as highly efficient usage of target material. The latter is particularly attractive for precious metals. Varying argon pressure during deposition, we achieved in operando changes of AgAu alloy nanoparticle composition of more than 13 at%. The alloy nanoparticles were characterized by x-ray photoelectron spectroscopy and energy dispersive x-ray spectroscopy. The characteristic plasmon resonances of multilayer nanoparticle composites were analyzed by UV-vis spectroscopy. Tuning of the number of particles per unit area (particle densities) within individual layers showed an additional degree of freedom to tailor the optical properties of multilayer nanocomposites. By extension of this technique to more complex systems, the presented results are expected to encourage and simplify further research based on plasmonic multi-element nanoparticles. The present method is by no means restricted to plasmonics or nanoparticle based applications, but is also highly relevant for conventional magnetron sputtering of alloys and can be extended to in operando control of alloy concentration by magnetic field.

  16. Understanding and controlling laser-matter interactions: From solvated dye molecules to polyatomic molecules in gas phase

    NASA Astrophysics Data System (ADS)

    Konar, Arkaprabha

    The goal of my research is to obtain a better understanding of the various processes that occur during and following laser-matter interactions from both the physical and chemical point of view. In particular I focused my research on understanding two very important aspects of laser-matter interaction; 1) Intense laser-matter interactions for polyatomic molecules in the gas phase in order to determine to what extent processes like excitation, ionization and fragmentation can be controlled by modifying the phase and amplitude of the laser field according to the timescales for electronic, vibrational and rotational energy transfer. 2) Developing pulse shaping based single beam methods aimed at studying solvated molecules in order to elucidate processes like inhomogeneous broadening, solvatochromic shift and to determine the electronic coherence lifetimes of solvated molecules. The effect of the chirped femtosecond pulses on fluorescence and stimulated emission from solvated dye molecules was studied and it was observed that the overall effect depends quadratically on pulse energy, even where excitation probabilities range from 0.02 to 5%, in the so-called "linear excitation regime". The shape of the chirp dependence is found to be independent of the energy of the pulse. It was found that the chirp dependence reveals dynamics related to solvent rearrangement following excitation and also depends on electronic relaxation of the chromophore. Furthermore, the chirped pulses were found to be extremely sensitive to solvent environment and that the complementary phases having the opposite sign provide information about the electronic coherence lifetimes. Similar to chirped pulses, the effects of a phase step on the excitation spectrum and the corresponding changes to the stimulated emission spectrum were also studied and it was found that the coherent feature on the spectrum is sensitive to the dephasing time of the system. Therefore a single phase scanning method can

  17. Nonequilibrium vibrational excitation of molecules behind a shock front in a gas mixture

    NASA Astrophysics Data System (ADS)

    Dobkin, S. V.; Son, E. E.

    1981-10-01

    It is shown that when a shock wave propagates in a light gas with a small admixture of heavy gas, the nonequilibrium vibrational excitation of molecules of the heavy gas can occur. In this case, the vibrational temperature can increase to values exceeding the gas temperature behind the shock wave, in contrast to the equilibrium case. Vibrational energy in a shock wave in a mixture of helium and uranium hexafluoride is calculated as an example. The possibility of experimentally observing this effect is discussed.

  18. Exploring the dynamic behaviors and transport properties of gas molecules in a transmembrane cyclic peptide nanotube.

    PubMed

    Li, Rui; Fan, Jianfen; Li, Hui; Yan, Xiliang; Yu, Yi

    2013-12-05

    The dynamic behaviors and transport properties of O2, CO2, and NH3 molecules through a transmembrane cyclic peptide nanotube (CPNT) of 8×cyclo-(WL)4/POPE have been investigated by steered molecular dynamics (SMD) simulations and adaptive biasing force (ABF) samplings. Different external forces are needed for three gas molecules to enter the channel. The periodic change of the pulling force curve for a gas traveling through the channel mainly arises from the regular and periodic arrangement of the composed CP subunits of the CPNT. Radial distribution functions (RDFs) between gas and water disclose the density decrease of channel water, which strongly aggravates the discontinuity of H-bond formation between a gas molecule and the neighboring water. Compared to hardly any H-bond formation between CO2 (or O2) and the framework of the CPNT, NH3 can form abundant H-bonds with the carbonyl/amide groups of the CPNT, leading to a fierce competition to NH3-water H-bonded interactions. In addition to direct H-bonded interactions, all three gases can form water bridges with the tube. The potential profile of mean force coincides with the occurring probability of a gas molecule along the tube axis. The energy barriers at two mouths of the CPNT elucidate the phenomenon that CO2 and O2 are thoroughly confined in the narrow lumen while NH3 can easily go outside the tube. Intermolecular interactions of each gas with channel water and the CPNT framework and the formation of H-bonds and water bridges illuminate the different gas translocation behaviors. The results uncover interesting and comprehensive mechanisms underlying the permeation characteristics of three gas molecules traveling through a transmembrane CPNT.

  19. Positron Impact Ionization in Noble Gas Atoms and Diatomic Molecules

    NASA Astrophysics Data System (ADS)

    Marler, J. P.

    2005-05-01

    Results are presented for absolute positronium formation and direct ionization by positron impact on Ne, Ar, Kr, Xe, N2, CO and O2 at energies from threshold up to 90 eV. The experiments use a high-resolution, trap-based positron beam and exploit the properties of positron orbits in a magnetic field [1]. Results for the noble gases are compared with theoretical predictions and with measurements obtained using a significantly different method [2]. Results for diatomic molecules are compared to other available measurements and theoretical calculations where available. There is generally good agreement between the experimental measurements, providing an important benchmark for theoretical calculations. Intriguing features in Ar and O2 will be discussed. [1] J.P. Sullivan, S.J. Gilbert, J.P. Marler, R.G. Greaves, S.J. Buckman and C.M. Surko., Phys. Rev. A. 66, 042708 (2002) [2] J.P. Marler, J.P. Sullivan and C.M. Surko, Phys. Rev. A (2005), in press.

  20. Effects of polymer coating on the adsorption of gas molecules on carbon nanotube networks

    SciTech Connect

    Kim, Sanghun; Lee, Hyeong Rag; Yun, Yong Ju; Ji, Seungmuk; Yoo, Kwonjae; Yun, Wan Soo; Koo, Ja-Yong; Ha, Dong Han

    2007-08-27

    Functionalization of carbon nanotubes (CNTs) with polymers such as polyethyleneimine or nafion was found to not change the adsorption properties of gas molecules on CNTs, although functionalization can remarkably enhance the sensitivity of gas sensors. Charge transfer between adsorbed molecules and single-walled carbon nanotubes (SWCNTs) at defect sites causes a steep and nonlinear conductance change at low gas concentrations, while molecules physically adsorbed on the pristine surfaces result in the linear electrical responses at higher concentrations. In addition, the molecular binding energies at defect sites of SWCNTs were measured to be 0.61 eV for NO{sub 2} and 0.53 eV for NH{sub 3}.

  1. PAHs molecules and heating of the interstellar gas

    NASA Technical Reports Server (NTRS)

    Verstraete, Laurent; Leger, Alain; Dhendecourt, Louis B.; Dutuit, O.; Defourneau, D.

    1989-01-01

    Until now it has remained difficult to account for the rather high temperatures seen in many diffuse interstellar clouds. Various heating mechanisms have been considered: photoionization of minor species, ionization of H by cosmic rays, and photoelectric effect on small grains. Yet all these processes are either too weak or efficient under too restricting conditions to balance the observed cooling rates. A major heat source is thus still missing in the thermal balance of the diffuse gas. Using photoionization cross sections measured in the lab, it was shown that in order to balance the observed cooling rates in cold diffuse clouds (T approx. 80 K) the PAHs would have to contain 15 percent of the cosmic abundance of carbon. This value does not contradict the former estimation of 6 percent deduced from the IR emission bands since this latter is to be taken as a lower limit. Further, it was estimated that the contribution to the heating rate due to PAH's in a warm HI cloud, assuming the same PAH abundance as for a cold HI cloud, would represent a significant fraction of the value required to keep the medium in thermal balance. Thus, photoionization of PAHs might well be a major heat source for the cold and warm HI media.

  2. Generation and orientation of organoxenon molecule H-Xe-CCH in the gas phase

    NASA Astrophysics Data System (ADS)

    Poterya, Viktoriya; Votava, Ondřej; Fárník, Michal; Ončák, Milan; Slavíček, Petr; Buck, Udo; Friedrich, Břetislav

    2008-03-01

    We report on the first observation of the organoxenon HXeCCH molecule in the gas phase. This molecule has been prepared in a molecular beam experiment by 193nm photolysis of an acetylene molecule on Xen clusters (n¯≈390). Subsequently the molecule has been oriented via the pseudo-first-order Stark effect in a strong electric field of the polarized laser light combined with the weak electrostatic field in the extraction region of a time-of-flight spectrometer. The experimental evidence for the oriented molecule has been provided by measurements of its photodissociation. For comparison, photolysis of C2H2 on Arn clusters (n¯≈280) has been measured. Here the analogous rare gas molecule HArCCH could not be generated. The interpretation of our experimental findings has been supported by ab initio calculations. In addition, the experiment together with the calculations reveals information on the photochemistry of the HXeCCH molecule. The 193nm radiation excites the molecule predominantly into the 2Σ+1 state, which cannot dissociate the Xe-H bond directly, but the system evolves along the Xe-C coordinate to a conical intersection of a slightly nonlinear configuration with the dissociative 1Π1 state, which then dissociates the Xe-H bond.

  3. Measurement of the orientation of buffer-gas-cooled, electrostatically-guided ammonia molecules

    NASA Astrophysics Data System (ADS)

    Steer, Edward W.; Petralia, Lorenzo S.; Western, Colin M.; Heazlewood, Brianna R.; Softley, Timothy P.

    2017-02-01

    The extent to which the spatial orientation of internally and translationally cold ammonia molecules can be controlled as molecules pass out of a quadrupole guide and through different electric field regions is examined. Ammonia molecules are collisionally cooled in a buffer gas cell, and are subsequently guided by a three-bend electrostatic quadrupole into a detection chamber. The orientation of ammonia molecules is probed using (2 + 1) resonance-enhanced multiphoton ionisation (REMPI), with the laser polarisation axis aligned both parallel and perpendicular to the time-of-flight axis. Even with the presence of a near-zero field region, the ammonia REMPI spectra indicate some retention of orientation. Monte Carlo simulations propagating the time-dependent Schrödinger equation in a full basis set including the hyperfine interaction enable the orientation of ammonia molecules to be calculated - with respect to both the local field direction and a space-fixed axis - as the molecules pass through different electric field regions. The simulations indicate that the orientation of ∼95% of ammonia molecules in JK =11 could be achieved with the application of a small bias voltage (17 V) to the mesh separating the quadrupole and detection regions. Following the recent combination of the buffer gas cell and quadrupole guide apparatus with a linear Paul ion trap, this result could enable one to examine the influence of molecular orientation on ion-molecule reaction dynamics and kinetics.

  4. Generation and orientation of organoxenon molecule H-Xe-CCH in the gas phase

    SciTech Connect

    Poterya, Viktoriya; Votava, Ondrej; Farnik, Michal; Oncak, Milan; Slavicek, Petr; Buck, Udo; Friedrich, Bretislav

    2008-03-14

    We report on the first observation of the organoxenon HXeCCH molecule in the gas phase. This molecule has been prepared in a molecular beam experiment by 193 nm photolysis of an acetylene molecule on Xe{sub n} clusters (n{approx_equal}390). Subsequently the molecule has been oriented via the pseudo-first-order Stark effect in a strong electric field of the polarized laser light combined with the weak electrostatic field in the extraction region of a time-of-flight spectrometer. The experimental evidence for the oriented molecule has been provided by measurements of its photodissociation. For comparison, photolysis of C{sub 2}H{sub 2} on Ar{sub n} clusters (n{approx_equal}280) has been measured. Here the analogous rare gas molecule HArCCH could not be generated. The interpretation of our experimental findings has been supported by ab initio calculations. In addition, the experiment together with the calculations reveals information on the photochemistry of the HXeCCH molecule. The 193 nm radiation excites the molecule predominantly into the 2 {sup 1}{sigma}{sup +} state, which cannot dissociate the Xe-H bond directly, but the system evolves along the Xe-C coordinate to a conical intersection of a slightly nonlinear configuration with the dissociative 1 {sup 1}{pi} state, which then dissociates the Xe-H bond.

  5. Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules.

    PubMed

    Boll, Rebecca; Rouzée, Arnaud; Adolph, Marcus; Anielski, Denis; Aquila, Andrew; Bari, Sadia; Bomme, Cédric; Bostedt, Christoph; Bozek, John D; Chapman, Henry N; Christensen, Lauge; Coffee, Ryan; Coppola, Niccola; De, Sankar; Decleva, Piero; Epp, Sascha W; Erk, Benjamin; Filsinger, Frank; Foucar, Lutz; Gorkhover, Tais; Gumprecht, Lars; Hömke, André; Holmegaard, Lotte; Johnsson, Per; Kienitz, Jens S; Kierspel, Thomas; Krasniqi, Faton; Kühnel, Kai-Uwe; Maurer, Jochen; Messerschmidt, Marc; Moshammer, Robert; Müller, Nele L M; Rudek, Benedikt; Savelyev, Evgeny; Schlichting, Ilme; Schmidt, Carlo; Scholz, Frank; Schorb, Sebastian; Schulz, Joachim; Seltmann, Jörn; Stener, Mauro; Stern, Stephan; Techert, Simone; Thøgersen, Jan; Trippel, Sebastian; Viefhaus, Jens; Vrakking, Marc; Stapelfeldt, Henrik; Küpper, Jochen; Ullrich, Joachim; Rudenko, Artem; Rolles, Daniel

    2014-01-01

    This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C(8)H(5)F) and dissociating, laser-aligned 1,4-dibromobenzene (C(6)H(4)Br(2)) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments.

  6. Sensitivity and resolution in frequency comb spectroscopy of buffer gas cooled polyatomic molecules

    NASA Astrophysics Data System (ADS)

    Changala, P. Bryan; Spaun, Ben; Patterson, David; Doyle, John M.; Ye, Jun

    2016-12-01

    We discuss the use of cavity-enhanced direct frequency comb spectroscopy in the mid-infrared region with buffer gas cooling of polyatomic molecules for high-precision rovibrational absorption spectroscopy. A frequency comb coupled to an optical enhancement cavity allows us to collect high-resolution, broad-bandwidth infrared spectra of translationally and rotationally cold (10-20 K) gas-phase molecules with high absorption sensitivity and fast acquisition times. The design and performance of the combined apparatus are discussed in detail. Recorded rovibrational spectra in the CH stretching region of several organic molecules, including vinyl bromide (CH_2CHBr), adamantane (C_{10}H_{16}), and diamantane (C_{14}H_{20}) demonstrate the resolution and sensitivity of this technique, as well as the intrinsic challenges faced in extending the frontier of high-resolution spectroscopy to large complex molecules.

  7. Small Molecules Detected by Second-Harmonic Generation Modulate the Conformation of Monomeric α-Synuclein and Reduce Its Aggregation in Cells*

    PubMed Central

    Moree, Ben; Yin, Guowei; Lázaro, Diana F.; Munari, Francesca; Strohäker, Timo; Giller, Karin; Becker, Stefan; Outeiro, Tiago F.; Zweckstetter, Markus; Salafsky, Joshua

    2015-01-01

    Proteins are structurally dynamic molecules that perform specialized functions through unique conformational changes accessible in physiological environments. An ability to specifically and selectively control protein function via conformational modulation is an important goal for development of novel therapeutics and studies of protein mechanism in biological networks and disease. Here we applied a second-harmonic generation-based technique for studying protein conformation in solution and in real time to the intrinsically disordered, Parkinson disease related protein α-synuclein. From a fragment library, we identified small molecule modulators that bind to monomeric α-synuclein in vitro and significantly reduce α-synuclein aggregation in a neuronal cell culture model. Our results indicate that the conformation of α-synuclein is linked to the aggregation of protein in cells. They also provide support for a therapeutic strategy of targeting specific conformations of the protein to suppress or control its aggregation. PMID:26396193

  8. Amyloid at the nanoscale: AFM and single-molecule investigations of early steps of aggregation and mature fibril growth, structure, and mechanics

    NASA Astrophysics Data System (ADS)

    Subramaniam, Vinod

    2013-03-01

    Misfolding and aggregation of proteins into nanometer-scale fibrillar assemblies is a hallmark of many neurodegenerative diseases. We have investigated the self-assembly of the human intrinsically disordered protein alpha-synuclein, involved in Parkinson's disease, into amyloid fibrils. A particularly relevant question is the role of early oligomeric aggregates in modulating the dynamics of protein nucleation and aggregation. We have used single molecule fluorescence spectroscopy to characterize conformational transitions of alpha-synuclein, and to gain insights into the structure and composition of oligomeric aggregates of alpha-synuclein. Quantitative atomic force microscopy and nanomechanical investigations provide information on amyloid fibril polymorphism and on nanoscale mechanical properties of mature fibrillar species, while conventional optical and super-resolution imaging have yielded insights into the growth of fibrils and into the assembly of suprafibrillar structures. We thank the Foundation for Fundamental Research on Matter (FOM), the Netherlands Organisation for Scientific Research (NWO), and the MESA+ Institute for Nanotechnology for support.

  9. The role of fibrinogen A alpha chains in ADP-induced platelet aggregation in the presence of fibrinogen molecules containing gamma' chains.

    PubMed

    Amrani, D L; Newman, P J; Meh, D; Mosesson, M W

    1988-09-01

    Human plasma fibrinogen (Fgn) is heterogenous with respect to the size of its gamma chains, which differ in that residues 408 to 411 of gammaA chains (93% of total) are replaced in gamma' chains by a unique 20 amino acid sequence (gamma408 to gamma427). In this study, we compared the contribution to adenosine diphosphate (ADP)-induced platelet aggregation of the A alpha chains in Fgn molecules containing predominantly (fraction 1-2) or exclusively (peak 1 Fgn) gammaA chains with that of molecules containing approximately 50% gamma' chains (peak 2 Fgn). Using washed human platelets, we confirmed that the number of peak 2 Fgn molecules binding to platelets in the presence of ADP was about half the number of peak 1 Fgn molecules (18,962 +/- 2,298 v 44,366 +/- 16,096 molecules per platelet), and that isolated S-carboxymethylated (SCM) gammaA chains supported ADP-induced platelet aggregation nearly as well as peak 1 Fgn. In contrast, SCM-gamma' chains alone supported aggregation poorly, whereas a mixture of SCM-gammaA and gamma' chains (1:1 ratio) gave intermediate results. Despite the findings with isolated SCM-gamma' chains, we found that peak 2 Fgn supported platelet aggregation nearly as well as peak 1 Fgn. However, peak 2 Fgn from which carboxy (COOH)-terminal A alpha chain segments had been removed by digestion with plasmin showed a markedly decreased platelet aggregation potential. Peak 1 Fgn core fraction from an 88% to 90% coagulable plasmin digest, or Fgn fraction 1-9, which has a high gammaA/gamma' chain ratio (93:7), but lacks COOH-terminal regions of A alpha chains, supported platelet aggregation to the same extent as did intact peak 2 Fgn. These findings indicate that Fgn molecules containing gamma' chains can approach the aggregation potential of Fgn molecules containing predominantly or exclusively gammaA chains only if intact A alpha chains are also present.

  10. Composite thermochemistry of gas phase U(VI)-containing molecules.

    PubMed

    Bross, David H; Peterson, Kirk A

    2014-12-28

    Reaction energies have been calculated for a series of reactions involving UF6, UO3, UO2(OH)2, and UO2F2 using coupled cluster singles and doubles with perturbative triples, CCSD(T), with a series of correlation consistent basis sets, including newly developed pseudopotential (PP)- and all-electron (AE) Douglas-Kroll-Hess-based sets for the U atom. The energies were calculated using a Feller-Peterson-Dixon composite approach in which CCSD(T) complete basis set (CBS) limits were combined with a series of additive contributions for spin-orbit coupling, outer-core correlation, and quantum electrodynamics effects. The calculated reaction enthalpies (both PP and AE) were combined with the accurately known heat of formation of UF6 to determine the enthalpies of formation of UO3, UO2(OH)2, and UO2F2. The contribution to the reaction enthalpies due to correlation of the 5s5p5d electrons of U was observed to be very slowly convergent with basis set and at the CBS limit their impact on the final enthalpies was on the order of 1 kcal/mol or less. For these closed shell molecules, spin-orbit effects contributed about 1 kcal/mol to the final enthalpies. Interestingly, the PP and AE approaches yielded quite different spin-orbit contributions (similar magnitude but opposite in sign), but the total scalar plus spin-orbit results from the two approaches agreed to within ∼1 kcal/mol of each other. The final composite heat of formation for UO2F2 was in excellent agreement with experiment, while the two results obtained for UO3 were just outside the ±2.4 kcal/mol error bars of the currently recommended experimental value. An improved enthalpy of formation (298 K) for UO2(OH)2 is predicted from this work to be -288.7 ± 3 kcal/mol, compared to the currently accepted experimental value of -292.7 ± 6 kcal/mol.

  11. Composite thermochemistry of gas phase U(VI)-containing molecules

    SciTech Connect

    Bross, David H.; Peterson, Kirk A.

    2014-12-28

    Reaction energies have been calculated for a series of reactions involving UF{sub 6}, UO{sub 3}, UO{sub 2}(OH){sub 2}, and UO{sub 2}F{sub 2} using coupled cluster singles and doubles with perturbative triples, CCSD(T), with a series of correlation consistent basis sets, including newly developed pseudopotential (PP)- and all-electron (AE) Douglas-Kroll-Hess-based sets for the U atom. The energies were calculated using a Feller-Peterson-Dixon composite approach in which CCSD(T) complete basis set (CBS) limits were combined with a series of additive contributions for spin-orbit coupling, outer-core correlation, and quantum electrodynamics effects. The calculated reaction enthalpies (both PP and AE) were combined with the accurately known heat of formation of UF{sub 6} to determine the enthalpies of formation of UO{sub 3}, UO{sub 2}(OH){sub 2}, and UO{sub 2}F{sub 2}. The contribution to the reaction enthalpies due to correlation of the 5s5p5d electrons of U was observed to be very slowly convergent with basis set and at the CBS limit their impact on the final enthalpies was on the order of 1 kcal/mol or less. For these closed shell molecules, spin-orbit effects contributed about 1 kcal/mol to the final enthalpies. Interestingly, the PP and AE approaches yielded quite different spin-orbit contributions (similar magnitude but opposite in sign), but the total scalar plus spin-orbit results from the two approaches agreed to within ∼1 kcal/mol of each other. The final composite heat of formation for UO{sub 2}F{sub 2} was in excellent agreement with experiment, while the two results obtained for UO{sub 3} were just outside the ±2.4 kcal/mol error bars of the currently recommended experimental value. An improved enthalpy of formation (298 K) for UO{sub 2}(OH){sub 2} is predicted from this work to be −288.7 ± 3 kcal/mol, compared to the currently accepted experimental value of −292.7 ± 6 kcal/mol.

  12. Composite thermochemistry of gas phase U(VI)-containing molecules

    NASA Astrophysics Data System (ADS)

    Bross, David H.; Peterson, Kirk A.

    2014-12-01

    Reaction energies have been calculated for a series of reactions involving UF6, UO3, UO2(OH)2, and UO2F2 using coupled cluster singles and doubles with perturbative triples, CCSD(T), with a series of correlation consistent basis sets, including newly developed pseudopotential (PP)- and all-electron (AE) Douglas-Kroll-Hess-based sets for the U atom. The energies were calculated using a Feller-Peterson-Dixon composite approach in which CCSD(T) complete basis set (CBS) limits were combined with a series of additive contributions for spin-orbit coupling, outer-core correlation, and quantum electrodynamics effects. The calculated reaction enthalpies (both PP and AE) were combined with the accurately known heat of formation of UF6 to determine the enthalpies of formation of UO3, UO2(OH)2, and UO2F2. The contribution to the reaction enthalpies due to correlation of the 5s5p5d electrons of U was observed to be very slowly convergent with basis set and at the CBS limit their impact on the final enthalpies was on the order of 1 kcal/mol or less. For these closed shell molecules, spin-orbit effects contributed about 1 kcal/mol to the final enthalpies. Interestingly, the PP and AE approaches yielded quite different spin-orbit contributions (similar magnitude but opposite in sign), but the total scalar plus spin-orbit results from the two approaches agreed to within ˜1 kcal/mol of each other. The final composite heat of formation for UO2F2 was in excellent agreement with experiment, while the two results obtained for UO3 were just outside the ±2.4 kcal/mol error bars of the currently recommended experimental value. An improved enthalpy of formation (298 K) for UO2(OH)2 is predicted from this work to be -288.7 ± 3 kcal/mol, compared to the currently accepted experimental value of -292.7 ± 6 kcal/mol.

  13. Exchange Bias Optimization by Controlled Oxidation of Cobalt Nanoparticle Films Prepared by Sputter Gas Aggregation.

    PubMed

    Antón, Ricardo López; González, Juan A; Andrés, Juan P; Normile, Peter S; Canales-Vázquez, Jesús; Muñiz, Pablo; Riveiro, José M; De Toro, José A

    2017-03-11

    Porous films of cobalt nanoparticles have been obtained by sputter gas aggregation and controllably oxidized by air annealing at 100 °C for progressively longer times (up to more than 1400 h). The magnetic properties of the samples were monitored during the process, with a focus on the exchange bias field. Air annealing proves to be a convenient way to control the Co/CoO ratio in the samples, allowing the optimization of the exchange bias field to a value above 6 kOe at 5 K. The occurrence of the maximum in the exchange bias field is understood in terms of the density of CoO uncompensated spins and their degree of pinning, with the former reducing and the latter increasing upon the growth of a progressively thicker CoO shell. Vertical shifts exhibited in the magnetization loops are found to correlate qualitatively with the peak in the exchange bias field, while an increase in vertical shift observed for longer oxidation times may be explained by a growing fraction of almost completely oxidized particles. The presence of a hummingbird-like form in magnetization loops can be understood in terms of a combination of hard (biased) and soft (unbiased) components; however, the precise origin of the soft phase is as yet unresolved.

  14. Exchange Bias Optimization by Controlled Oxidation of Cobalt Nanoparticle Films Prepared by Sputter Gas Aggregation

    PubMed Central

    Antón, Ricardo López; González, Juan A.; Andrés, Juan P.; Normile, Peter S.; Canales-Vázquez, Jesús; Muñiz, Pablo; Riveiro, José M.; De Toro, José A.

    2017-01-01

    Porous films of cobalt nanoparticles have been obtained by sputter gas aggregation and controllably oxidized by air annealing at 100 °C for progressively longer times (up to more than 1400 h). The magnetic properties of the samples were monitored during the process, with a focus on the exchange bias field. Air annealing proves to be a convenient way to control the Co/CoO ratio in the samples, allowing the optimization of the exchange bias field to a value above 6 kOe at 5 K. The occurrence of the maximum in the exchange bias field is understood in terms of the density of CoO uncompensated spins and their degree of pinning, with the former reducing and the latter increasing upon the growth of a progressively thicker CoO shell. Vertical shifts exhibited in the magnetization loops are found to correlate qualitatively with the peak in the exchange bias field, while an increase in vertical shift observed for longer oxidation times may be explained by a growing fraction of almost completely oxidized particles. The presence of a hummingbird-like form in magnetization loops can be understood in terms of a combination of hard (biased) and soft (unbiased) components; however, the precise origin of the soft phase is as yet unresolved. PMID:28336895

  15. Interference-free coherence dynamics of gas-phase molecules using spectral focusing.

    PubMed

    Wrzesinski, Paul J; Roy, Sukesh; Gord, James R

    2012-10-08

    Spectral focusing using broadband femtosecond pulses to achieve highly selective measurements has been employed for numerous applications in spectroscopy and microspectroscopy. In this work we highlight the use of spectral focusing for selective excitation and detection of gas-phase species. Furthermore, we demonstrate that spectral focusing, coupled with time-resolved measurements based upon probe delay, allows the observation of interference-free coherence dynamics of multiple molecules and gas-phase temperature making this technique ideal for gas-phase measurements of reacting flows and combustion processes.

  16. From molecules to aggregates

    NASA Astrophysics Data System (ADS)

    Roesky, Herbert W.

    2001-11-01

    The preparation of organometallic oxides, imides and nitrides is described. The molecular structures of these compounds resemble those found in binary systems. However, due to the organic envelope of the molecular solids, they are soluble in organic solvents, easy to crystallize and unambiguously characterizable by single X-ray structural analysis and NMR investigations. Moreover, inorganic oxides can be incorporated in organometallic phosphonates or organoalumoxanes. Herein we describe the organometallic phosphonates as hosts with a hydrophobic exterior.

  17. A Gas Chromatography Experiment for Proving the Application of Quantum Symmetry Restrictions in Homonuclear Diatomic Molecules.

    ERIC Educational Resources Information Center

    Dosiere, M.

    1985-01-01

    Background information, procedures used, and typical results obtained are provided for an experiment in which gas chromatography is used to prove the application of quantum symmetry restrictions in homonuclear diatomic molecules. Comparisons between experimental results and theoretical computed values show good agreement, within one to two…

  18. A Gas Chromatography Experiment for Proving the Application of Quantum Symmetry Restrictions in Homonuclear Diatomic Molecules.

    ERIC Educational Resources Information Center

    Dosiere, M.

    1985-01-01

    Background information, procedures used, and typical results obtained are provided for an experiment in which gas chromatography is used to prove the application of quantum symmetry restrictions in homonuclear diatomic molecules. Comparisons between experimental results and theoretical computed values show good agreement, within one to two…

  19. Probing Buffer-Gas Cooled Molecules with Direct Frequency Comb Spectroscopy in the Mid-Infrrared

    NASA Astrophysics Data System (ADS)

    Spaun, Ben; Changala, Bryan; Bjork, Bryce J.; Heckl, Oliver H.; Patterson, David; Doyle, John M.; Ye, Jun

    2015-06-01

    We present the first demonstration of cavity-enhanced direct frequency comb spectroscopy on buffer-gas cooled molecules.By coupling a mid-infrared frequency comb to a high-finesse cavity surrounding a helium buffer-gas chamber, we can gather rotationally resolved absorption spectra with high sensitivity over a broad wavelength region. The measured ˜10 K rotational and translational temperatures of buffer-gas cooled molecules drastically simplify the observed spectra, compared to those of room temperature molecules, and allow for high spectral resolution limited only by Doppler broadening (10-100 MHz). Our system allows for the extension of high-resolution spectroscopy to larger molecules, enabling detailed analysis of molecular structure and dynamics, while taking full advantage of the powerful optical properties of frequency combs. A. Foltynowicz et al. Cavity-enhanced optical frequency comb spectroscopy in the mid-infrared application to trace detection of hydrogen peroxide. Applied Physics B, vol. 110, pp. 163-175, 2013. {D. Patterson and J. M. Doyle. Cooling molecules in a cell for FTMW spectroscopy. Molecular Physics 110, 1757-1766, 2012

  20. Bombardment of gas molecules on single graphene layer at high temperature

    NASA Astrophysics Data System (ADS)

    Murugesan, Ramki; Park, Jae Hyun; Ha, Dong Sung

    2014-12-01

    Graphite is widely used as a material for rocket-nozzle inserts due to its excellent thermo-physical properties as well as low density. During the operation of rockets, the surface of the graphite nozzle is subjected to very high heat fluxes and the undesirable erosion of the surface occurs due to the bombardment of gas molecules with high kinetic energy, which causes a significant reduction of nozzle performance. However, the understanding and quantification of such bombardment is not satisfactory due to its complexity: The bond breaking-forming happens simultaneously for the carbon atoms of graphene, some gas molecules penetrate through the surface, some of them are reflected from the surface, etc. In the present study, we perform extensive molecular dynamics (MD) simulations to examine the bombardment phenomena in high temperature environment (several thousand Kelvin). Advanced from the previous studies that have focused on the bombardment by light molecules (e.g., H2), we will concentrate on the impact by realistic molecules (e.g., CO2 and H2O ). LAMMPS is employed for the MD simulations with NVE ensemble and AIREBO potential for graphene. The molecular understanding of the interaction between graphene and highly energetic gas molecules will enable us to design an efficient thermo-mechanical protection system.

  1. Bombardment of gas molecules on single graphene layer at high temperature

    SciTech Connect

    Murugesan, Ramki; Park, Jae Hyun; Ha, Dong Sung

    2014-12-09

    Graphite is widely used as a material for rocket-nozzle inserts due to its excellent thermo-physical properties as well as low density. During the operation of rockets, the surface of the graphite nozzle is subjected to very high heat fluxes and the undesirable erosion of the surface occurs due to the bombardment of gas molecules with high kinetic energy, which causes a significant reduction of nozzle performance. However, the understanding and quantification of such bombardment is not satisfactory due to its complexity: The bond breaking-forming happens simultaneously for the carbon atoms of graphene, some gas molecules penetrate through the surface, some of them are reflected from the surface, etc. In the present study, we perform extensive molecular dynamics (MD) simulations to examine the bombardment phenomena in high temperature environment (several thousand Kelvin). Advanced from the previous studies that have focused on the bombardment by light molecules (e.g., H{sub 2}), we will concentrate on the impact by realistic molecules (e.g., CO{sub 2} and H{sub 2}O). LAMMPS is employed for the MD simulations with NVE ensemble and AIREBO potential for graphene. The molecular understanding of the interaction between graphene and highly energetic gas molecules will enable us to design an efficient thermo-mechanical protection system.

  2. Laboratory Studies of Stabilities of Heterocyclic Aromatic Molecules: Suggested Gas Phase Ion-Molecule Routes to Production in Interstellar Gas Clouds

    NASA Technical Reports Server (NTRS)

    Adams, Nigel G.; Fondren, L. Dalila; McLain, Jason L.; Jackson, Doug M.

    2006-01-01

    Several ring compounds have been detected in interstellar gas clouds, ISC, including the aromatic, benzene. Polycyclic aromatic hydrocarbons, PAHs, have been implicated as carriers of diffuse interstellar bands (DIBs) and unidentified infrared (UIR) bands. Heterocyclic aromatic rings of intermediate size containing nitrogen, possibly PreLife molecules, were included in early searches but were not detected and a recent search for Pyrimidine was unsuccessful. Our laboratory investigations of routes to such molecules could establish their existence in ISC and suggest conditions under which their concentrations would be maximized thus aiding the searches. The stability of such ring compounds (C5H5N, C4H4N2, C5H11N and C4H8O2) has been tested in the laboratory using charge transfer excitation in ion-molecule reactions. The fragmentation paths, including production of C4H4(+), C3H3N(+) and HCN, suggest reverse routes to the parent molecules, which are presently under laboratory investigation as production sources.

  3. Guest Molecule Exchange Kinetics for the 2012 Ignik Sikumi Gas Hydrate Field Trial

    SciTech Connect

    White, Mark D.; Lee, Won Suk

    2014-05-14

    A commercially viable technology for producing methane from natural gas hydrate reservoirs remains elusive. Short-term depressurization field tests have demonstrated the potential for producing natural gas via dissociation of the clathrate structure, but the long-term performance of the depressurization technology ultimately requires a heat source to sustain the dissociation. A decade of laboratory experiments and theoretical studies have demonstrated the exchange of pure CO2 and N2-CO2 mixtures with CH4 in sI gas hydrates, yielding critical information about molecular mechanisms, recoveries, and exchange kinetics. Findings indicated the potential for producing natural gas with little to no production of water and rapid exchange kinetics, generating sufficient interest in the guest-molecule exchange technology for a field test. In 2012 the U.S. DOE/NETL, ConocoPhillips Company, and Japan Oil, Gas and Metals National Corporation jointly sponsored the first field trial of injecting a mixture of N2-CO2 into a CH4-hydrate bearing formation beneath the permafrost on the Alaska North Slope. Known as the Ignik Sikumi #1 Gas Hydrate Field Trial, this experiment involved three stages: 1) the injection of a N2-CO2 mixture into a targeted hydrate-bearing layer, 2) a 4-day pressurized soaking period, and 3) a sustained depressurization and fluid production period. Data collected during the three stages of the field trial were made available after an extensive quality check. These data included continuous temperature and pressure logs, injected and recovered fluid compositions and volumes. The Ignik Sikumi #1 data set is extensive, but contains no direct evidence of the guest-molecule exchange process. This investigation is directed at using numerical simulation to provide an interpretation of the collected data. A numerical simulator, STOMP-HYDT-KE, was recently completed that solves conservation equations for energy, water, mobile fluid guest molecules, and hydrate guest

  4. Ultracold Dipolar Gas of Fermionic 23Na 40K Molecules in Their Absolute Ground State

    NASA Astrophysics Data System (ADS)

    Park, Jee Woo; Will, Sebastian A.; Zwierlein, Martin W.

    2015-05-01

    We report on the creation of an ultracold dipolar gas of fermionic 23Na 40K molecules in their absolute rovibrational and hyperfine ground state. Starting from weakly bound Feshbach molecules, we demonstrate hyperfine resolved two-photon transfer into the singlet X 1Σ+ |v =0 ,J =0 ⟩ ground state, coherently bridging a binding energy difference of 0.65 eV via stimulated rapid adiabatic passage. The spin-polarized, nearly quantum degenerate molecular gas displays a lifetime longer than 2.5 s, highlighting NaK's stability against two-body chemical reactions. A homogeneous electric field is applied to induce a dipole moment of up to 0.8 D. With these advances, the exploration of many-body physics with strongly dipolar Fermi gases of 23Na 40K molecules is within experimental reach.

  5. Ultracold Dipolar Gas of Fermionic 23Na40 K Molecules in Their Absolute Ground State.

    PubMed

    Park, Jee Woo; Will, Sebastian A; Zwierlein, Martin W

    2015-05-22

    We report on the creation of an ultracold dipolar gas of fermionic 23Na40 K molecules in their absolute rovibrational and hyperfine ground state. Starting from weakly bound Feshbach molecules, we demonstrate hyperfine resolved two-photon transfer into the singlet X 1Σ+|v=0,J=0⟩ ground state, coherently bridging a binding energy difference of 0.65 eV via stimulated rapid adiabatic passage. The spin-polarized, nearly quantum degenerate molecular gas displays a lifetime longer than 2.5 s, highlighting NaK's stability against two-body chemical reactions. A homogeneous electric field is applied to induce a dipole moment of up to 0.8 D. With these advances, the exploration of many-body physics with strongly dipolar Fermi gases of 23Na40K molecules is within experimental reach.

  6. Ground state of a hydrogen ion molecule immersed in an inhomogeneous electron gas

    NASA Astrophysics Data System (ADS)

    Diaz-Valdes, J.; Gutierrez, F. A.; Matamala, A. R.; Denton, C. D.; Vargas, P.; Valdes, J. E.

    2007-01-01

    In this work we have calculated the ground state energy of the hydrogen molecule, H2+, immersed in the highly inhomogeneous electron gas around a metallic surface within the local density approximation. The molecule is perturbed by the electron density of a crystalline surface of Au <1 0 0> with the internuclear axis parallel to the surface. The surface spatial electron density is calculated through a linearized band structure method (LMTO-DFT). The ground state of the molecule-ion was calculated using the Born-Oppenheimer approximation for a fixed-ion while the screening effects of the inhomogeneous electron gas are depicted by a Thomas-Fermi like electrostatic potential. We found that within our model the molecular ion dissociates at the critical distance of 2.35 a.u. from the first atomic layer of the solid.

  7. Noble gas-actinide compounds: complexation of the CUO molecule by Ar, Kr, and Xe atoms in noble gas matrices.

    PubMed

    Li, Jun; Bursten, Bruce E; Liang, Binyong; Andrews, Lester

    2002-03-22

    The CUO molecule, formed from the reaction of laser-ablated U atoms with CO in a noble gas, exhibits very different stretching frequencies in a solid argon matrix [804.3 and 852.5 wave numbers (cm(-1))] than in a solid neon matrix (872.2 and 1047.3 cm(-1)). Related experiments in a matrix consisting of 1% argon in neon suggest that the argon atoms are interacting directly with the CUO molecule. Relativistic density functional calculations predict that CUO can bind directly to one argon atom (U-Ar = 3.16 angstroms; binding energy = 3.2 kilocalories per mole), accompanied by a change in the ground state from a singlet to a triplet. Our experimental and theoretical results also suggest that multiple argon atoms can bind to a single CUO molecule.

  8. Noble Gas-Actinide Compounds: Complexation of the CUO Molecule by Ar, Kr, and Xe Atoms in Noble Gas Matrices

    SciTech Connect

    Li, Jun; Bursten, Bruce E.; Liang, Binyong; Andrews, Lester

    2002-03-22

    The CUO molecule, formed from the reaction of laser-ablated U atoms with CO in a noble gas, exhibits very different stretching frequencies in a solid argon matrix (804.3 and 852.5 cm -1 ) than in a solid neon matrix (872.2 and 1047.3 cm -1 ). Related experiments in a matrix consisting of 1% Ar in Ne suggest that the Ar atoms are interacting directly with the CUO molecule. Relativistic density functional calculations predict that CUO can bind directly to an Ar atom (U-Ar= 3.16 angstroms; binding energy= 3.2 kcal/mol), accompanied by a change in the ground state from a singlet to a triplet. The experimental and theoretical results suggest the possibility that multiple Ar atoms can bind to a single CUO molecule.

  9. Energy accommodation of gas molecules with free-standing films of vertically aligned single-walled carbon nanotubes

    SciTech Connect

    Ryu, K.; Harada, Y.; Kinefuchi, I.; Ishikawa, K.; Shiomi, J.; Takagi, S.; Maruyama, S.; Matsumoto, Y.

    2011-05-20

    The scattering process of gas molecules on vertically aligned single-walled carbon nanotubes (VA-SWNTs) was investigated by the molecular beam technique. To investigate interactions between VA-SWNT films themselves and helium gas molecules without the presence of substrates, free-standing films were used. The scattered molecules are divided into three components; reflected molecules, diffusively transmitted molecules, and directly transmitted molecules without interaction with SWNTs. Even with the thin film, most molecules have interacted with the films, which suggests that most molecules have interacted at the randomly oriented layer at the topmost of the films. Because of low accommodation coefficients of helium gas, VA-SWNTs films are thought to be useful as a surface modification to enhance energy accommodation.

  10. Interface-Induced Ordering of Gas Molecules Confined in a Small Space

    PubMed Central

    Lu, Yi-Hsien; Yang, Chih-Wen; Fang, Chung-Kai; Ko, Hsien-Chen; Hwang, Ing-Shouh

    2014-01-01

    The thermodynamic properties of gases have been understood primarily through phase diagrams of bulk gases. However, observations of gases confined in a nanometer space have posed a challenge to the principles of classical thermodynamics. Here, we investigated interfacial structures comprising either O2 or N2 between water and a hydrophobic solid surface by using advanced atomic force microscopy techniques. Ordered epitaxial layers and cap-shaped nanostructures were observed. In addition, pancake-shaped disordered layers that had grown on top of the epitaxial base layers were observed in oxygen-supersaturated water. We propose that hydrophobic solid surfaces provide low-chemical-potential sites at which gas molecules dissolved in water can be adsorbed. The structures are further stabilized by interfacial water. Here we show that gas molecules can agglomerate into a condensed form when confined in a sufficiently small space under ambient conditions. The crystalline solid surface may even induce a solid-gas state when the gas-substrate interaction is significantly stronger than the gas-gas interaction. The ordering and thermodynamic properties of the confined gases are determined primarily according to interfacial interactions. PMID:25424443

  11. Size controlled deposition of Cu and Si nano-clusters by an ultra-high vacuum sputtering gas aggregation technique

    NASA Astrophysics Data System (ADS)

    Banerjee, A. N.; Krishna, R.; Das, B.

    2008-02-01

    In this paper we have reported the syntheses of copper and silicon nano-clusters by a sputtering-gas-aggregation type growth technique. The process involves typical magnetron sputtering vaporization of target materials followed by an inert gas condensation to form clusters of varying sizes. The size-distributions of the clusters typically follow a normal-distribution and the peak cluster sizes of the distributions depends on several factors, which include gas-flow rate, length of the growth region, deposition pressure etc. We have observed a variation in the peak cluster size with the variation of the gas (argon) flow rates. The experimental values are compared with the existing models and the results are found to be in good agreement. The results are significant since it demonstrates that proper optimization of operation conditions can lead to desired cluster sizes as well as desired cluster-size distributions.

  12. Enhancement of Sublimation of Single Graphene Layer by Interacting with Gas Molecules in Rarefied Environment

    NASA Astrophysics Data System (ADS)

    Murugesan, Ramki; Park, Jae Hyun

    2014-11-01

    Graphene has excellent mechanical properties. One of them is the resistance to high temperature environment. Since the sublimation temperature of graphene is over 4500 K, it has been used for diverse high temperature applications in order to protect the system. In this study, using extensive molecular dynamics simulations, we show that the sublimation of graphene could be enhanced (occurs at the lower temperature) by interacting with the gas molecules. With increase in temperature, the bonds in graphene becomes so sensitive to interact with the incoming gas molecules. When the temperature is low, the graphene is stable to the impingement of gas molecules: The light H2 gases are stick to the graphene surface and remains being attached while the heavy CO2 and H2O are bounced back from the surface. However, at high temperature H2 gases are absorbed on the graphene and destroy the C -C bonds by forming C -H bonds. The local breakage of bond at the impingement spot spreads the entire graphene soon, causing a complete sublimation. Even though the heavy CO2 and H2O molecules also break the C -C bonds at high temperature,but their impingement effect is localized and the breakage does not propagate over the entire surface. This research was supported by Agency for Defence Development (ADD).

  13. High Resolution Rovibrational Spectroscopy of Large Molecules Using Infrared Frequency Combs and Buffer Gas Cooling

    NASA Astrophysics Data System (ADS)

    Changala, Bryan; Spaun, Ben; Patterson, David; Bjork, Bryce J.; Heckl, Oliver H.; Doyle, John M.; Ye, Jun

    2016-06-01

    We have recently demonstrated the integration of cavity-enhanced direct frequency comb spectroscopy with buffer gas cooling to acquire high resolution infrared spectra of translationally and rotationally cold (˜10 K) gas-phase molecules. Here, we extend this method to significantly larger systems, including naphthalene (C10H_8), a prototypical polyaromatic hydrocarbon, and adamantane (C10H_{16}), the fundamental building block of diamonoids. To the authors' knowledge, the latter molecule represents the largest system for which rotationally resolved spectra in the CH stretch region (3 μm) have been obtained. In addition to the measured spectra, we present several details of our experimental methods. These include introducing non-volatile species into the cold buffer gas cell and obtaining broadband spectra with single comb mode resolution. We also discuss recent modifications to the apparatus to improve its absorption sensitivity and time resolution, which facilitate the study of both larger molecular systems and cold chemical dynamics. B. Spaun, et al. Probing buffer-gas cooled molecules with direct frequency comb spectroscopy in the mid-infrared, WF02, 70th International Symposium on Molecular Spectroscopy, Champaign-Urbana, IL, 2015.

  14. Superradiance from Two Dimensional Brick-Wall Aggregates of Dye Molecules: The Role of Size and Shape for the Temperature Dependence

    NASA Astrophysics Data System (ADS)

    Eisfeld, Alexander; Marquardt, Christian; Paulheim, Alexander; Sokolowski, Moritz

    2017-09-01

    Aggregates of interacting molecules can exhibit electronically excited states that are coherently delocalized over many molecules. This can lead to a strong enhancement of the fluorescence decay rate which is referred to as superradiance (SR). To date, the temperature dependence of SR is described by a 1 /T law. Using an epitaxial dye layer and a Frenkel-exciton based model we provide both experimental and theoretical evidence that significant deviations from the 1 /T behavior can occur for brick-wall-type aggregates of finite size leading even to a maximum of the SR at finite temperature. This is due to the presence of low energy excitations of weak or zero transition strength. These findings are relevant for designing light-emitting molecular materials.

  15. Prospect for the formation of a gas of ultracold polar NaRb molecules

    NASA Astrophysics Data System (ADS)

    Quéméner, Goulven; Vexiau, Romain; Wang, Gaoren; Lepers, Maxence; Luc, Eliane; Bouloufa-Maafa, Nadia; Dulieu, Olivier; Wang, Dajun

    2015-05-01

    We present a complete theoretical model for the formation of an ultracold gas of polar NaRb molecules, based on high-precision spectroscopic data completed with accurate quantum chemistry calculations. Weakly-bound molecules are first created via a Feshbach resonance with main triplet character. The population is transfered down to the lowest rovibrational level of the ground state by a coherent STIRAP process. The efficiency of various paths via different electronically-excited molecular states is discussed in relation of the ongoing experimental implementation. Supported by Agence Nationale de la Recherche (ANR), project COPOMOL (# ANR-13-IS04-0004-01).

  16. Formation of complex organic molecules in cold objects: the role of gas-phase reactions

    NASA Astrophysics Data System (ADS)

    Balucani, Nadia; Ceccarelli, Cecilia; Taquet, Vianney

    2015-04-01

    While astrochemical models are successful in reproducing many of the observed interstellar species, they have been struggling to explain the observed abundances of complex organic molecules. Current models tend to privilege grain surface over gas-phase chemistry in their formation. One key assumption of those models is that radicals trapped in the grain mantles gain mobility and react on lukewarm ( ≳ 30 K) dust grains. Thus, the recent detections of methyl formate (MF) and dimethyl ether (DME) in cold objects represent a challenge and may clarify the respective role of grain-surface and gas-phase chemistry. We propose here a new model to form DME and MF with gas-phase reactions in cold environments, where DME is the precursor of MF via an efficient reaction overlooked by previous models. Furthermore, methoxy, a precursor of DME, is also synthesized in the gas phase from methanol, which is desorbed by a non-thermal process from the ices. Our new model reproduces fairly well the observations towards L1544. It also explains, in a natural way, the observed correlation between DME and MF. We conclude that gas-phase reactions are major actors in the formation of MF, DME and methoxy in cold gas. This challenges the exclusive role of grain-surface chemistry and favours a combined grain-gas chemistry.

  17. Infrared Action Spectroscopy of Low-Temperature Neutral Gas-Phase Molecules of Arbitrary Structure

    NASA Astrophysics Data System (ADS)

    Yatsyna, Vasyl; Bakker, Daniël J.; Salén, Peter; Feifel, Raimund; Rijs, Anouk M.; Zhaunerchyk, Vitali

    2016-09-01

    We demonstrate a technique for IR action spectroscopy that enables measuring IR spectra in a background-free fashion for low-temperature neutral gas-phase molecules of arbitrary structure. The method is exemplified experimentally for N -methylacetamide molecules in the mid-IR spectral range of 1000 - 1800 cm-1 , utilizing the free electron laser FELIX. The technique involves the resonant absorption of multiple mid-IR photons, which induces molecular dissociation. The dissociation products are probed with 10.49 eV vacuum ultraviolet photons and analyzed with a mass spectrometer. We also demonstrate the capability of this method to record, with unprecedented ease, mid-IR spectra for the molecular associates, such as clusters and oligomers, present in a molecular beam. In this way the mass-selected spectra of low-temperature gas-phase dimers and trimers of N -methylacetamide are measured in the full amide I-III range.

  18. Molecular conformation of linear alkane molecules: From gas phase to bulk water through the interface

    NASA Astrophysics Data System (ADS)

    Murina, Ezequiel L.; Fernández-Prini, Roberto; Pastorino, Claudio

    2017-08-01

    We studied the behavior of long chain alkanes (LCAs) as they were transferred from gas to bulk water, through the liquid-vapor interface. These systems were studied using umbrella sampling molecular dynamics simulation and we have calculated properties like free energy profiles, molecular orientation, and radius of gyration of the LCA molecules. The results show changes in conformation of the solutes along the path. LCAs adopt pronounced molecular orientations and the larger ones extend appreciably when partially immersed in the interface. In bulk water, their conformations up to dodecane are mainly extended. However, larger alkanes like eicosane present a more stable collapsed conformation as they approach bulk water. We have characterized the more probable configurations in all interface and bulk regions. The results obtained are of interest for the study of biomatter processes requiring the transfer of hydrophobic matter, especially chain-like molecules like LCAs, from gas to bulk aqueous systems through the interface.

  19. Molecular conformation of linear alkane molecules: From gas phase to bulk water through the interface.

    PubMed

    Murina, Ezequiel L; Fernández-Prini, Roberto; Pastorino, Claudio

    2017-08-14

    We studied the behavior of long chain alkanes (LCAs) as they were transferred from gas to bulk water, through the liquid-vapor interface. These systems were studied using umbrella sampling molecular dynamics simulation and we have calculated properties like free energy profiles, molecular orientation, and radius of gyration of the LCA molecules. The results show changes in conformation of the solutes along the path. LCAs adopt pronounced molecular orientations and the larger ones extend appreciably when partially immersed in the interface. In bulk water, their conformations up to dodecane are mainly extended. However, larger alkanes like eicosane present a more stable collapsed conformation as they approach bulk water. We have characterized the more probable configurations in all interface and bulk regions. The results obtained are of interest for the study of biomatter processes requiring the transfer of hydrophobic matter, especially chain-like molecules like LCAs, from gas to bulk aqueous systems through the interface.

  20. New structural types of Mn16 single-molecule magnets: W-shaped topology from reductive aggregation.

    PubMed

    Thuijs, Annaliese E; King, Philippa; Abboud, Khalil A; Christou, George

    2015-09-21

    Two new Mn16 clusters are reported: [Mn16O10(OH)3(OMe)8(O2CPhBut)17(MeOH)5] (2) and [Mn16O16(OMe)6(O2CPh)12(NO3)4(MeOH)2(H2O)4] (3). The complexes were obtained by reductive aggregation of MnO4– in CH2Cl2/MeOH, and oxidation of MnII and preformed (NnBu4)[Mn4IIIO2(O2CPh)9(H2O)] with CeIV, respectively. The core of 2 has a Mn16III core with an unusual 1:2:3:4:3:2:1 layer structure and a W-shaped pleated topology, whereas 3 contains a central 2 × 3 Mn6IV planar grid held within a nonplanar Mn10III loop and is a rare example of a complex with nitrate ions bridging like carboxylate ions. Variable-temperature, solid-state dc susceptibility, and ac susceptibility studies reveal that 2 and 3 possess S = 12 and S = 8 ground states, respectively. Fits of dc magnetization data collected over a temperature range of 1.8–4.0 K and a magnetization range of 0.1–4 T were fit to give S = 12, D = −0.16(2) cm–1, g = 1.98(3) for 2 and S = 8, D = −0.22(1) cm–1, g = 1.99(2) for 3, where D is the axial zero-field splitting parameter. The ac in-phase (χM′T) susceptibility below 15 K confirmed the ground-state spin values of 2 and 3, as determined from dc data, and the appearance of frequency-dependent out-of-phase (χM″) signals revealed that both complexes are new single-molecule magnets (SMMs). Fits of the ac data gave Ueff = 49.7(1) K and τ0 = 4.32 × 10–9 s for 2 and Ueff ≈ 14.0 ± 2 cm–1 and τ0 ≈ 3.2 ± 0.5 × 10–8 s for 3, where Ueff is the effective barrier to magnetization relaxation and τ0 is the pre-exponential factor. Thus, complexes 2 and 3 are two new members of a growing family of Mn16 clusters, and two new examples of high-nuclearity SMMs, with the Ueff for 2 approaching the value for the prototypical SMM family, [Mn12O12(O2CR)16(H2O)4].

  1. Intermediate energy proton stopping power for hydrogen molecules and monoatomic helium gas

    NASA Technical Reports Server (NTRS)

    Xu, Y. J.; Khandelwal, G. S.; Wilson, J. W.

    1984-01-01

    Stopping power in the intermediate energy region (100 keV to 1 MeV) was investigated, based on the work of Lindhard and Winther, and on the local plasma model. The theory is applied to calculate stopping power of hydrogen molecules and helium gas for protons of energy ranging from 100 keV to 2.5 MeV. Agreement with the experimental data is found to be within 10 percent.

  2. Intermediate energy proton stopping power for hydrogen molecules and monoatomic helium gas

    NASA Technical Reports Server (NTRS)

    Xu, Y. J.; Khandelwal, G. S.; Wilson, J. W.

    1984-01-01

    Stopping power in the intermediate energy region (100 keV to 1 MeV) was investigated, based on the work of Lindhard and Winther, and on the local plasma model. The theory is applied to calculate stopping power of hydrogen molecules and helium gas for protons of energy ranging from 100 keV to 2.5 MeV. Agreement with the experimental data is found to be within 10 percent.

  3. Buffer Gas Modifiers Effect Resolution in Ion Mobility Spectrometry through Selective Ion-Molecule Clustering Reactions

    PubMed Central

    Fernández-Maestre, Roberto; Wu, Ching; Hill, Herbert H.

    2013-01-01

    RATIONALE When polar molecules (modifiers) are introduced into the buffer gas of an ion mobility spectrometer, most ion mobilities decrease due to the formation of ion-modifier clusters. METHODS We used ethyl lactate, nitrobenzene, 2-butanol, and tetrahydrofuran-2-carbonitrile as buffer gas modifiers and electrospray ionization ion mobility spectrometry (IMS) coupled to quadrupole mass spectrometry. Ethyl lactate, nitrobenzene, and tetrahydrofuran-2-carbonitrile had not been tested as buffer gas modifiers and 2-butanol had not been used with basic amino acids. RESULTS The ion mobilities of several diamines (arginine, histidine, lysine, and atenolol) were not affected or only slightly reduced when these modifiers were introduced into the buffer gas (3.4% average reduction in an analyte's mobility for the three modifiers). Intramolecular bridges caused limited change in the ion mobilities of diamines when modifiers were added to the buffer gas; these bridges hindered the attachment of modifier molecules to the positive charge of ions and delocalized the charge, which deterred clustering. There was also a tendency towards large changes in ion mobility when the mass of the analyte decreased; ethanolamine, the smallest compound tested, had the largest reduction in ion mobility with the introduction of modifiers into the buffer gas (61%). These differences in mobilities, together with the lack of shift in bridge-forming ions, were used to separate ions that overlapped in IMS, such as isoleucine and lysine, and arginine and phenylalanine, and made possible the prediction of separation or not of overlapping ions. CONCLUSIONS The introduction of modifiers into the buffer gas in IMS can selectively alter the mobilities of analytes to aid in compound identification and/or enable the separation of overlapping analyte peaks. PMID:22956312

  4. The Strong Light-Emission Materials in the Aggregated State: What Happens from a Single Molecule to the Collective Group.

    PubMed

    Li, Qianqian; Li, Zhen

    2017-07-01

    The strong light emission of organic luminogens in the aggregated state is essential to their applications as optoelectronic materials with good performance. In this review, with respect to the aggregation-induced emission and room-temperature phosphorescence luminogens, the important role of molecular packing modes is highlighted. As demonstrated in the selected examples, the molecular packing status in the aggregate state is affected by many factors, including the molecular configurations, the inherent electronic properties, the special functional groups, and so on. With the consideration of all these parameters, the strong fluorescence and phosphorescence in the aggregated state could be achieved in the rationally designed organic luminogens, providing some guidance for the further development.

  5. High-order-harmonic generation using gas-phase H{sub 2}O molecules

    SciTech Connect

    Zhao Songfeng; Jin, Cheng; Le, Anh-Thu; Lin, C. D.; Lucchese, R. R.

    2011-03-15

    We investigate high-order-harmonic generation of isotropically distributed gas-phase H{sub 2}O molecules exposed to an intense laser field. The induced dipole of each individual molecule by the laser field is first calculated using the recently developed quantitative rescattering theory. In a thin medium, harmonic spectra generated coherently from all the molecules are then calculated by solving Maxwell's equation of propagation. By using accurate transition dipoles of H{sub 2}O, we show that the harmonics in the lower plateau region are quite different from models that employ the simpler strong-field approximation. We also examine the magnitude and phase of the harmonics and their dependence on laser focusing conditions.

  6. Responses of the Microalga Chlorophyta sp. to Bacterial Quorum Sensing Molecules (N-Acylhomoserine Lactones): Aromatic Protein-Induced Self-Aggregation.

    PubMed

    Zhou, Dandan; Zhang, Chaofan; Fu, Liang; Xu, Liang; Cui, Xiaochun; Li, Qingcheng; Crittenden, John C

    2017-03-21

    Bacteria and microalgae often coexist during the recycling of microalgal bioresources in wastewater treatment processes. Although the bacteria may compete with the microalgae for nutrients, they could also facilitate microalgal harvesting by forming algal-bacterial aggregates. However, very little is known about interspecies interactions between bacteria and microalgae. In this study, we investigated the responses of a model microalga, Chlorophyta sp., to the typical quorum sensing (QS) molecules N-acylhomoserine lactones (AHLs) extracted from activated sludge bacteria. Chlorophyta sp. self-aggregated in 200 μm bioflocs by secreting 460-1000 kDa aromatic proteins upon interacting with AHLs, and the settling efficiency of Chlorophyta sp. reached as high as 41%. However, Chlorophyta sp. cells were essentially in a free suspension in the absence of AHLs. Fluorescence intensity of the aromatic proteins had significant (P < 0.05) relationship with the Chlorophyta sp. settleability, and showed a positive correlation, indicating that aromatic proteins helped aggregate microalga. Transcriptome results further revealed up-regulation of synthesis pathways for aromatic proteins from tyrosine and phenylalanine that was assisted by anthranilate accumulation. To the best of our knowledge, this is the first study to confirm that eukaryotic microorganisms can sense and respond to prokaryotic QS molecules.

  7. An Experimental Study on the Structure of Cosmic Dust Aggregates and Their Alignment by Motion Relative to Gas.

    PubMed

    Wurm; Blum

    2000-01-20

    We experimentally studied the shape of dust grains grown in a cluster-cluster type of aggregation (CCA) and derived characteristic axial ratios to describe the nonsphericity. CCAs might be described by an axial ratio rhoCCA=rg,max&solm0;rg,min approximately 2.0 in the limit of large aggregates, where rg,min and rg,max describe the minimum and maximum radius of gyration, while small aggregates show a somewhat larger value in their mean axial ratio up to rhoCCA approximately 3.0 but rapidly decrease to the limit rhoCCA approximately 2.0. The axial ratios for large aggregates are in agreement with the general findings of different authors for axial ratios of interstellar dust grains that are generally described by rods or spheroids. Beyond this kind of agreement, our approach does not necessarily require a special shape for individual dust grains but rather offers a physical process to generate nonsphericity. Although the simple shapes might be sufficient for first-order applications and are easier to handle analytically, our results offer a firm ground of special axial ratios for rods or spheroids on a more physical basis apart from any ad hoc assumptions. We also find an alignment of the aggregates during sedimentation in a gas along the drift axis leading to an axial ratio of rhoCCA,align=1.21+/-0.02 with respect to the drift axis and an axis perpendicular to this drift. This result is directly applicable to dust grains in protoplanetary disks and planetary atmospheres.

  8. Numerical analysis on gas-surface interaction by molecular dynamics method. I - Simulation with Lennard-Jones molecules

    NASA Astrophysics Data System (ADS)

    Matsumoto, Yoichiro; Matsui, Jun; Ohashi, Hideo

    1992-07-01

    Rarefied gas flows in various situations are calculated successfully by the direct simulation Monte Carlo method. In the simulation, the Maxwell model, where a gas molecule reflects diffusely with the probability alpha and reflects specularly with the probability 1 - alpha, is widely used for boundary conditions on solid surfaces. However, the value of alpha is determined empirically and varies greatly with conditions such as degree of contamination and temperature of the surface. Rational prediction of the value and analysis of the interaction between gas and solid surface are required. In this paper, the behavior of a gas molecule with collides onto the solid surface is simulated by the molecular dynamics method. The numerical results reveal that the scattering behavior of the gas molecule is neither specular, diffuse, nor Maxwell-type reflection, and that the sticking probability is affected by the initial gas velocity and the potential well depth.

  9. Enhanced fluorescence and aggregation of rhodamine molecules dispersed in a thin polymer film in the presence of plasmonic nanostructures

    NASA Astrophysics Data System (ADS)

    Kamalieva, Aisylu N.; Toropov, Nikita A.; Vartanyan, Tigran A.

    2016-04-01

    Optical properties of composite structures comprised of the island films of silver nanoparticles with a thin molecular layer of a dye rhodamine 6G were obtained and studied in this paper. In the near field of plasmonic nanoparticles enhancement and shifting of the maximums of the absorption and fluorescence spectra were observed. In the absorption and fluorescence spectra of thin molecular films with nanoparticles the new red-shifted band in comparison with spectra of thin films without nanoparticles was found. This band was associated with the formation of aggregates. Thus, the silver nanoparticles can contribute to fluorescence enhancement and formation of the aggregates in the rhodamine thin films.

  10. New quantum chemical computations of formamide deuteration support gas-phase formation of this prebiotic molecule

    NASA Astrophysics Data System (ADS)

    Skouteris, D.; Vazart, F.; Ceccarelli, C.; Balucani, N.; Puzzarini, C.; Barone, V.

    2017-06-01

    Based on recent work, formamide might be a potentially very important molecule in the emergence of terrestrial life. Although detected in the interstellar medium for decades, its formation route is still debated, whether in the gas phase or on the dust grain surfaces. Molecular deuteration has proven to be, in other cases, an efficient way to identify how a molecule is synthesized. For formamide, new published observations towards the IRAS16293-2422 B hot corino show that its three deuterated forms have all the same deuteration ratio, 2-5 per cent and that this is a factor of 3-8 smaller than that measured for H2CO towards the IRAS16293-2422 protostar. Following a previous work on the gas-phase formamide formation via the reaction NH2 + H2CO → HCONH2 + H, we present here new calculations of the rate coefficients for the production of monodeuterated formamide through the same reaction, starting from monodeuterated NH2 or H2CO. Some misconceptions regarding our previous treatment of the reaction are also cleared up. The results of the new computations show that, at the 100 K temperature of the hot corino, the rate of deuteration of the three forms is the same, within 20 per cent. On the contrary, the reaction between non-deuterated species proceeds three times faster than that with deuterated ones. These results confirm that a gas-phase route for the formation of formamide is perfectly in agreement with the available observations.

  11. A flexible metal–organic framework: Guest molecules controlled dynamic gas adsorption

    DOE PAGES

    Mahurin, Shannon Mark; Li, Man -Rong; Wang, Hailong; ...

    2015-04-13

    A flexible metal–organic framework (MOF) of [Zn3(btca)2(OH)2]·(guest)n (H2btca = 1,2,3-benzotriazole-5-carboxylic acid) that exhibits guest molecule-controlled dynamic gas adsorption is reported in which carbon dioxide molecules rather than N2, He, and Ar induce a structural transition with a corresponding appearance of additional steps in the isotherms. Physical insights into the dynamic adsorption behaviors of flexible compound 1 were detected by gas adsorption at different temperatures and different pressures and confirmed by Fourier transform infrared spectroscopy and molecular simulations. Interestingly, by taking advantage of the flexible nature inherent to the framework, this MOF material enables highly selective adsorption of CO2/N2, CO2/Ar, andmore » CO2/He of 36.3, 32.6, and 35.9, respectively, at 298 K. Furthermore, this class of flexible MOFs has potential applications for controlled release, molecular sensing, noble gas separation, smart membranes, and nanotechnological devices.« less

  12. A flexible metal–organic framework: Guest molecules controlled dynamic gas adsorption

    SciTech Connect

    Mahurin, Shannon Mark; Li, Man -Rong; Wang, Hailong; Lu, Zhengliang; Chen, Banglin; Dai, Sheng; Yue, Yanfeng; Rabone, Jeremy A.; Liu, Hongjun; Wang, Jihang; Fang, Youxing

    2015-04-13

    A flexible metal–organic framework (MOF) of [Zn3(btca)2(OH)2]·(guest)n (H2btca = 1,2,3-benzotriazole-5-carboxylic acid) that exhibits guest molecule-controlled dynamic gas adsorption is reported in which carbon dioxide molecules rather than N2, He, and Ar induce a structural transition with a corresponding appearance of additional steps in the isotherms. Physical insights into the dynamic adsorption behaviors of flexible compound 1 were detected by gas adsorption at different temperatures and different pressures and confirmed by Fourier transform infrared spectroscopy and molecular simulations. Interestingly, by taking advantage of the flexible nature inherent to the framework, this MOF material enables highly selective adsorption of CO2/N2, CO2/Ar, and CO2/He of 36.3, 32.6, and 35.9, respectively, at 298 K. Furthermore, this class of flexible MOFs has potential applications for controlled release, molecular sensing, noble gas separation, smart membranes, and nanotechnological devices.

  13. Exobiological implications of dust aggregation in planetary atmospheres: An experiment for the gas-grain simulation facility

    NASA Technical Reports Server (NTRS)

    Huntington, J. L.; Schwartz, D. E.; Marshall, J. R.

    1991-01-01

    The Gas-Grain Simulation Facility (GGSF) will provide a microgravity environment where undesirable environmental effects are reduced, and thus, experiments involving interactions between small particles and grains can be more suitably performed. Slated for flight aboard the Shuttle in 1992, the ESA glovebox will serve as a scientific and technological testbed for GGSF exobiology experiments as well as generating some basic scientific data. Initial glovebox experiments will test a method of generating a stable, mono-dispersed cloud of fine particles using a vibrating sprinkler system. In the absence of gravity and atmospheric turbulence, it will be possible to determine the influence of interparticle forces in controlling the rate and mode of aggregation. The experimental chamber can be purged of suspended matter to enable multiple repetitions of the experiments. Of particular interest will be the number of particles per unit volume of the chamber, because it is suspected that aggregation will occur extremely rapidly if the number exceeds a critical value. All aggregation events will be recorded on high-resolution video film. Changes in the experimental procedure as a result of surprise events will be accompanied by real-time interaction with the mission specialist during the Shuttle flight.

  14. Reactions of metal cluster anions with inorganic and organic molecules in the gas phase.

    PubMed

    Zhao, Yan-Xia; Liu, Qing-Yu; Zhang, Mei-Qi; He, Sheng-Gui

    2016-07-28

    The study of gas phase ion-molecule reactions by state-of-the-art mass spectrometric experiments in conjunction with quantum chemistry calculations offers an opportunity to clarify the elementary steps and mechanistic details of bond activation and conversion processes. In the past few decades, a considerable number of publications have been devoted to the ion-molecule reactions of metal clusters, the experimentally and theoretically tractable models for the active phase of condensed phase systems. The focus of this perspective concerns progress on activation and transformation of important inorganic and organic molecules by negatively charged metal clusters. The metal cluster anions cover bare metal clusters as well as ligated systems with oxygen, carbon, and nitrogen, among others. The following important issues have been summarized and discussed: (i) dependence of chemical reactivity and selectivity on cluster structures and sizes, metals and metal oxidation states, odd-even electron numbers, etc. and (ii) effects of doping, ligation, and pre-adsorption on the reactivity of metal clusters toward rather inert molecules.

  15. The double dark resonance in a cold gas of Cs atoms and molecules.

    PubMed

    Feng, ZhiFang; Li, WeiDong; Xiao, LianTuan; Jia, SuoTang

    2008-09-29

    We theoretically investigated the properties of the effective four-level stimulated Raman adiabatic passage scheme in a cold gas of Cs atoms and molecules, where exists the tunnelling coupling between two excited molecular states due to the 0(g)- (6S,6P(3/2)) double well structure. The double dark resonance is predicted in the absorption spectrum when the tunnelling coupling strength is large enough. The double dark resonance not only reveals the formation of the ultra-cold molecules, but also provides further evidence for the tunnelling as one effective coupling mechanism between the two excited molecular states. The effect of the various experimental conditions on this phenomena has been discussed.

  16. Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis

    PubMed Central

    Moser, Adam; Range, Kevin; York, Darrin M.

    2010-01-01

    Benchmark quantum calculations of proton affinities and gas phase basicities of molecules relevant to biochemical processes, particulsarly acid/base catalysis, are presented and compared for a variety of multi-level and density-functional quantum models. Included are nucleic acid bases in both keto and enol tautomeric forms, ribose in B-form and A-form sugar pucker conformations, amino acid side chains and backbone molecules, and various phosphates and phosphoranes including thio substitutions. This work presents a high-level thermodynamic characterization of biologically relevant protonation states, and provides a benchmark database for development of next-generation semiempirical and approximate density-functional quantum models, and parameterization of methods to predict pKa values and relative solvation energies. PMID:20942500

  17. The Buffer-Gas Positron Accumulator and Resonances in Positron-Molecule Interactions

    NASA Technical Reports Server (NTRS)

    Surko, C.M.

    2007-01-01

    This is a personal account of the development of our buffer-gas positron trap and the new generation of cold beams that these traps enabled. Dick Drachman provided much appreciated advice to us from the time we started the project. The physics underlying trap operation is related to resonances (or apparent resonances) in positron-molecule interactions. Amusingly, experiments enabled by the trap allowed us to understand these processes. The positron-resonance "box score" to date is one resounding "yes," namely vibrational Feshbach resonances in positron annihilation on hydrocarbons; a "probably" for positron-impact electronic excitation of CO and NZ;an d a "maybe" for vibrational excitation of selected molecules. Two of these processes enabled the efficient operation of the trap, and one almost killed it in infancy. We conclude with a brief overview of further applications of the trapping technology discussed here, such as "massive" positron storage and beams with meV energy resolution.

  18. Dynamics of the water molecule density in a discharge chamber filled with a low-pressure humid gas

    SciTech Connect

    Bernatskiy, A. V. Ochkin, V. N.; Bafoev, R. N.; Antipenkov, A. B.

    2016-10-15

    The dynamics of the H{sub 2}O molecule density in a metal gas-discharge chamber filled with low-pressure water vapor or its mixtures with noble gases was investigated by manometric and spectral methods. Regimes both with and without discharge excitation were studied. In the absence of a discharge, the molecule density dynamics is governed by the heterogeneous interaction of molecules with the chamber walls. In the presence of a discharge, in addition to the heterogeneous interaction, fast plasmachemical molecule dissociation also contributes to the initial stage of H{sub 2}O molecule loss. The role of heating of the chamber walls is discussed.

  19. Methods for Using Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules

    DTIC Science & Technology

    2014-08-20

    Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules The focus of this research was to apply efficient...methods for using ab initio potential energy surfaces (PESs) computed with high levels of quantum chemistry theory to predict chemical reaction properties...in non peer-reviewed journals: Methods for Using Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules Report

  20. Linear dichroism spectroscopy of gas phase biological molecules embedded in superfluid helium droplets

    NASA Astrophysics Data System (ADS)

    Kong, Wei; Pei, Linsen; Zhang, Jie

    This article presents the current status of gas phase linear dichroism (LD) spectroscopy, including the theoretical background, the experimental technique, and a few examples in the UV/VIS and IR. Orientation and alignment of gas phase samples are achieved using a DC electric field. To reach the necessary degree of alignment, biological molecules vaporized from a heated oven need to be embedded in superfluid helium droplets. Excitation under different polarization directions of the light source relative to the alignment field can then be used to derive the direction of the transition dipole, or the size of the permanent dipole, or both. For biological molecules that have no resonance lines or too many resonance lines, LD offers an additional parameter for spectroscopic assignment and tautomeric and conformational identification. The direction of the vibrational transition dipole is proven more reliable for vibrational and tautomeric assignment than the energy or frequency information, which is often problematic because of its sensitivity to basis sets and calculation methods. Several examples of vibrational LD of nucleic acid bases will be discussed. On the other hand, if a chromophore with a known electronic transition dipole is attached to a biological molecule, as demonstrated in the case of tryptamine, the permanent dipole determined from LD is then representative of the molecular conformation. This method of conformational determination does not rely on detailed spectroscopic assignment, thus it is applicable to molecules that do not have resolvable vibronic bands. However, its application is currently limited to the availability of an effective chromophore, and the search for such a chromophore is an on-going effort.

  1. Intermediate energy proton stopping power for hydrogen molecules and monoatomic helium gas

    NASA Technical Reports Server (NTRS)

    Xu, Y. J.; Khandelwal, G. S.; Wilson, J. W.

    1984-01-01

    Stopping power in the intermediate energy region (100 keV to 1 MeV) was investigated, based on the work of Lindhard and Winther, and on the local plasma model. The theory is applied to calculate stopping power of hydrogen molecules and helium gas for protons of energy ranging from 100 keV to 2.5 MeV. Agreement with the experimental data is found to be within 10 percent. Previously announced in STAR as N84-16955

  2. Intermediate energy proton stopping power for hydrogen molecules and monoatomic helium gas

    NASA Technical Reports Server (NTRS)

    Xu, Y. J.; Khandelwal, G. S.; Wilson, J. W.

    1984-01-01

    Stopping power in the intermediate energy region (100 keV to 1 MeV) was investigated, based on the work of Lindhard and Winther, and on the local plasma model. The theory is applied to calculate stopping power of hydrogen molecules and helium gas for protons of energy ranging from 100 keV to 2.5 MeV. Agreement with the experimental data is found to be within 10 percent. Previously announced in STAR as N84-16955

  3. The structures of tellurium(IV) halides in the gas phase and as solvated molecules.

    PubMed

    Shlykov, Sergey A; Giricheva, Nina I; Titov, Anton V; Szwak, Małgorzata; Lentz, Dieter; Girichev, Georgiy V

    2010-04-07

    The structures of molecular tellurium tetrafluoride and tellurium tetrachloride were determined by a combination of gas-phase electron diffraction, mass spectrometry and quantum chemical calculations. The combined GED/MS experiments showed no evidence of decomposition of TeF(4) and TeCl(4). No ions of oligomeric (dimeric, trimeric, etc.) or any other composition were found in the mass spectra. The monomeric molecules possess a pseudo trigonal bipyramidal structure (C(2v) symmetry) with the equatorial Te-X distances being shorter than the axial ones. The fluorine atoms are bent away from the lone pair resulting in X(eq)-Te-X(eq) and X(eq)-Te-X(ax) bond angles smaller than 120 and 90 degrees, respectively. The structure of solvates TeF(4) (THF)(2), TeF(4) (dioxane) TeF(4) (DME)(2), TeF(4)(Et(2)O) TeF(4)(toluene), TeCl(4)(CH(3)CN)(2), TeCl(4)(DME)(2) and TeCl(4)(dioxane) were determined by X-ray diffraction. The structures of tellurium tetrafluoride solvates are strongly influenced by the choice of the solvent molecules. Monomeric TeF(4) units were obtained with THF, DME and dioxane whereas fluoride bridged coordination polymers were formed using diethyl ether or toluene. All tellurium tetrachloride solvates studied contain monomeric TeCl(4) units with coordinated solvent molecules. Coordination numbers range from four in the gas phase to eight in the TeF(4) dimethoxyethane solvate. Geometric parameters of the TeX(4) molecules in the crystal, solvates and gas phase were compared. DFT, MP2, CCSD, CCSD(T) methods were applied for calculation of geometric and vibrational characteristics of free TeX(4) molecules (X = F, Cl). The pseudorotation barriers were estimated and an NBO analysis was performed. It was shown that both, GED and theoretical, quantitative results are in agreement with the qualitative results of the VSEPR model.

  4. Properties of clusters in the gas phase. V - Complexes of neutral molecules onto negative ions

    NASA Technical Reports Server (NTRS)

    Keesee, R. G.; Lee, N.; Castleman, A. W., Jr.

    1980-01-01

    Ion-molecules association reactions of the form A(-)(B)n-1 + B = A(-)(B)n were studied over a range of temperatures in the gas phase using high pressure mass spectrometry. Enthalpy and entropy changes were determined for the stepwise clustering reactions of (1) sulfur dioxide onto Cl(-), I(-), and NO2(-) with n ranging from one to three or four, and onto SO2(-) and SO3(-) with n equal to one; and (2) carbon dioxide onto Cl(-), I(-), NO2(-), CO3(-), and SO3(-) with n equal to one. From these data and earlier hydration results, the order of the magnitude of the enthalpy changes on the association of the first neutral for a series of negative ions was found to parallel the gas-phase basicity of those anions.

  5. Prebiotic molecules formation through the gas-phase reaction between HNO and CH2CHOH2+

    NASA Astrophysics Data System (ADS)

    Redondo, Pilar; Martínez, Henar; Largo, Antonio; Barrientos, Carmen

    2017-07-01

    Context. Knowing how the molecules that are present in the ISM can evolve to more complex ones is an interesting topic in interstellar chemistry. The study of possible reactions between detected species can help to understand the evolution in complexity of the interstellar matter and also allows knowing the formation of new molecules which could be candidates to be detected. We focus our attention on two molecules detected in space, vinyl alcohol (CH2CHOH) and azanone (HNO). Aims: We aim to carry out a theoretical study of the ion-molecule reaction between protonated vinyl alcohol and azanone. The viability of formation of complex organic molecules (COMs) from these reactants is expected to provide some insight into the formation of prebiotic species through gas phase reactions. Methods: The reaction of protonated vinyl alcohol with azanone has been theoretically studied by using ab initio methods. Stationary points on the potential energy surface (PES) were characterized at the second-order Moller-Plesset level in conjunction with the aug-cc-pVTZ (correlation-consistent polarized valence triple-zeta) basis set. In addition, the electronic energies were refined by means of single-point calculations at the CCSD(T) level (coupled cluster single and double excitation model augmented with a non-iterative treatment of triple excitations) with the same basis set. Results: From a thermodynamic point of view, twelve products, composed of carbon, oxygen, nitrogen, and hydrogen which could be precursors in the formation of more complex biological molecules, can be obtained from this reaction. Among these, we focus especially on ionized glycine and two of its isomers. The analysis of the PES shows that only formation of cis- and trans-O-protonated imine acetaldehyde, CH2NHCOH+ and, CHNHCHOH+, are viable under interstellar conditions. Conclusions: The reaction of protonated vinyl alcohol with azanone can evolve in the interstellar medium to more complex organic molecules of

  6. Laser-driven rotational dynamics of gas-phase molecules: Control and applications

    NASA Astrophysics Data System (ADS)

    Ren, Xiaoming

    In this thesis, our work on developing new techniques to measure and enhance field-free molecular alignment and orientation is described. Non-resonant femtosecond laser pulses are used to align and orient rotationally-cold gas-phase molecules. The time-dependent Schrodinger equation is solved to simulate the experimental results. A single-shot kHz velocity map imaging (VMI) spectrometer is developed for characterizing 1D and 3D alignment. Stimulated by a novel metric for 3D alignment proposed by Makhija et al. [Phys. Rev. A 85,033425 (2012)], a multi-pulse scheme to improve 3D alignment is demonstrated experimentally on difluoro-iodobenzene molecules and the best field-free 3D alignment is achieved. A degenerate four wave mixing probe is developed to overcome limitations in VMI measurement; experiments on different types of molecules show good agreement with computational results. Highly aligned linear molecules are used for high harmonic generation experiments. Due to the high degree of alignment, fractional revivals, variation of revival structure with harmonic order and the shape resonance and Cooper minimum in the photoionization cross section of molecular nitrogen are all observed directly in experiment for the first time. Enhanced orientation from rotationally cold heteronuclear molecules is also demonstrated. We follow the theory developed by Zhang et al. [Phys. Rev. A 83, 043410 (2011)] and demonstrate experimentally for the first time that for rotationally cold carbon monoxide an aligning laser pulse followed by a two-color laser pulse can increase field-free orientation level by almost a factor of three compared to using just the two-color pulse.

  7. Production efficiencies of U.S. electric generation plants: Effects of data aggregation and greenhouse gas and renewable energy policy

    NASA Astrophysics Data System (ADS)

    Lynes, Melissa Kate

    Over the last few decades there has been a shift in electricity production in the U.S. Renewable energy sources are becoming more widely used. In addition, electric generation plants that use coal inputs are more heavily regulated than a couple decades ago. This shift in electricity production was brought on by changes in federal policy -- a desire for electricity produced in the U.S. which led to policies being adopted that encourage the use of renewable energy. The change in production practices due to policies may have led to changes in the productivity of electric generation plants. Multiple studies have examined the most efficient electric generation plants using the data envelopment analysis (DEA) approach. This study builds on past research to answer three questions: 1) Does the level of aggregation of fuel input variables affect the plant efficiency scores and how does the efficiency of renewable energy input compare to nonrenewable energy inputs; 2) Are policies geared toward directly or indirectly reducing greenhouse gas emissions affecting the production efficiencies of greenhouse gas emitting electric generation plants; and 3) Do renewable energy policies and the use of intermittent energy sources (i.e. wind and solar) affect the productivity growth of electric generation plants. All three analysis, presented in three essays, use U.S. plant level data obtained from the Energy Information Administration to answer these questions. The first two essays use DEA to determine the pure technical, overall technical, and scale efficiencies of electric generation plants. The third essay uses DEA within the Malmquist index to assess the change in productivity over time. Results indicate that the level of aggregation does matter particularly for scale efficiency. This implies that valuable information is likely lost when fuel inputs are aggregated together. Policies directly focused on reducing greenhouse gas emissions may improve the production efficiencies of

  8. Monte Carlo calculations of diatomic molecule gas flows including rotational mode excitation

    NASA Technical Reports Server (NTRS)

    Yoshikawa, K. K.; Itikawa, Y.

    1976-01-01

    The direct simulation Monte Carlo method was used to solve the Boltzmann equation for flows of an internally excited nonequilibrium gas, namely, of rotationally excited homonuclear diatomic nitrogen. The semi-classical transition probability model of Itikawa was investigated for its ability to simulate flow fields far from equilibrium. The behavior of diatomic nitrogen was examined for several different nonequilibrium initial states that are subjected to uniform mean flow without boundary interactions. A sample of 1000 model molecules was observed as the gas relaxed to a steady state starting from three specified initial states. The initial states considered are: (1) complete equilibrium, (2) nonequilibrium, equipartition (all rotational energy states are assigned the mean energy level obtained at equilibrium with a Boltzmann distribution at the translational temperature), and (3) nonequipartition (the mean rotational energy is different from the equilibrium mean value with respect to the translational energy states). In all cases investigated the present model satisfactorily simulated the principal features of the relaxation effects in nonequilibrium flow of diatomic molecules.

  9. Photochemical reactions of triplet benzophenone and anthraquinone molecules with amines in the gas phase

    NASA Astrophysics Data System (ADS)

    Zalesskaya, G. A.; Sambor, E. G.; Belyĭ, N. N.

    2004-07-01

    The intermolecular photoinduced reactions between triplet ketone molecules and aliphatic amines and pyridine are studied by the quenching of delayed fluorescence of anthraquinone and benzophenone vapors by diethylamine, dibutylamine, cyclohexylamine, triethylamine, and pyridine. In the temperature range 423-573 K, the delayed fluorescence quenching rate constants k q are estimated from changes in the decay rate constant and the intensity of delayed fluorescence upon increasing pressure of bath gases. It is ascertained that, in the gas phase, the mixtures under study exhibit both a negative and a positive dependence of k q on temperature, which indicates that some photoinduced reactions do not have activation barriers. The rate constant k q is shown to increase with decreasing ionization potential of the electron donors. This points to the importance of interactions with charge transfer in the photoreaction of triplet ketone molecules with aliphatic amines and pyridine in the gas phase. The relationship between k q and the change in the free energy Δ G upon the photoinduced intermolecular electron transfer, which is the primary stage of the photochemical reaction, is studied. It is shown that the dependence k q (Δ G) for the donor-acceptor pairs under study is described well by the Marcus equation, in which the average vibrational energies of the donor and acceptor are taken into account for the estimate of Δ G.

  10. Relativistic ultrafast electron diffraction from molecules in the gas phase (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Yang, Jie; Guehr, Markus; Vecchione, Theodore; Robinson, Matthew S.; Li, Renkai; Hartmann, Nick; Shen, Xiaozhe; Centurion, Martin; Wang, Xijie

    2016-10-01

    Ultrafast electron diffraction (UED) is a powerful technique that can be used to resolve structural changes of gas molecules during a photochemical reaction. However, the temporal resolution in pump-probe experiments has been limited to the few-ps level by the space-charge effect that broadens the electron pulse duration and by velocity mismatch between the pump laser pulses and the probe electron pulses, making only long-lived intermediate states accessible. Taking advantage of relativistic effects, Mega-electron-volt (MeV) electrons can be used to suppress both the space-charge effect and the velocity mismatch, and hence to achieve a temporal resolution that is fast enough to follow coherent nuclear motion in the target molecules. In this presentation, we show the first MeV UED experiments on gas phase targets. These experiments not only demonstrate that femtosecond temporal resolution is achieved, but also show that the spatial resolution is not compromised. This unprecedented combination of spatiotemporal resolution is sufficient to image coherent nuclear motions, and opens the door to a new class of experiments where the structural changes can be followed simultaneously in both space and time.

  11. Dispersion and Functionalization of Nanoparticles Synthesized by Gas Aggregation Source: Opening New Routes Toward the Fabrication of Nanoparticles for Biomedicine.

    PubMed

    Oprea, B; Martínez, L; Román, E; Vanea, E; Simon, S; Huttel, Y

    2015-12-29

    The need to find new nanoparticles for biomedical applications is pushing the limits of the fabrication methods. New techniques with versatilities beyond the extended chemical routes can provide new insight in the field. In particular, gas aggregation sources offer the possibility to fabricate nanoparticles with controlled size, composition, and structure out of thermodynamics. In this context, the milestone is the optimization of the dispersion and functionalization processes of nanoparticles once fabricated by these routes as they are generated in the gas phase and deposited on substrates in vacuum or ultra-high vacuum conditions. In the present work we propose a fabrication route in ultra-high vacuum that is compatible with the subsequent dispersion and functionalization of nanoparticles in aqueous media and, which is more remarkable, in one single step. In particular, we will present the fabrication of nanoparticles with a sputter gas aggregation source using a Fe50B50 target and their further dispersion and functionalization with polyethyleneglycol (PEG). Characterization of these nanoparticles is carried out before and after PEG functionalization. During functionalization, significant boron dissolution occurs, which facilitates nanoparticle dispersion in the aqueous solution. The use of different complementary techniques allows us to prove the PEG attachment onto the surface of the nanoparticles, creating a shell to make them biocompatible. The result is the formation of nanoparticles with a structure mainly composed by a metallic Fe core and an iron oxide shell, surrounded by a second PEG shell dispersed in aqueous solution. Relaxivity measurements of these PEG-functionalized nanoparticles assessed their effectiveness as contrast agents for magnetic resonance imaging (MRI) analysis. Therefore, this new fabrication route is a reliable alternative for the synthesis of nanoparticles for biomedicine.

  12. The study of excited oxygen molecule gas species production and quenching on thermal protection system materials

    NASA Technical Reports Server (NTRS)

    Nordine, Paul C.; Fujimoto, Gordon T.; Greene, Frank T.

    1987-01-01

    The detection of excited oxygen and ozone molecules formed by surface catalyzed oxygen atom recombination and reaction was investigated by laser induced fluorescence (LIF), molecular beam mass spectrometric (MBMS), and field ionization (FI) techniques. The experiment used partially dissociated oxygen flows from a microwave discharge at pressures in the range from 60 to 400 Pa or from an inductively coupled RF discharge at atmospheric pressure. The catalyst materials investigated were nickel and the reaction cured glass coating used for Space Shuttle reusable surface insulation tiles. Nonradiative loss processes for the laser excited states makes LIF detection of O2 difficult such that formation of excited oxygen molecules could not be detected in the flow from the microwave discharge or in the gaseous products of atom loss on nickel. MBMS experiments showed that ozone was a product of heterogeneous O atom loss on nickel and tile surfaces at low temperatures and that ozone is lost on these materials at elevated temperatures. FI was separately investigated as a method by which excited oxygen molecules may be conveniently detected. Partial O2 dissociation decreases the current produced by FI of the gas.

  13. Gas-phase ion/molecule reactions of corannulene, a fullerene subunit

    SciTech Connect

    Becker, H.; Schwarz, H. ); Javahery, G.; Petrie, S.; Bohme, D.K. ); Cheng, P.C.; Scott, L.T. )

    1993-12-01

    Corannulene is intriguing, not only because of its highly-strained bowl-like structure, but also as a subunit of C[sub 60] and other fullerenes. The carbon skeleton of corannulene appears several times in C[sub 60], and its curvature mimics the curvature of C[sub 60]. Inspired by this curiosity, and having previously investigated ion/molecule reactions of C[sub 60] cations, we began an unprecedented experimental investigation of ion/molecule reactions of corannulene. Here we report the first observations of gas-phase ion/molecule reactions with corannulene: reactions of the corannulene cation (cor[sup [sm bullet]+]) with C[sub 60] and of neutral corannulene with Ar[sup [sm bullet]+], cor[sup [sm bullet]+], C[sub 60][sup [sm bullet]+], C[sub 60][sup 2+], and C[sub 60][sup [sm bullet]3+]. Both electronic and topographical features are expected to be of consequence in many of these reactions. 22 refs., 1 tab.

  14. Computational study of peptide bond formation in the gas phase through ion-molecule reactions.

    PubMed

    Redondo, Pilar; Martínez, Henar; Cimas, Alvaro; Barrientos, Carmen; Largo, Antonio

    2013-08-21

    A computational study of peptide bond formation from gas-phase ion-molecule reactions has been carried out. We have considered the reaction between protonated glycine and neutral glycine, as well as the reaction between two neutral glycine molecules for comparison purposes. Two different mechanisms, concerted and stepwise, were studied. Both mechanisms show significant energy barriers for the neutral reaction. The energy requirements for peptide bond formation are considerably reduced upon protonation of one of the glycine molecules. For the reaction between neutral glycine and N-protonated glycine the lowest energy barrier is observed for the concerted mechanism. For the reaction between neutral glycine and protonated glycine at carbonyl oxygen, the preferred mechanism is the stepwise one, with a relatively small energy barrier (23 kJ mol(-1) at 0 K) and leading to the lowest-lying protonated glycylglycine isomer. In the case that the reaction could be initiated by protonated glycine at hydroxyl oxygen the process would be barrier-free and clearly exothermic. In that case peptide bond formation could take place even under interstellar conditions if glycine is present in space.

  15. Gasotransmitters are emerging as new guard cell signaling molecules and regulators of leaf gas exchange.

    PubMed

    García-Mata, Carlos; Lamattina, Lorenzo

    2013-03-01

    Specialized guard cells modulate plant gas exchange through the regulation of stomatal aperture. The size of the stomatal pore is a direct function of the volume of the guard cells. The transport of solutes across channels in plasma membrane is a crucial process in the maintenance of guard cell water status. The fine tuned regulation of that transport requires an integrated convergence of multiple endogenous and exogenous signals perceived at both the cellular and the whole plant level. Gasotransmitters are novel signaling molecules with key functions in guard cell physiology. Three gasotransmitters, nitric oxide (NO), carbon monoxide (CO), and hydrogen sulfide (H(2)S) are involved in guard cell regulatory processes. These molecules are endogenously produced by plant cells and are part of the guard cells responses to drought stress conditions through ABA-dependent pathways. In this review, we summarize the current knowledge of gasotransmitters as versatile molecules interacting with different components of guard cell signaling network and propose them as players in new paradigms to study ABA-independent guard cell responses to water deficit. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  16. Probing the role of metal cations on the aggregation behavior of amyloid β-peptide at a single molecule level by AFM

    NASA Astrophysics Data System (ADS)

    Xie, Yang; Wang, Jianhua; Liu, Chundong

    2016-09-01

    With the development of nanotechnology, understanding of intermolecular interactions on a single molecule level by atomic force spectroscopy (AFM) has played an important role in molecular biology and biomedical science. In recent years, some research suggested that the presence of metal cations is an important regulator in the processes of misfolding and aggregation of the amyloid β-protein (Aβ), which may be an important etiological factor of Alzheimer's disease. However, the knowledge on the principle of interactions between Aβ and metal cations at the single molecule level is still poor understood. In this paper, the amyloid β-protein (Aβ) was fabricated on substrate of mixed thiol-modified gold nanoparticles using self-assembled monolayer method and the adhesion force in the longitudinal direction between metal cations and Aβ42 were investigated by AFM. The role of metal ions on Aβ aggregation is discussed from the perspective of single molecular force. The force results showed that the specific adhesion force F i and the nonspecific force F 0 between a single Aβ-Aβ pair in control experiment were calculated as 42 ± 3 and 80 pN, respectively. However, F i between a single Aβ-Aβ pair in the presence of Cu2+, Zn2+, Ca2+ and Al3+ increased dramatically to 84 ± 6, 89 ± 3, 73 ± 5, 95 ± 5 pN successively, which indicated that unbinding between Aβ proteins is accelerated in the presence of metal cations. What is more, the imaging results showed that substoichiometric copper cations accelerate the formation of fibrils within 3 days. The combined atomic force spectroscopy and imaging analysis indicate that metal cations play a role in promoting the aggregating behavior of Aβ42.

  17. Stereochemical determination of chlorophyll-d molecule from Acaryochloris marina and its modification to a self-aggregative chlorophyll as a model of green photosynthetic bacterial antennae.

    PubMed

    Mizoguchi, Tadashi; Shoji, Ayumi; Kunieda, Michio; Miyashita, Hideaki; Tsuchiya, Tohru; Mimuro, Mamoru; Tamiaki, Hitoshi

    2006-03-01

    Acaryochloris marina is a unique photosynthetic prokaryote containing chlorophyll(Chl)-d as a major photoactive pigment (over 95%). The molecular structure of Chl-d is proposed as the 3-formyl analog of Chl-a. However, the stereochemistry of Chl-d at the 13(2)-, 17- and 18-positions has not yet been established unambiguously. In the first part of this paper, we describe the determination of their stereochemistries to be 13(2)-(R)-, 17-(S)- and 18-(S)-configurations by using 1H-1H NOE correlations in 1H-NMR and circular dichroism spectra as well as chemical modification of Chl-a to produce stereochemically defined Chl derivatives. In the second part of the paper, we report a facile synthesis of a self-aggregative Chl by modifying isolated Chl-d. Since Chl-d was characterized by its reactive 3-formyl group, the formyl group was reduced with t-BuNH2BH3 to afford the desirable Chl, 3-deformyl-3-hydroxymethyl-pyrochlorophyll-d (3(1)-OH-pyroChl-d). The synthetic 3(1)-OH-pyroChl-d molecules spontaneously self-organized to form well-ordered aggregates in a non-polar organic solvent. The self-aggregates are a good model of major light-harvesting antenna systems of green photosynthetic bacteria, chlorosomes, in terms of the following three findings. (1) Both the red-shifted electronic absorption band above 750 nm and its induced reverse S-shape CD signal around 750 nm were observed in 0.5% (v/v) THF-cyclohexane. (2) The stretching mode of the 13-carbonyl group was downshifted by about 35 cm(-1) from the wavenumber of its free carbonyl. (3) The self-aggregates were quite stable on titration of pyridine to the suspension, in comparison with those of natural chlorosomal bacteriochlorophyll-d possessing the 3-(1-hydroxyethyl) group.

  18. Interaction of gas molecules with crystalline polymer separation membranes: Atomic-scale modeling and first-principles calculations

    SciTech Connect

    Sergey N. Rashkeev; Eric S. Peterson

    2011-11-01

    Carbon dioxide (CO2)-induced plasticization can significantly decrease the gas separation performance of membranes in high-temperature or high pressure conditions, such as industrial methane (CH4) separations. In this paper, we investigated the crystalline phase of three polymers (polybenzimidazole (PBI), Bis(isobutylcarboxy)polybenzimidazole (PBI-Butyl), and KaptonTM) and interactions between gas molecules (CO2 and N2) and these polymers. A novel, molecular dynamics (MD) based, computational technique was employed to find unknown crystalline structures of these polymer materials. The interaction of CO2 and N2 gases with these crystals was studied by first-principles calculations and by classical MD simulations. The results showed that the packing structure and the interlayer coupling in polymer crystals determine the permeability and diffusivity of gas molecules. This methodology also allows prediction of plastic swelling in these materials caused by gas molecules absorbed in the polymer matrix.

  19. The Scattering of Gas Phase Molecules and Van Der Waals Clusters from Surfaces

    NASA Astrophysics Data System (ADS)

    Beauregard, John Norman

    The interaction of gas phase species with surfaces plays an important role in a myriad of processes such as heterogeneous catalysis, corrosion and the etching of semiconductor surfaces in the microelectronics industry. Thus, the study of gas-surface interactions has become a field of intense research. In this dissertation, we present the results of a computational study of the scattering of gas phase molecules and van der Waals clusters from surfaces. We have used molecular dynamics calculations which allow for the examination of the microscopic details of gas-surface scattering. In this work we study four distinct systems. In Chapter I the focus is on the scattering of van der Waals clusters of N_2 from crystal surfaces. We find that the cluster-surface scattering dynamics are very different from those observed in monomer-surface scattering. Furthermore, our results are in qualitative agreement with a recent experimental study of the scattering of nitrogen clusters from metal surfaces. The focus of Chapter II is on the effect of reagent rotation and rotational alignment on the dissociative chemisorption of H_2 on metal surfaces. We find that the probability of dissociative chemisorption depends strongly on both the rotational energy and the plane of rotation of the reactant H_2. Our results suggest that such information might be useful in uncovering intricate details of the potential energy surface governing these reactions. In Chapter III we examine the dissociative trapping of HD on a tungsten surface. In dissociative trapping only one atom becomes bound to the surface while the other returns to the gas phase. We observe a novel isotope effect in this channel which is explained in terms of a simple mechanism for the dissociative trapping process. Finally, in Chapter IV we examine the effect of dissolving an H_2 molecule in an argon microcluster on the dissociative chemisorption of H_2 on a silicon surface. We find that this does, in fact, facilitate the reaction

  20. Poly(ethylene glycol)-poly(L-lactide) diblock copolymer prevents aggregation of poly(L-lactide) microspheres during ethylene oxide gas sterilization.

    PubMed

    Choi, Y; Kim, S Y; Moon, M H; Kim, S H; Lee, K S; Byun, Y

    2001-05-01

    Sterilization procedure is one of the most important obstacles in the clinical applications of biodegradable microspheres. The microspheres prepared with poly(alpha-hydroxy acid) were severely aggregated during ethylene oxide (EO) gas sterilization, and could not be used in clinical applications. In this study, the effects of EO gas sterilization on the poly(L-lactide) (PLLA) microspheres were analyzed by nuclear magnetic resonance spectroscopy (1H-NMR), differential scanning calorimetry (DSC), gel permeation chromatography (GPC), scanning electron microscope (SEM) and size fractionation. The aggregation between the microspheres might be stimulated by high mobility of amorphous regions of PLLA on the microsphere surfaces since both water vapor and gas mixture can reduce glass transition temperature (Tg) of PLLA below the sterilization temperature. During EO gas sterilization, there were no changes in the molecular structure and the molecular weight of PLLA in microspheres, but there were changes in the crystallinity of PLLA in microspheres. In this study, poly(L-lactide)-poly(ethylene glycol) diblock copolymers (PLE) were blended with PLLA homopolymers in various ratios to design the microsphere suitable for EO gas sterilization. Aggregation of PLLA microspheres was markedly prevented when more than 4wt% of PLE was blended in the microspheres. This inhibition effect on aggregation may be due to the increased initial crystallinity of the microspheres, which help to maintain the microsphere morphology during EO gas sterilization.

  1. A gas sensor using a multi-walled carbon nanotube sheet to detect oxygen molecules.

    PubMed

    Jung, Daewoong; Lee, Kyung H; Kim, Donghyun; Overzet, Lawrence J; Lee, Gil S

    2013-12-01

    A gas sensor using a multi-walled carbon nanotube (MWCNT) sheet, which can detect oxygen (O2) gas, is presented and its output characteristics are evaluated in this study. A simple, cost effective and novel fabrication technique is described compared to dispersing CNTs into a liquid or polymer. The sheets are spun from a MWCNT forest grown on a silicon substrate; its electrical resistance decreases linearly with O2 exposure. The MWCNT sheet has a large surface area and many individual MWCNT contact points; this leads to a linear sensitivity, a fast response time, repeatability, and stability. It is well known that the surface distribution and areal density of MWCNTs have a significantly affect on their sensing characteristics. The sensors fabricated using dispersed CNTs on a substrate, either with separated CNTs of low density or with overlapping CNTs of low resistance, reveal much lower sensitivities. The large surface area and uniform distribution of the gas sensor, however, allow for the higher interaction of the MWCNTs with the O2 molecules, increasing the sensor's characteristics. Moreover, the MWCNT sheet does not need purification or a complex transfer process to be used as a sensor, making it suitable for practical applications.

  2. Gas molecule scattering & ion mobility measurements for organic macro-ions in He versus N2 environments.

    PubMed

    Larriba-Andaluz, Carlos; Fernández-García, Juan; Ewing, Michael A; Hogan, Christopher J; Clemmer, David E

    2015-06-14

    A pending issue in linking ion mobility measurements to ion structures is that the collisional cross section (CCS, the measured structural parameter in ion mobility spectrometry) of an ion is strongly dependent upon the manner in which gas molecules effectively impinge on and are reemitted from ion surfaces (when modeling ions as fixed structures). To directly examine the gas molecule impingement and reemission processes and their influence, we measured the CCSs of positively charged ions of room temperature ionic liquids 1-ethyl-3-methylimidazolium dicyanamide (EMIM-N(CN)2) and 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM-BF4) in N2 using a differential mobility analyzer-mass spectrometer (DMA-MS) and in He using a drift tube mobility spectrometer-mass spectrometer (DT-MS). Cluster ions, generated via electrosprays, took the form (AB)N(A)z, spanning up to z = 20 and with masses greater than 100 kDa. As confirmed by molecular dynamics simulations, at the measurement temperature (∼300 K), such cluster ions took on globular conformations in the gas phase. Based upon their attained charge levels, in neither He nor N2 did the ion-induced dipole potential significantly influence gas molecule-ion collisions. Therefore, differences in the CCSs measured for ions in the two different gases could be primarily attributed to differences in gas molecule behavior upon collision with ions. Overwhelmingly, by comparison of predicted CCSs with selected input impingement-reemission laws to measurements, we find that in N2, gas molecules collide with ions diffusely--they are reemitted at random angles relative to the gas molecule incoming angle--and inelastically. Meanwhile, in He, gas molecules collide specularly and elastically and are emitted from ion surfaces at determined angles. The results can be rationalized on the basis of the momentum transferred per collision; in the case of He, individual gas molecule collisions minimally perturb the atoms within a cluster ion

  3. Salt bridge stabilization of charged zwitterionic arginine aggregates in the gas phase.

    PubMed

    Julian, R R; Hodyss, R; Beauchamp, J L

    2001-04-18

    The discovery of several new unusually stable aggregates of arginine that are intermolecularly bound by salt bridges is reported. Quadrupole ion-trap mass spectrometry provides evidence for the stability of arginine in the zwitterionic state, where the protonated guanidinium group of one arginine interacts strongly with the carboxylate of another to form stable noncovalent complexes, coordinated to either a cation or anion. Clusters of arginine with itself, sodium, potassium, lithium, magnesium, chloride, fluoride, bromide, iodide, and nitrate are observed. DFT calculations at the B3LYP/6-31G level are used to assess the structures and energetics of particularly prominent clusters. An examination of mixtures of D-arginine with isotopically labeled L-arginine indicates that the stability of these clusters does not depend on arginine enantiomeric purity. The cyclic trimers of arginine, capped with either Cl(-) or NO(3)(-), possess exceptional stability.

  4. X-ray absorption and Mössbauer spectroscopies characterization of iron nanoclusters prepared by the gas aggregation technique.

    PubMed

    Sánchez-Marcos, J; Laguna-Marco, M A; Martínez-Morillas, R; Céspedes, E; Menéndez, N; Jiménez-Villacorta, F; Prieto, C

    2012-11-01

    Partially oxidized iron nanoclusters have been prepared by the gas-phase aggregation technique with typical sizes of 2-3 nm. This preparation technique has been reported to obtain clusters with interesting magnetic properties such as very large exchange bias. In this paper, a sample composition study carried out by Mössbauer and X-ray absorption spectroscopies is reported. The information reached by these techniques, which is based on the iron short range order, results to be an ideal way to have a characterization of the whole sample since the obtained data are an average over a very large amount of the clusters. In addition, our results indicate the presence of ferrihydrite, which is a compound typically ignored when studying this type of systems.

  5. A redox-active, compact molecule for cross-linking amyloidogenic peptides into nontoxic, off-pathway aggregates: In vitro and in vivo efficacy and molecular mechanisms

    SciTech Connect

    Derrick, Jeffrey S.; Kerr, Richard A.; Nam, Younwoo; Oh, Shin Bi; Lee, Hyuck Jin; Earnest, Kaylin G.; Suh, Nayoung; Peck, Kristy L.; Ozbil, Mehmet; Korshavn, Kyle J.; Ramamoorthy, Ayyalusamy; Prabhakar, Rajeev; Merino, Edward J.; Shearer, Jason; Lee, Joo -Yong; Ruotolo, Brandon T.; Lim, Mi Hee

    2015-11-17

    Chemical reagents targeting and controlling amyloidogenic peptides have received much attention for helping identify their roles in the pathogenesis of protein-misfolding disorders. In this paper, we report a novel strategy for redirecting amyloidogenic peptides into nontoxic, off-pathway aggregates, which utilizes redox properties of a small molecule (DMPD, N,N-dimethyl-p-phenylenediamine) to trigger covalent adduct formation with the peptide. In addition, for the first time, biochemical, biophysical, and molecular dynamics simulation studies have been performed to demonstrate a mechanistic understanding for such an interaction between a small molecule (DMPD) and amyloid-β (Aβ) and its subsequent anti-amyloidogenic activity, which, upon its transformation, generates ligand–peptide adducts via primary amine-dependent intramolecular cross-linking correlated with structural compaction. Furthermore, in vivo efficacy of DMPD toward amyloid pathology and cognitive impairment was evaluated employing 5xFAD mice of Alzheimer’s disease (AD). Such a small molecule (DMPD) is indicated to noticeably reduce the overall cerebral amyloid load of soluble Aβ forms and amyloid deposits as well as significantly improve cognitive defects in the AD mouse model. Altogether our in vitro and in vivo studies of DMPD toward Aβ with the first molecular-level mechanistic investigations present the feasibility of developing new, innovative approaches that employ redox-active compounds without the structural complexity as next-generation chemical tools for amyloid management.

  6. A Redox-Active, Compact Molecule for Cross-Linking Amyloidogenic Peptides into Nontoxic, Off-Pathway Aggregates: In Vitro and In Vivo Efficacy and Molecular Mechanisms

    SciTech Connect

    Derrick, Jeffrey S.; Kerr, Richard A.; Nam, Younwoo; Oh, Shin Bi; Lee, Hyuck Jin; Earnest, Kaylin G.; Suh, Nayoung; Peck, Kristy L.; Ozbil, Mehmet; Korshavn, Kyle J.; Ramamoorthy, Ayyalusamy; Prabhakar, Rajeev; Merino, Edward J.; Shearer, Jason; Lee, Joo-Yong; Ruotolo, Brandon T.; Lim, Mi Hee

    2015-11-25

    Chemical reagents targeting and controlling amyloidogenic peptides have received much attention for helping identify their roles in the pathogenesis of protein-misfolding disorders. Herein, we report a novel strategy for redirecting amyloidogenic peptides into nontoxic, off-pathway aggregates, which utilizes redox properties of a small molecule (DMPD, N,N-dimethyl-p-phenylenediamine) to trigger covalent adduct formation with the peptide. In addition, for the first time, biochemical, biophysical, and molecular dynamics simulation studies have been performed to demonstrate a mechanistic understanding for such an interaction between a small molecule (DMPD) and amyloid-β (Aβ) and its subsequent anti-amyloidogenic activity, which, upon its transformation, generates ligand–peptide adducts via primary amine-dependent intramolecular cross-linking correlated with structural compaction. Furthermore, in vivo efficacy of DMPD toward amyloid pathology and cognitive impairment was evaluated employing 5xFAD mice of Alzheimer’s disease (AD). Such a small molecule (DMPD) is indicated to noticeably reduce the overall cerebral amyloid load of soluble Aβ forms and amyloid deposits as well as significantly improve cognitive defects in the AD mouse model. Overall, our in vitro and in vivo studies of DMPD toward Aβ with the first molecular-level mechanistic investigations present the feasibility of developing new, innovative approaches that employ redox-active compounds without the structural complexity as next-generation chemical tools for amyloid management.

  7. A redox-active, compact molecule for cross-linking amyloidogenic peptides into nontoxic, off-pathway aggregates: In vitro and in vivo efficacy and molecular mechanisms

    DOE PAGES

    Derrick, Jeffrey S.; Kerr, Richard A.; Nam, Younwoo; ...

    2015-11-17

    Chemical reagents targeting and controlling amyloidogenic peptides have received much attention for helping identify their roles in the pathogenesis of protein-misfolding disorders. In this paper, we report a novel strategy for redirecting amyloidogenic peptides into nontoxic, off-pathway aggregates, which utilizes redox properties of a small molecule (DMPD, N,N-dimethyl-p-phenylenediamine) to trigger covalent adduct formation with the peptide. In addition, for the first time, biochemical, biophysical, and molecular dynamics simulation studies have been performed to demonstrate a mechanistic understanding for such an interaction between a small molecule (DMPD) and amyloid-β (Aβ) and its subsequent anti-amyloidogenic activity, which, upon its transformation, generates ligand–peptidemore » adducts via primary amine-dependent intramolecular cross-linking correlated with structural compaction. Furthermore, in vivo efficacy of DMPD toward amyloid pathology and cognitive impairment was evaluated employing 5xFAD mice of Alzheimer’s disease (AD). Such a small molecule (DMPD) is indicated to noticeably reduce the overall cerebral amyloid load of soluble Aβ forms and amyloid deposits as well as significantly improve cognitive defects in the AD mouse model. Altogether our in vitro and in vivo studies of DMPD toward Aβ with the first molecular-level mechanistic investigations present the feasibility of developing new, innovative approaches that employ redox-active compounds without the structural complexity as next-generation chemical tools for amyloid management.« less

  8. NMR dynamics of quantum discord for spin-carrying gas molecules in a closed nanopore

    SciTech Connect

    Yurishchev, M. A.

    2014-11-15

    A local orthogonal transformation that transforms any centrosymmetric density matrix of a two-qubit system to the X form has been found. A piecewise-analytic-numerical formula Q = min(Q{sub π/2}, Q{sub θ}, Q{sub 0}), where Q{sub π/2} and Q{sub 0} are analytical expressions and the branch Q{sub 0θ} can be obtained only by numerically searching for the optimal measurement angle θ ∈ (0, π/2), is proposed to calculate the quantum discord Q of a general X state. The developed approaches have been applied for a quantitative description of the recently predicted flickering (periodic disappearance and reappearance) of the quantum-information pair correlation between nuclear 1/2 spins of atoms or molecules of a gas (for example, {sup 129}Xe) in a bounded volume in the presence of a strong magnetic field.

  9. Accurate Structure Parameters for Tunneling Ionization Rates of Gas-Phase Linear Molecules

    NASA Astrophysics Data System (ADS)

    Zhao, Song-Feng; Li, Jian-Ke; Wang, Guo-Li; Li, Peng-Cheng; Zhou, Xiao-Xin

    2017-03-01

    In the molecular Ammosov-Delone-Krainov (MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402], the ionization rate depends on the structure parameters of the molecular orbital from which the electron is removed. We determine systematically and tabulate accurate structure parameters of the highest occupied molecular orbital (HOMO) for 123 gas-phase linear molecules by solving time-independent Schrödinger equation with B-spline functions and molecular potentials which are constructed numerically using the modified Leeuwen-Baerends (LBα) model. Supported by National Natural Science Foundation of China under Grant Nos. 11664035, 11674268, 11465016, 11364038, 11364039, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001 and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province

  10. Generation, Detection and characterization of Gas-Phase Transition Metal containing Molecules

    SciTech Connect

    Steimle, Timothy

    2015-12-15

    The objective of this project was to generate, detect, and characterize small, gas-phase, metal containing molecules. In addition to being relevant to high temperature chemical environments (e.g. plasmas and combustion), gas-phase experiments on metal containing molecules serve as the most direct link to a molecular-level theoretical model for catalysis. Catalysis (i.e. the addition of a small about of recoverable material to control the rate and direction of a chemical reaction) is critical to the petroleum and pharmaceutical industries as well as environmental remediation. Currently, the majority of catalytic materials are based on very expensive metals such as platinum (Pt), palladium (Pd), iridium (Ir,) rhenium (Re), and rhodium (Rh). For example, the catalyst used for converting linear hydrocarbon molecules (e.g. hexane) to cyclic molecules (e.g. cyclohexane) is a mixture of Pt and Re suspended on alumina. It enables straight chain alkanes to be converted into branched-chain alkanes, cyclohexanes and aromatic hydrocarbons which are used, amongst other things, to enhance the octane number of petrol. A second example is the heterogeneous catalysis used in automobile exhaust systems to: a) decrease nitrogen oxide; b) reduce carbon monoxide; and c) oxidize unburned hydrocarbons. The exhaust is vented through a high-surface area chamber lined with Pt, Pd, and Rh. For example, the carbon monoxide is catalytically converted to carbon dioxide by reaction with oxygen. The research results from this work have been published in readily accessible journals1-28. The ground and excited electronic state properties of small metal containing molecules that we determine were: a) electronic state distributions and lifetimes, b) vibrational frequencies, c) bond lengths and angles, d) hyperfine interactions, e) permanent electric dipole moments, mel, and f) magnetic dipoles, μm. In general terms, μel, gives insight into the charge distribution and mm into

  11. Markedly different adsorption behaviors of gas molecules on defective monolayer MoS2: a first-principles study.

    PubMed

    Li, Hongxing; Huang, Min; Cao, Gengyu

    2016-06-01

    Sulfur vacancy (SV) is one of the most typical defects in two-dimensional monolayer MoS2, leading to reactive sites. We presented a systematic study of the adsorption behaviors of gas molecules, CO2, N2, H2O, CO, NH3, NO, O2, H2 and NO2, on monolayer MoS2 with single SV by first-principles calculations. It was found that CO2, N2 and H2O molecules physisorbed at the proximity of single SV. Our adsorption energy calculations and charge transfer analysis showed that the interactions between CO2, N2 and H2O molecules and defective MoS2 are stronger than the cases of CO2, N2 and H2O molecules adsorbed on pristine MoS2, respectively. The defective MoS2 based gas sensors may be more sensitive to CO2, N2 and H2O molecules than pristine MoS2 based ones. CO, NO, O2 and NH3 molecules were found to chemisorb at the S vacancy site and thus modify the electronic properties of defective monolayer MoS2. Magnetism was induced upon adsorption of NO molecules and the defective states induced by S vacancy can be completely removed upon adsorption of O2 molecules, which may provide some helpful information for designing new MoS2 based nanoelectronic devices in future. The H2 and NO2 molecules were found to dissociate at S vacancy. The dissociation of NO2 molecules resulted in O atoms located at the S vacancy site and NO molecules physisorbed on O-doped MoS2. The calculated results showed that NO2 molecules can help heal the S vacancy of the MoS2 monolayer.

  12. Dissociation Chemistry of Gas Molecules on Carbon Nanotubes - Applications to Chemical Sensing.

    SciTech Connect

    Govind, Niri; Andzelm, Jan; Maiti, Amitesh

    2008-06-01

    It is well known in the literature that carbon nanotubes (CNTs) interact weakly with many gas molecules like H2O, CO, NH3, H2, NO2 and so on. Exposure to NO2, O2, and NH3 significantly affects the electrical conductance of a single wall nanotube (SWNT). These can be explained using a simple charge transfer picture, which results in the observed changes in the hole conduction of the tubes. It is also known that pure SWNTs only weakly interact with these molecules. We have recently investigated [AGM2006] how common defects in CNTs (Stone-Wales (SW), monovacancy, and interstitial) influence the chemisorption of NH3. This paper is a continuation of our previous work. Here we further investigate, via Density Functional Theory (DFT) calculations, the effects of Stone-Wales (SW) defects on the adsorption/dissociation of O2 and H2O. We also study the diffusion of adsorbed oxygen atoms on the nanotube surface in the vicinity of the SW defect as well as the dissociation of NH3 in the presence of adsorbed oxygen atoms.

  13. Detection of water molecules in inert gas based plasma by the ratios of atomic spectral lines

    NASA Astrophysics Data System (ADS)

    Bernatskiy, A. V.; Ochkin, V. N.

    2017-01-01

    A new approach is considered to detect the water leaks in inert plasma-forming gas present in the reactor chamber. It is made up of the intensity ratio of D α and H α spectral lines in combination with O, Ar and Xe lines intensity. The concentrations of H2O, O, H and D particles have been measured with high sensitivity. At the D2 admixture pressure {{p}{{\\text{D}\\text{2}}}}   =  0.025 mbar, we used the acquisition time of 10 s to measure the rate of water molecules injected from the outside, Γ0  =  1.4 · 10-9 mbar · m3 · s-1, and the incoming water molecules to plasma, Γ  =  5 ·10-11 mbar · m3 · s-1. The scaling proves that at small D2 admixtures (10-4 mbar), the leaks with the rates Γ0  ≈  6 · 10-12 mbar · m3 · s-1 and Γ  ≈  2 · 10-13 mbar · m3 · s-1 can be detected and measured. The difference between Γ0 and Γ values is due to the high degree of H2O dissociation, which can be up to 97-98%.

  14. Influence of a magnetic field on the viscosity of a dilute gas consisting of linear molecules.

    PubMed

    Hellmann, Robert; Vesovic, Velisa

    2015-12-07

    The viscomagnetic effect for two linear molecules, N2 and CO2, has been calculated in the dilute-gas limit directly from the most accurate ab initio intermolecular potential energy surfaces presently available. The calculations were performed by means of the classical trajectory method in the temperature range from 70 K to 3000 K for N2 and 100 K to 2000 K for CO2, and agreement with the available experimental data is exceptionally good. Above room temperature, where no experimental data are available, the calculations provide the first quantitative information on the magnitude and the behavior of the viscomagnetic effect for these gases. In the presence of a magnetic field, the viscosities of nitrogen and carbon dioxide decrease by at most 0.3% and 0.7%, respectively. The results demonstrate that the viscomagnetic effect is dominated by the contribution of the jj¯ polarization at all temperatures, which shows that the alignment of the rotational axes of the molecules in the presence of a magnetic field is primarily responsible for the viscomagnetic effect.

  15. First-principles investigation of armchair boron nitride nanoribbons for sensing PH3 gas molecules

    NASA Astrophysics Data System (ADS)

    Srivastava, Pankaj; Jaiswal, Neeraj K.; Sharma, Varun

    2014-09-01

    The present work exhibits density functional theory (DFT) based first-principles calculations to explore the sensing properties of bare armchair boron nitride nanoribbons (ABNNR) for PH3 gas molecules. Edges of the ribbon were considered as the sites of possible adsorption with two different configurations i.e. adsorption at one edge and adsorption at both edges of the ribbon. It is revealed that B atoms of the ribbons are more energetically favorable sites for the adsorption of PH3 molecules as compared with N atoms. The adsorption of PH3 affects the electronic properties of nanoribbons. One edge PH3 adsorbed ribbons are metallic whereas in both edges PH3 adsorption, the band gap is decreased than that of bare ribbon. The changes in electronic properties caused by PH3 adsorption are further supported by the current-voltage (I-V) characteristics of the considered configurations. The results show that ABNNR can serve as a potential candidate for PH3 sensing applications.

  16. Gas phase ion - molecule reactions studied by Fourier transform ion cyclotron resonance mass spectrometry

    SciTech Connect

    Ross, C.W. III.

    1993-01-01

    Intrinsic thermodynamic information of molecules can easily be determined in the low pressure FT/ICR mass spectrometer. The gas phase basicity of two carbenes were measured by isolating the protonated carbene ion and reacting it with neutral reference compounds by the bracketing method. A fundamentally new-dimensional FT/ICR/MS experiment, SWIM (stored waveform ion modulation) 2D-FT/ICR MS/MS, is described. Prior encodement of the second dimension by use of two identical excitation waveforms separated by a variable delay period is replaced by a new encodement in which each row of the two-dimensional data array is obtained by use of a single stored excitation waveform whose frequency-domain magnitude spectrum is a sinusoid whose frequency increases from one row to the next. In the two-dimensional mass spectrum, the conventional one-dimensional FT/ICR mass spectrum appears along the diagonal, and each off-diagonal peak corresponds to an ion-neutral reaction whose ionic components may be identified by horizontal and vertical projections to the diagonal spectrum. All ion-molecule reactions in a gaseous mixture may be identified from a single 2D-FT/ICR MS/MS experiment, without any prior knowledge of the system. In some endoergic reactions there is a minimum energy threshold that must overcome for a reaction to occur. Hence, a simple sinusoidal modulation of parent ion cyclotron radius leads to a clipped sinusoidal signal of the product ion abundance in the second dimension, which upon Fourier transformation produces signals with harmonic and combination ion cyclotron resonance frequencies. Moreover, ion-molecule reaction rates may vary directly within kinetic energy rather than cyclotron radius. With SWIM, it is possible to tailor the excitation profile so as to produce a sinusoidal modulation of ion kinetic energy as a function of cyclotron frequency.

  17. Complex Organic Molecules Formation in Space Through Gas Phase Reactions: A Theoretical Approach

    NASA Astrophysics Data System (ADS)

    Redondo, Pilar; Barrientos, Carmen; Largo, Antonio

    2017-02-01

    Chemistry in the interstellar medium (ISM) is capable of producing complex organic molecules (COMs) of great importance to astrobiology. Gas phase and grain surface chemistry almost certainly both contribute to COM formation. Amino acids as building blocks of proteins are some of the most interesting COMs. The simplest one, glycine, has been characterized in meteorites and comets and, its conclusive detection in the ISM seems to be highly plausible. In this work, we analyze the gas phase reaction of glycine and {{{CH}}5}+ to establish the role of this process in the formation of alanine or other COMs in the ISM. Formation of protonated α- and β-alanine in spite of being exothermic processes is not viable under interstellar conditions because the different paths leading to these isomers present net activation energies. Nevertheless, glycine can evolve to protonated 1-imide-2, 2-propanediol, protonated amino acetone, protonated hydroxyacetone, and protonated propionic acid. However, formation of acetic acid and protonated methylamine is also a favorable process and therefore will be a competitive channel with the evolution of glycine to COMs.

  18. Properties of clusters in the gas phase: V. Complexes of neutral molecules onto negative ions

    SciTech Connect

    Keesee, R.G.; Lee, N.; Castleman, A.W. Jr.

    1980-09-01

    Ion--molecules association reactions of the form A/sup -/(B)/sub n1/-+B=A/sup -/(B)/sub n/ were studied over a range of temperatures in the gas phase using high pressure mass spectrometry. Enthalpy and entropy changes were determined for the stepwise clustering reactions of (1) sulfur dioxide onto Cl/sup -/, I/sup -/, and NO/sub 2//sup -/ with n ranging from one to three or four, and onto SO/sub 2//sup -/ and SO/sub 3//sup -/ with n equal to one; and (2) carbon dioxide onto Cl/sup -/, I/sup -/, NO/sub 2//sup -/, CO/sub 3//sup -/, and SO/sub 3//sup -/ with n equal to one. From these data and earlier hydration results, the order of the magnitude of the enthalpy changes on the association of the first neutral for a series of negative ions was found to parallel the gas-phase basicity of those anions. For any given ion, the relative order of the addition enthalpies among the neutrals was found to be dependent on the polarizabilities of the neutrals and on the covalency in the ion-neutral bond. Dispersion of charge via covalent bonding was found to affect significantly the succeeding clustering steps.

  19. Applying ion-molecule reactions to studies of gas-phase protein structure

    SciTech Connect

    Ogorzalek Loo, R.R.; Loo, J.A.; Smith, R.D.

    1992-06-01

    Whether solution phase differences in protein higher order structure persist in the gas phase, is examined by means of proton transfer reactions on ions generated by electrospray ionization of different solution conformations. Ion-molecule reactions were carried out in the atmosphere-vacuum interface of a quadrupole mass spectrometer with a Y-shaped capillary inlet-reactor. An amine (dimethyl-, trimethyl-, or diethyl-) were delivered to one inlet arm. Reactivities of bovine cytochrome c ions sprayed from denatured and native solutions were determined; the ions generated shifted to about the same charge states. Addition of equal amounts of amine to ions generated from different solution conformations of bovine ubiquitin also yielded similar final charge states; however, the average charge state increased with temperature. Myoglobin and apomyoglobin also yielded similar final charge states. The results suggest that for the non-disulfide linked proteins, either there are not significant differences in gas phase higher order structure, or proton transfer reactions are not sensitive enough to detect higher order structural differences arising from noncovalent interactions. 2 refs, 2 figs. (DLC)

  20. J-aggregates of organic dye molecules complexed with iron oxide nanoparticles for imaging-guided photothermal therapy under 915-nm light.

    PubMed

    Song, Xuejiao; Gong, Hua; Liu, Teng; Cheng, Liang; Wang, Chao; Sun, Xiaoqi; Liang, Chao; Liu, Zhuang

    2014-11-12

    Recently, the development of nano-theranostic agents aiming at imaging guided therapy has received great attention. In this work, a near-infrared (NIR) heptamethine indocyanine dye, IR825, in the presence of cationic polymer, polyallylamine hydrochloride (PAH), forms J-aggregates with red-shifted and significantly enhanced absorbance. After further complexing with ultra-small iron oxide nanoparticles (IONPs) and the followed functionalization with polyethylene glycol (PEG), the obtained IR825@PAH-IONP-PEG composite nanoparticles are highly stable in different physiological media. With a sharp absorbance peak, IR825@PAH-IONP-PEG can serve as an effective photothermal agent under laser irradiation at 915 nm, which appears to be optimal in photothermal therapy application considering its improved tissue penetration compared with 808-nm light and much lower water heating in comparison to 980-nm light. As revealed by magnetic resonance (MR) imaging, those nanoparticles after intravenous injection exhibit high tumor accumulation, which is then harnessed for in vivo photothermal ablation of tumors, achieving excellent therapeutic efficacy in a mouse tumor model. This study demonstrates for the first time that J-aggregates of organic dye molecules are an interesting class of photothermal material, which when combined with other imageable nanoprobes could serve as a theranostic agent for imaging-guided photothermal therapy of cancer.

  1. Detecting the Formation and Transformation of Oligomers during Insulin Fibrillation by a Dendrimer Conjugated with Aggregation-Induced Emission Molecule.

    PubMed

    Huang, Qin; Xie, Jing; Liu, Yanpeng; Zhou, Anna; Li, Jianshu

    2017-04-19

    The fibrillation of protein is harmful and impedes the use of protein drugs. It also relates to various debilitating diseases such as Alzheimer's diseases. Thus, investigating the protein fibrillation process is necessary. In this study, poly(amido amine) dendrimers (PAMAM) of generation 3 (G3) and generation 4 (G4) were synthesized and conjugated with 4-aminobiphenyl, an aggregation-induced emission (AIE) moiety, at varied grafting ratios. Among them, one fluorescence probe named G3-biph-3 that was grafted average 3.25 4-aminobiphenyl to the G3, can detect the transformations both from native insulin to oligomers and from oligomers to fibrils. The size difference of native insulin, oligomers, and fibrils was proposed to be the main factor leading to the detection of the above transformations. Different molecular weights of sodium polyacrylate (PAAS) were also applied as a model to interact with G3-biph-3 to further reveal the mechanism. The results indicated that PAMAM with a certain generation and grafted with appropriate AIE groups can detect the oligomer formation and transformation during the insulin fibrillation process.

  2. Adsorption of gas molecules on Ga-doped graphene and effect of applied electric field: A DFT study

    NASA Astrophysics Data System (ADS)

    Liang, Xiong-Yi; Ding, Ning; Ng, Siu-Pang; Wu, Chi-Man Lawrence

    2017-07-01

    Density functional theory calculations have been carried out to study the adsorption of varous gas molecules (H2O, NH3, CO, NO2 and NO) on pristine graphene and Ga-doped graphene in order to explore the feasibility of Ga-doped graphene based gas sensor. For each gas molecule, various adsorption positions and orientations were considered. The most stable configuration was determined and the adsorption energies with van der Waals interactions were calculated. Further, electronic properties such as electron density, density of states, charge transfer and band structure were investigated to understand the mechanism of adsorption. The results showed that the gas molecules studied were only weakly adsorbed on pristine graphene with small adsorption energies. On the other hand, the adsorption energies of all gas molecules on Ga-doped graphene increased by various amounts. Adsorption of gas molecules on Ga-doped graphene can open a relatively large band gap ranging from 0.267 to 0.397 eV. NO2 was found to be very sensitive to Ga-doped graphene with adsorption energy of -1.928 eV due to strong orbital hybridization and large charge transfer. Furthermore, our study suggests that the affinity and electronic properties of NO2 on Ga-doped graphene can be dramatically changed by an external electric field. A negative electric field enhances the adsorption of NO2 on Ga-doped graphene as reflected in the increase in adsorption energy. In contrast, the interaction will be weakened under a positive electric field. The results of the DFT calculation indicates the potential application of Ga-doped graphene in gas sensing for NO2 detection, and the advantage to use external electric field to tune the sensitivity for NO2.

  3. Relevance of the Pharmacokinetic and Pharmacodynamic Profiles of Puerariae lobatae Radix to Aggregation of Multi-Component Molecules in Aqueous Decoctions.

    PubMed

    Su, Bili; Kan, Yongjun; Xie, Jianwei; Hu, Juan; Pang, Wensheng

    2016-06-28

    The complexity of traditional Chinese medicines (TCMs) is related to their multi-component system. TCM aqueous decoction is a common clinical oral formulation. Between molecules in solution, there exist intermolecular strong interactions to form chemical bonds or weak non-bonding interactions such as hydrogen bonds and Van der Waals forces, which hold molecules together to form "molecular aggregates". Taking the TCM Puerariae lobatae Radix (Gegen) as an example, we explored four Gegen decoctions of different concentration of 0.019, 0.038, 0.075, and 0.30 g/mL, named G-1, G-2, G-3, and G-4. In order of molecular aggregate size (diameter) the four kinds of solution were ranked G-1 < G-2 < G-3 < G-4 by Flow Cell 200S IPAC image analysis. A rabbit vertebrobasilar artery insufficiency (VBI) model was set up and they were given Gegen decoction (GGD) at a clinical dosage of 0.82 g/kg (achieved by adjusting the gastric perfusion volume depending on the concentration). The HPLC fingerprint of rabbit plasma showed that the chemical component absorption into blood in order of peak area values was G-1 < G-2 > G-3 > G-4. Puerarin and daidzin are the major constituents of Gegen, and the pharmacokinetics of G-1 and G-2 puerarin conformed with the two compartment open model, while for G-3 and G-4, they conformed to a one compartment open model. For all four GGDs the pharmacokinetics of daidzin complied with a one compartment open model. FQ-PCR assays of rabbits' vertebrobasilar arterial tissue were performed to determine the pharmacodynamic profiles of the four GGDs. GGD markedly lowered the level of AT₁R mRNA, while the AT₂R mRNA level was increased significantly vs. the VBI model, and G-2 was the most effective. In theory the dosage was equal to the blood drug concentration and should be consistent; however, the formation of molecular aggregates affects drug absorption and metabolism, and therefore influences drugs' effects. Our data provided references for the rational use

  4. Inhalation of Whole Diesel Exhaust but not Gas-Phase Components Affects In Vitro Platelet Aggregation in Hypertensive Rats

    EPA Science Inventory

    Rationale: Intravascular thrombosis and platelet aggregation are enhanced following exposure to diesel exhaust (DE) and other respirable particulate matter; however, the roles of endothelial and circulating mediators on platelet aggregation remain unclear. We hypothesized that ad...

  5. Inhalation of Whole Diesel Exhaust but not Gas-Phase Components Affects In Vitro Platelet Aggregation in Hypertensive Rats

    EPA Science Inventory

    Rationale: Intravascular thrombosis and platelet aggregation are enhanced following exposure to diesel exhaust (DE) and other respirable particulate matter; however, the roles of endothelial and circulating mediators on platelet aggregation remain unclear. We hypothesized that ad...

  6. Definitive Ideal-Gas Thermochemical Functions of the H216O Molecule

    NASA Astrophysics Data System (ADS)

    Furtenbacher, Tibor; Szidarovszky, Tamás; Hrubý, Jan; Kyuberis, Aleksandra A.; Zobov, Nikolai F.; Polyansky, Oleg L.; Tennyson, Jonathan; Császár, Attila G.

    2016-12-01

    A much improved temperature-dependent ideal-gas internal partition function, Qint(T), of the H216O molecule is reported for temperatures between 0 and 6000 K. Determination of Qint(T) is principally based on the direct summation technique involving all accurate experimental energy levels known for H216O (almost 20 000 rovibrational energies including an almost complete list up to a relative energy of 7500 cm-1), augmented with a less accurate but complete list of first-principles computed rovibrational energy levels up to the first dissociation limit, about 41 000 cm-1 (the latter list includes close to one million bound rovibrational energy levels up to J = 69, where J is the rotational quantum number). Partition functions are developed for ortho- and para-H216O as well as for their equilibrium mixture. Unbound rovibrational states of H216O above the first dissociation limit are considered using an approximate model treatment. The effect of the excited electronic states on the thermochemical functions is neglected, as their contribution to the thermochemical functions is negligible even at the highest temperatures considered. Based on the high-accuracy Qint(T) and its first two moments, definitive results, in 1 K increments, are obtained for the following thermochemical functions: Gibbs energy, enthalpy, entropy, and isobaric heat capacity. Reliable uncertainties (approximately two standard deviations) are estimated as a function of temperature for each quantity determined. These uncertainties emphasize that the present results are the most accurate ideal-gas thermochemical functions ever produced for H216O. It is recommended that the new value determined for the standard molar enthalpy increment at 298.15 K, 9.904 04 ± 0.000 01 kJ mol-1, should replace the old CODATA datum, 9.905 ± 0.005 kJ mol-1.

  7. Potential interstellar noble gas molecules: ArOH+ and NeOH+ rovibrational analysis from quantum chemical quartic force fields

    NASA Astrophysics Data System (ADS)

    Theis, Riley A.; Fortenberry, Ryan C.

    2016-03-01

    The discovery of ArH+ in the interstellar medium has shown that noble gas chemistry may be of more chemical significance than previously believed. The present work extends the known chemistry of small noble gas molecules to NeOH+ and ArOH+. Besides their respective neonium and argonium diatomic cation cousins, these hydroxyl cation molecules are the most stable small noble gas molecules analyzed of late. ArOH+ is once again more stable than the neon cation, but both are well-behaved enough for a complete quartic force field analysis of their rovibrational properties. The Ar-O bond in ArOH+ , for instance, is roughly three-quarters of the strength of the Ar-H bond in ArH+ highlighting the rigidity of this system. The rotational constants, geometries, and vibrational frequencies for both molecules and their various isotopologues are computed from ab initio quantum chemical theory at high-level, and it is shown that these cations may form in regions where peroxy or weakly-bound alcohols may be present. The resulting data should be of significant assistance for the laboratory or observational analysis of these potential interstellar molecules.

  8. Three new defined proton affinities for polybasic molecules in the gas-phase: Proton microaffinity, proton macroaffinity and proton overallaffinity

    NASA Astrophysics Data System (ADS)

    Salehzadeh, Sadegh; Bayat, Mehdi

    2006-08-01

    A theoretical study on complete protonation of a series of tetrabasic molecules with general formula N[(CH 2) nNH 2][(CH 2) mNH 2][(CH 2) pNH 2] (tren, pee, ppe, tpt, epb and ppb) is reported. For first time, three kinds of gas-phase proton affinities for each polybasic molecule are defined as: 'proton microaffinity (PA n, i)', 'proton macroaffinity (PA)' and 'proton overall affinity ( PA)'. The variations of calculated logPA in the series of these molecules is very similar to that of their measured log Kn. There is also a good correlation between the calculated gas-phase proton macroaffinities and proton overallaffinities with corresponding equilibrium macroconstants and overall protonation constants in solution.

  9. Comparative investigation of pure and mixed rare gas atoms on coronene molecules

    NASA Astrophysics Data System (ADS)

    Rodríguez-Cantano, Rocío; Bartolomei, Massimiliano; Hernández, Marta I.; Campos-Martínez, José; González-Lezana, Tomás; Villarreal, Pablo; Pérez de Tudela, Ricardo; Pirani, Fernando; Hernández-Rojas, Javier; Bretón, José

    2017-01-01

    Clusters formed by the combination of rare gas (RG) atoms of He, Ne, Ar, and Kr on coronene have been investigated by means of a basin-hopping algorithm and path integral Monte Carlo calculations at T = 2 K. Energies and geometries have been obtained and the role played by the specific RG-RG and RG-coronene interactions on the final results is analysed in detail. Signatures of diffuse behavior of the He atoms on the surface of the coronene are in contrast with the localization of the heavier species, Ar and Kr. The observed coexistence of various geometries for Ne suggests the motion of the RG atoms on the multi-well potential energy surface landscape offered by the coronene. Therefore, the investigation of different clusters enables a comparative analysis of localized versus non-localized features. Mixed Ar-He-coronene clusters have also been considered and the competition of the RG atoms to occupy the docking sites on the molecule is discussed. All the obtained information is crucial to assess the behavior of coronene, a prototypical polycyclic aromatic hydrocarbon clustering with RG atoms at a temperature close to that of interstellar medium, which arises from the critical balance of the interactions involved.

  10. Collisions of ideal gas molecules with a rough/fractal surface. A computational study.

    PubMed

    Panczyk, Tomasz

    2007-02-01

    The frequency of collisions of ideal gas molecules (argon) with a rough surface has been studied. The rough/fractal surface was created using random deposition technique. By applying various depositions, the roughness of the surface was controlled and, as a measure of the irregularity, the fractal dimensions of the surfaces were determined. The surfaces were next immersed in argon (under pressures 2 x 10(3) to 2 x 10(5) Pa) and the numbers of collisions with these surfaces were counted. The calculations were carried out using a simplified molecular dynamics simulation technique (only hard core repulsions were assumed). As a result, it was stated that the frequency of collisions is a linear function of pressure for all fractal dimensions studied (D = 2, ..., 2.5). The frequency per unit pressure is quite complex function of the fractal dimension; however, the changes of that frequency with the fractal dimension are not strong. It was found that the frequency of collisions is controlled by the number of weakly folded sites on the surfaces and there is some mapping between the shape of adsorption energy distribution functions and this number of weakly folded sites. The results for the rough/fractal surfaces were compared with the prediction given by the Langmuir-Hertz equation (valid for smooth surface), generally the departure from the Langmuir-Hertz equation is not higher than 48% for the studied systems (i.e. for the surfaces created using the random deposition technique).

  11. Comparative investigation of pure and mixed rare gas atoms on coronene molecules.

    PubMed

    Rodríguez-Cantano, Rocío; Bartolomei, Massimiliano; Hernández, Marta I; Campos-Martínez, José; González-Lezana, Tomás; Villarreal, Pablo; Pérez de Tudela, Ricardo; Pirani, Fernando; Hernández-Rojas, Javier; Bretón, José

    2017-01-21

    Clusters formed by the combination of rare gas (RG) atoms of He, Ne, Ar, and Kr on coronene have been investigated by means of a basin-hopping algorithm and path integral Monte Carlo calculations at T = 2 K. Energies and geometries have been obtained and the role played by the specific RG-RG and RG-coronene interactions on the final results is analysed in detail. Signatures of diffuse behavior of the He atoms on the surface of the coronene are in contrast with the localization of the heavier species, Ar and Kr. The observed coexistence of various geometries for Ne suggests the motion of the RG atoms on the multi-well potential energy surface landscape offered by the coronene. Therefore, the investigation of different clusters enables a comparative analysis of localized versus non-localized features. Mixed Ar-He-coronene clusters have also been considered and the competition of the RG atoms to occupy the docking sites on the molecule is discussed. All the obtained information is crucial to assess the behavior of coronene, a prototypical polycyclic aromatic hydrocarbon clustering with RG atoms at a temperature close to that of interstellar medium, which arises from the critical balance of the interactions involved.

  12. Excitation and dissociation of molecules by femtosecond IR laser radiation in the gas phase and on dielectric surfaces

    SciTech Connect

    Kompanets, V O; Laptev, Vladimir B; Makarov, Aleksandr A; Pigulskii, S V; Ryabov, Evgenii A; Chekalin, Sergei V

    2013-04-30

    This paper presents an overview of early studies and new experimental data on the effect of near-IR (0.8-1.8 {mu}m) and mid-IR (3.3-5.8 {mu}m) intense femtosecond (130-350 fs) laser pulses on polyatomic molecules in the gas phase and on the surface of substrates. We examine the vibrational dynamics of nine molecules containing a C=O chromophore group, which are initiated by resonance femtosecond IR laser radiation at a wavelength of {approx}5 {mu}m, and report measured characteristic times of intramolecular vibrational redistribution. The characteristic time of molecules containing a single C=O group lies in the range 2.4-20 ps and that of the Fe(CO){sub 5} and Cr(CO){sub 6} molecules lies in the nanosecond range ({approx}1.0 and {approx}1.5 ns, respectively). Carbon structures have been observed for the first time to result from the decomposition of (CF{sub 3}){sub 2}CCO molecules on the surface of metal fluorides under the effect of femtosecond IR laser radiation in the wavelength range 3.3-5.4 {mu}m with no gas-phase decomposition of the molecules. (extreme light fields and their applications)

  13. C-C stretching Raman spectra and stabilities of hydrocarbon molecules in natural gas hydrates: a quantum chemical study.

    PubMed

    Liu, Yuan; Ojamäe, Lars

    2014-12-11

    The presence of specific hydrocarbon gas molecules in various types of water cavities in natural gas hydrates (NGHs) are governed by the relative stabilities of these encapsulated guest molecule-water cavity combinations. Using molecular quantum chemical dispersion-corrected hybrid density functional computations, the interaction (ΔE(host--guest)) and cohesive energies (ΔE(coh)), enthalpies, and Gibbs free energies for the complexes of host water cages and hydrocarbon guest molecules are calculated at the ωB97X-D/6-311++G(2d,2p) level of theory. The zero-point energy effect of ΔE(host-guest) and ΔE(coh) is found to be quite substantial. The energetically optimal host-guest combinations for seven hydrocarbon gas molecules (CH4, C2H6, C3H6, C3H8, C4H8, i-C4H10, and n-C4H10) and various water cavities (D, ID, T, P, H, and I) in NGHs are found to be CH4@D, C2H6@T, C3H6@T, C3H8@T, C4H8@T/P/H, i-C4H10@H, and n-C4H10@H, as the largest cohesive energy magnitudes will be obtained with these host-guest combinations. The stabilities of various water cavities enclosing hydrocarbon molecules are evaluated from the computed cohesive Gibbs free energies: CH4 prefers to be trapped in a ID cage; C2H6 prefer T cages; C3H6 and C3H8 prefer T and H cages; C4H8 and i-C4H10 prefer H cages; and n-C4H10 prefer I cages. The vibrational frequencies and Raman intensities of the C-C stretching vibrational modes for these seven hydrocarbon molecules enclosed in each water cavity are computed. A blue shift results after the guest molecule is trapped from gas phase into various water cages due to the host-guest interactions between the water cage and hydrocarbon molecule. The frequency shifts to the red as the radius of water cages increases. The model calculations support the view that C-C stretching vibrations of hydrocarbon molecules in the water cavities can be used as a tool to identify the types of crystal phases and guest molecules in NGHs.

  14. Collision lifetimes of polyatomic molecules at low temperatures: Benzene–benzene vs benzene–rare gas atom collisions

    SciTech Connect

    Cui, Jie; Krems, Roman V.; Li, Zhiying

    2014-10-28

    We use classical trajectory calculations to study the effects of the interaction strength and the geometry of rigid polyatomic molecules on the formation of long-lived collision complexes at low collision energies. We first compare the results of the calculations for collisions of benzene molecules with rare gas atoms He, Ne, Ar, Kr, and Xe. The comparison illustrates that the mean lifetimes of the collision complexes increase monotonically with the strength of the atom–molecule interaction. We then compare the results of the atom–benzene calculations with those for benzene–benzene collisions. The comparison illustrates that the mean lifetimes of the benzene–benzene collision complexes are significantly reduced due to non-ergodic effects prohibiting the molecules from sampling the entire configuration space. We find that the thermally averaged lifetimes of the benzene–benzene collisions are much shorter than those for Xe with benzene and similar to those for Ne with benzene.

  15. Collision lifetimes of polyatomic molecules at low temperatures: Benzene-benzene vs benzene-rare gas atom collisions

    NASA Astrophysics Data System (ADS)

    Cui, Jie; Li, Zhiying; Krems, Roman V.

    2014-10-01

    We use classical trajectory calculations to study the effects of the interaction strength and the geometry of rigid polyatomic molecules on the formation of long-lived collision complexes at low collision energies. We first compare the results of the calculations for collisions of benzene molecules with rare gas atoms He, Ne, Ar, Kr, and Xe. The comparison illustrates that the mean lifetimes of the collision complexes increase monotonically with the strength of the atom-molecule interaction. We then compare the results of the atom-benzene calculations with those for benzene-benzene collisions. The comparison illustrates that the mean lifetimes of the benzene-benzene collision complexes are significantly reduced due to non-ergodic effects prohibiting the molecules from sampling the entire configuration space. We find that the thermally averaged lifetimes of the benzene-benzene collisions are much shorter than those for Xe with benzene and similar to those for Ne with benzene.

  16. Collision lifetimes of polyatomic molecules at low temperatures: benzene-benzene vs benzene-rare gas atom collisions.

    PubMed

    Cui, Jie; Li, Zhiying; Krems, Roman V

    2014-10-28

    We use classical trajectory calculations to study the effects of the interaction strength and the geometry of rigid polyatomic molecules on the formation of long-lived collision complexes at low collision energies. We first compare the results of the calculations for collisions of benzene molecules with rare gas atoms He, Ne, Ar, Kr, and Xe. The comparison illustrates that the mean lifetimes of the collision complexes increase monotonically with the strength of the atom-molecule interaction. We then compare the results of the atom-benzene calculations with those for benzene-benzene collisions. The comparison illustrates that the mean lifetimes of the benzene-benzene collision complexes are significantly reduced due to non-ergodic effects prohibiting the molecules from sampling the entire configuration space. We find that the thermally averaged lifetimes of the benzene-benzene collisions are much shorter than those for Xe with benzene and similar to those for Ne with benzene.

  17. Tracking all-vapor instant gas-hydrate formation and guest molecule populations: A possible probe for molecules trapped in water nanodroplets

    NASA Astrophysics Data System (ADS)

    Uras-Aytemiz, Nevin; Cwiklik, Lukasz; Paul Devlin, J.

    2012-11-01

    Quantitative Fourier-transform infrared spectra for low-temperature (160-200 K) aerosols of clathrate-hydrate nanoparticles that contain large-cage catalysts and small-cage nonpolar guests have been extended to a broad range of vapor compositions and sampling conditions. The data better reveal the stages by which room-temperature vapor mixtures, when cooled below ˜220 K, instantly generate aerosols with particles composed exclusively of the corresponding clathrate hydrates. In particular the quantitative data help relate the nature of the hydrates that form to the composition of the aqueous nanodroplets of the first stages of the rapid transition from the all-vapor mixture. The overall transition from an all-vapor mixture to "gas"-hydrate nanocrystals is a multistage one that has been characterized as homogeneous nucleation and growth of solution nanodroplets (˜240 K) followed by nucleation and growth of the gas-hydrate particles (˜220 K); all occurring within a subsecond that follows pulsing of the warm vapor into a sampling cold chamber. This may serve well as a general description of the instantaneous generation of the gas-hydrate aerosols, but closer consideration of the nature of the sampling method, in context with recent computation-based insights to (a) gas-hydrate nucleation stages/rates and (b) the lifetimes of trapped small nonpolar molecules in cold aqueous nanodroplets, suggests a more complex multistage transition. The simulated lifetimes and extensive new quantitative infrared data significantly broaden the knowledge base in which the instantaneous transition from vapor to crystalline hydrate particles is viewed. The apparent need for a high occupancy of large-cage catalytic guest molecules currently limits the practical value of the all-vapor method. Only through greater clarity in the molecular-level description of the transition will the ultimate limits be defined.

  18. Molecular dynamics study of the equilibrium flux of gas molecules to a fractal/rough surface. Effects of gas atom diameter

    NASA Astrophysics Data System (ADS)

    Panczyk, T.; Warzocha, T.; Rudzinski, W.

    2007-04-01

    The frequency of collisions of ideal gas molecules (argon) with a rough surface has been studied. The rough/fractal surface was created using the random deposition technique. By applying various depositions the surface roughness was controlled and, as a measure of irregularity, the fractal dimensions of the surfaces were determined. The surfaces were next immersed in ideal gas and the numbers of collisions with these surfaces were counted. The calculations were carried out using the simplified molecular dynamics simulation technique (only hard core repulsions were assumed). The calculations were performed for various ratios of gas phase atoms diameter to the surface substrate atoms diameter. The results obtained showed that the size of a gas phase atom has crucial influence on the relation between the frequency of collision and the surface fractal dimension

  19. Absolute configuration assignment of a chiral molecule in the gas phase using foil-induced Coulomb explosion imaging

    NASA Astrophysics Data System (ADS)

    Herwig, Philipp; Zawatzky, Kerstin; Schwalm, Dirk; Grieser, Manfred; Heber, Oded; Jordon-Thaden, Brandon; Krantz, Claude; Novotný, Oldřich; Repnow, Roland; Schurig, Volker; Vager, Zeev; Wolf, Andreas; Trapp, Oliver; Kreckel, Holger

    2014-11-01

    Chiral molecules exist in two configurations that are nonsuperposable mirror images of one another. The underlying molecular structure is referred to as the absolute configuration. In chiral environments, the handedness of molecules influences their chemical characteristics dramatically, and therefore the determination of absolute configurations is of fundamental interest in organic chemistry and biology. Commonly applied techniques to assign absolute configuration are anomalous single-crystal x-ray diffraction and vibrational circular dichroism. However, these techniques become increasingly more challenging when applied to molecules that are made out of light atoms exclusively. Furthermore, there is no established method to determine the absolute handedness of gas-phase molecules that are not optically active. In this work, we apply the foil-induced Coulomb explosion imaging technique to determine directly the absolute configuration of the chiral molecule trans-2,3-dideuterooxirane (C2OD2H2) in the gas phase. The experiment leads to the definitive assignment of the (R ,R ) configuration to an enantio-selected dideuterooxirane sample with a statistical confidence of 5 σ . As the handedness of trans-2,3-dideuterooxirane is unambiguously linked by chemical synthesis to the stereochemical key reference glyceraldehyde, our results provide an independent verification of the absolute configuration of the stereochemical reference standard.

  20. Calculation of Ground State Rotational Populations for Kinetic Gas Homonuclear Diatomic Molecules including Electron-Impact Excitation and Wall Collisions

    SciTech Connect

    David R. Farley

    2010-08-19

    A model has been developed to calculate the ground-state rotational populations of homonuclear diatomic molecules in kinetic gases, including the effects of electron-impact excitation, wall collisions, and gas feed rate. The equations are exact within the accuracy of the cross sections used and of the assumed equilibrating effect of wall collisions. It is found that the inflow of feed gas and equilibrating wall collisions can significantly affect the rotational distribution in competition with non-equilibrating electron-impact effects. The resulting steady-state rotational distributions are generally Boltzmann for N≥3, with a rotational temperature between the wall and feed gas temperatures. The N=0,1,2 rotational level populations depend sensitively on the relative rates of electron-impact excitation versus wall collision and gas feed rates.

  1. Molecular orbital studies of gas-phase interactions between complex molecules.

    PubMed

    Gaudreault, Roger; Whitehead, M A; van de Ven, Theo G M

    2006-03-16

    Describing interactions among large molecules theoretically is a challenging task. As an example, we investigated gas-phase interactions between a linear nonionic oligomer and various model compounds (cofactors), which have been reported to associate experimentally, using PM3 semiempirical molecular orbital theory. As oligomer, we studied the hexamer of poly(ethylene oxide) (PEO), and as cofactors, we studied corilagin and related compounds containing phenolic groups (R-OH). These systems are of interest because they are models for PEO/cofactor flocculation systems, used in industrial applications. The PM3 delocalized molecular orbitals (DLMO) describe the bonding between (PEO)6 and cofactors, and some of them cover the complete complex. The DLMOs which cover the traditionally considered hydrogen bonds R-OH...O or R-CH...O show a distinct "pinch", a decrease of the electron density, between the H...O atoms. Calculations of Gibbs free energy, entropy, and enthalpy show that the PEO/cofactor complexes do not form at room temperature, because the loss of entropy exceeds the increase in enthalpy. The change in enthalpy is linearly related to the change in entropy for the different complexes. Even though bond lengths, bond angles, DLMOs, and electron densities for the PEO/cofactor complexes are consistent with the definition of hydrogen bonds, the number of intermolecular R-OH...O and R-CH...O bonds does not correlate with the enthalpy of association, indicating that the bonding mechanism for these systems is the sum of many small contributions of many delocalized orbitals.

  2. Photodissociation of HBr molecules in clusters: from rare gas clusters to water nanoparticles

    NASA Astrophysics Data System (ADS)

    Fárník, M.; Buck, Udo

    2007-09-01

    Experiments on the photodissociation of molecules in different cluster environments are described and illustrated based on the example of HBr molecules photolysed at 193 nm in various clusters. The photolysis of HBr molecules incorporated in the hydrogen bonded network of (HBr)n clusters exhibits pronounced direct exits of the H-fragments. On the other hand, the H-fragments from HBr molecules bound by much weaker van der Waals forces at the surface of large Arn clusters are trapped efficiently by the cluster cage. These observations are mainly explained by the geometry of the molecule bound to the cluster. The HBr molecules deposited on the large (H2O)n clusters behave quite differently. They undergo acid dissociation and the resulting zwitterionic form is excited by the radiation giving rise to the generation of the hydronium H3O molecule and its subsequent dissociation.

  3. Xyloketal-derived small molecules show protective effect by decreasing mutant Huntingtin protein aggregates in Caenorhabditis elegans model of Huntington’s disease

    PubMed Central

    Zeng, Yixuan; Guo, Wenyuan; Xu, Guangqing; Wang, Qinmei; Feng, Luyang; Long, Simei; Liang, Fengyin; Huang, Yi; Lu, Xilin; Li, Shichang; Zhou, Jiebin; Burgunder, Jean-Marc; Pang, Jiyan; Pei, Zhong

    2016-01-01

    Huntington’s disease is an autosomal-dominant neurodegenerative disorder, with chorea as the most prominent manifestation. The disease is caused by abnormal expansion of CAG codon repeats in the IT15 gene, which leads to the expression of a glutamine-rich protein named mutant Huntingtin (Htt). Because of its devastating disease burden and lack of valid treatment, development of more effective therapeutics for Huntington’s disease is urgently required. Xyloketal B, a natural product from mangrove fungus, has shown protective effects against toxicity in other neurodegenerative disease models such as Parkinson’s and Alzheimer’s diseases. To identify potential neuroprotective molecules for Huntington’s disease, six derivatives of xyloketal B were screened in a Caenorhabditis elegans Huntington’s disease model; all six compounds showed a protective effect. Molecular docking studies indicated that compound 1 could bind to residues GLN369 and GLN393 of the mutant Htt protein, forming a stable trimeric complex that can prevent the formation of mutant Htt aggregates. Taken together, we conclude that xyloketal derivatives could be novel drug candidates for treating Huntington’s disease. Molecular target analysis is a good method to simulate the interaction between proteins and drug compounds. Further, protective candidate drugs could be designed in future using the guidance of molecular docking results. PMID:27110099

  4. Xyloketal-derived small molecules show protective effect by decreasing mutant Huntingtin protein aggregates in Caenorhabditis elegans model of Huntington's disease.

    PubMed

    Zeng, Yixuan; Guo, Wenyuan; Xu, Guangqing; Wang, Qinmei; Feng, Luyang; Long, Simei; Liang, Fengyin; Huang, Yi; Lu, Xilin; Li, Shichang; Zhou, Jiebin; Burgunder, Jean-Marc; Pang, Jiyan; Pei, Zhong

    2016-01-01

    Huntington's disease is an autosomal-dominant neurodegenerative disorder, with chorea as the most prominent manifestation. The disease is caused by abnormal expansion of CAG codon repeats in the IT15 gene, which leads to the expression of a glutamine-rich protein named mutant Huntingtin (Htt). Because of its devastating disease burden and lack of valid treatment, development of more effective therapeutics for Huntington's disease is urgently required. Xyloketal B, a natural product from mangrove fungus, has shown protective effects against toxicity in other neurodegenerative disease models such as Parkinson's and Alzheimer's diseases. To identify potential neuroprotective molecules for Huntington's disease, six derivatives of xyloketal B were screened in a Caenorhabditis elegans Huntington's disease model; all six compounds showed a protective effect. Molecular docking studies indicated that compound 1 could bind to residues GLN369 and GLN393 of the mutant Htt protein, forming a stable trimeric complex that can prevent the formation of mutant Htt aggregates. Taken together, we conclude that xyloketal derivatives could be novel drug candidates for treating Huntington's disease. Molecular target analysis is a good method to simulate the interaction between proteins and drug compounds. Further, protective candidate drugs could be designed in future using the guidance of molecular docking results.

  5. Aggregated silver nanoparticles based surface-enhanced Raman scattering enzyme-linked immunosorbent assay for ultrasensitive detection of protein biomarkers and small molecules.

    PubMed

    Liang, Jiajie; Liu, Hongwu; Huang, Caihong; Yao, Cuize; Fu, Qiangqiang; Li, Xiuqing; Cao, Donglin; Luo, Zhi; Tang, Yong

    2015-06-02

    Lowering the detection limit is critical to the design of bioassays required for medical diagnostics, environmental monitoring, and food safety regulations. The current sensitivity of standard color-based analyte detection limits the further use of enzyme-linked immunosorbent assays (ELISAs) in research and clinical diagnoses. Here, we demonstrate a novel method that uses the Raman signal as the signal-generating system of an ELISA and combines surface-enhanced Raman scattering (SERS) with silver nanoparticles aggregation for ultrasensitive analyte detection. The enzyme label of the ELISA controls the dissolution of Raman reporter-labeled silver nanoparticles through hydrogen peroxide and generates a strong Raman signal when the analyte is present. Using this assay, prostate-specific antigen (PSA) and the adrenal stimulant ractopamine (Rac) were detected in whole serum and urine at the ultralow concentrations of 10(-9) and 10(-6) ng/mL, respectively. The methodology proposed here could potentially be applied to other molecules detection as well as PSA and Rac.

  6. Thermodynamic properties of water in the lattice gas model with consideration of the vibrational motions of molecules

    NASA Astrophysics Data System (ADS)

    Titov, S. V.; Tovbin, Yu. K.

    2016-11-01

    A molecular model developed earlier for a polar fluid within the lattice gas model is supplemented by considering the vibrational motions of molecules using water as an example. A combination of point dipole and Lennard-Jones potentials from SPC parametrization is chosen as the force field model for the molecule. The main thermodynamic properties of liquid water (density, internal energy, and entropy) are studied as functions of temperature. There is qualitative agreement between the calculation results and the experimental data. Ways of refining the molecular theory are discussed.

  7. Ab initio potential energy surface for the carbon dioxide molecule pair and thermophysical properties of dilute carbon dioxide gas

    NASA Astrophysics Data System (ADS)

    Hellmann, Robert

    2014-10-01

    A four-dimensional intermolecular potential energy surface (PES) for two rigid carbon dioxide molecules was determined from quantum-chemical ab initio calculations. Interaction energies for 1229 CO2-CO2 configurations were computed at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. An analytical site-site potential function with seven sites per CO2 molecule was fitted to the interaction energies. The PES was validated by calculating the second virial coefficient as well as viscosity and thermal conductivity in the dilute-gas limit.

  8. A Comparative High-Resolution Electron Microscope Study of Ag Clusters Produced by a Sputter-Gas Aggregation and Ion Cluster Beam Technique

    NASA Astrophysics Data System (ADS)

    Hohl, Georg-Friedrich; Hihara, Takehiko; Sakurai, Masaki; Oishi, Takashi; Wakoh, Kimio; Sumiyama, Kenji; Suzuki, Kenji

    1994-03-01

    Ag clusters were formed by a sputter-gas-aggregation process [H. Haberland et al..: J. Vac. Sci. Technol. A 10 (1992) 3266] and the ionized cluster beam (ICB) [T. Takagi: Ionized-Cluster Beam Deposition and Epitaxy (Noyes, Park Ridge, 1988)] technique. The Ag clusters deposited on collodion-coated microgrids were investigated by high-resolution transmission electron microscopy. The diameter of those clusters, d, ranges from 1 nm up to about 10 nm for specimens produced by the sputter-gas aggregation technique, depending on the sputter condition and the deposition time. Comparable times of the ICB deposition lead to a broader distribution up to d≈20 nm, suggesting the formation of islands with extremely flat shapes. High percentages of crystalline particles obtained by both techniques are either single crystals or multiple twins with clear lattice images.

  9. High-resolution optical spectroscopy with a buffer-gas-cooled beam of BaH molecules

    NASA Astrophysics Data System (ADS)

    Iwata, G. Z.; McNally, R. L.; Zelevinsky, T.

    2017-08-01

    Barium monohydride (BaH) is an attractive candidate for extending laser cooling and trapping techniques to diatomic hydrides. The apparatus and high-resolution optical spectroscopy presented here demonstrate progress toward this goal. A cryogenic buffer-gas-cooled molecular beam of BaH was constructed and characterized. Pulsed laser ablation into cryogenic helium buffer gas delivers ˜1 ×1010 molecules/sr/pulse in the X +2Σ (v''=0 ,N''=1 ) state of primary interest. More than 1 ×107 of these molecules per pulse enter the downstream science region with forward velocities below 100 m/s and transverse temperature of 0.1 K. This molecular beam enabled high-resolution optical spectra of BaH in quantum states relevant to laser slowing and cooling. The reported measurements include hyperfine structure and magnetic g factors in the X +2Σ , B +2Σ , and A 1/2 2Π states.

  10. Spectral Luminescent Properties of the Glycine Molecule in a Gas Discharge

    NASA Astrophysics Data System (ADS)

    General, A. A.; Migovich, M. I.; Kelman, V. A.; Zhmenyak, Yu. V.; Zvenigorodsky, V. V.

    2016-01-01

    We have experimentally studied the luminescence spectra of glycine powder in the plasma of a repetitively pulsed longitudinal discharge in argon-glycine and helium-glycine mixtures. We have identified the main fragments of the glycine molecule emitting in the 200-1000 nm region. The emitting molecules due to fragmentation of glycine and dissociation of the carboxyl (-COOH) and amino (-NH2) groups are nitrogen, carbon monoxide, and cyanogen molecules.

  11. Controlled Gas Molecules Doping of Monolayer MoS2 via Atomic-Layer-Deposited Al2O3 Films.

    PubMed

    Li, Yuanzheng; Li, Xinshu; Chen, Heyu; Shi, Jia; Shang, Qiuyu; Zhang, Shuai; Qiu, Xiaohui; Liu, Zheng; Zhang, Qing; Xu, Haiyang; Liu, Weizhen; Liu, Xinfeng; Liu, Yichun

    2017-08-23

    MoS2 as atomically thin semiconductor is highly sensitive to ambient atmosphere (e.g., oxygen, moisture, etc.) in optical and electrical properties. Here we report a controlled gas molecules doping of monolayer MoS2 via atomic-layer-deposited Al2O3 films. The deposited Al2O3 films, in the shape of nanospheres, can effectively control the contact areas between ambient atmosphere and MoS2 that allows precise modulation of gas molecules doping. By analyzing photoluminescence (PL) emission spectra of MoS2 with different thickness of Al2O3, the doped carrier concentration is estimated at ∼2.7 × 10(13) cm(-2) based on the mass action model. Moreover, time-dependent PL measurements indicate an incremental stability of single layer MoS2 as the thicknesses of Al2O3 capping layer increase. Effective control of gas molecules doping in monolayer MoS2 provides us a valuable insight into the applications of MoS2 based optical and electrical devices.

  12. Molecule and polaron in a highly polarized two-dimensional fermi gas with spin-orbit coupling.

    PubMed

    Yi, Wei; Zhang, Wei

    2012-10-05

    We show that spin-orbit coupling (SOC) gives rise to pairing instability in a highly polarized two-dimensional Fermi gas for an arbitrary interaction strength. The pairing instability can lead to a Fulde-Ferrell-Larkin-Ovchinnikov-like molecular state, which undergoes a first-order transition into a pairing state with zero center-of-mass momentum as the parameters are tuned. These pairing states are metastable against a polaron state dressed by particle-hole fluctuations for small SOC. At large SOC, a polaron-molecule transition exists, which suggests a phase transition between the topological superfluid state and the normal state for a highly polarized Fermi gas in the thermodynamic limit. As polarization in a Fermi gas with SOC is induced by the effective Zeeman field, we also discuss the influences of the effective Zeeman field on the ground state of the system. Our findings may be tested directly in future experiments.

  13. Cooperative Reformable Channel System with Unique Recognition of Small Gas Molecules in a two-dimensional ZIF-membrane

    NASA Astrophysics Data System (ADS)

    Motevalli, Benyamin; Taherifar, Neda; Liu, Zhe

    We report a cooperative reformable channel system in a coordination porous polymer, named as ZIF-L. Three types of local flexible ligands coexist in the crystal structure of this polymer, resulting in ultra-flexibility. The reformable channel is able to regulate permeation of a nonspherical guest molecule, such as N2 or CO2, based on its longer molecular dimension, which is in a striking contrast to conventional molecular sieves that regulate the shorter cross-sectional dimension of the guest molecules. Our density functional theory (DFT) calculations reveal that the guest molecule induces dynamic motion of the flexible ligands, leading to the channel reformation, and then the guest molecule reorientates itself to fit in the reformed channel. Such a unique ``induced fit-in'' mechanism causes the gas molecule to pass through 6 membered-ring windows in the c- crystal direction of ZIF-L with its longer axis parallel to the window plane. Our experimental permeance of N2 through the ZIF-L membranes is about three times greater than that of CO2, supporting the DFT simulation predictions.

  14. Radiation-induced degradation of alkane molecules in solid rare gas matrices

    NASA Astrophysics Data System (ADS)

    Feldman, V. I.; Sukhov, F. F.; Slovokhotova, N. A.; Bazov, V. P.

    1996-09-01

    The radiation-induced degradation of heptane molecules in solid argon and xenon matrices at 15 K was studied using low-temperature IR spectroscopy. The total radiation-chemical yield of the destruction of heptane molecules in argon (mole ratio 500:1) was estimated to be 1.4 molecule per 100 eV. Methane, vinyl- and trans-vinylene-type olefins, and allyl-type radicals were identified among the main radiolysis products in both matrices. The C-C bond rupture is favoured in argon probably due to formation of excited heptane cations in the hole transfer in this matrix. An indication of the radical cation trapping was obtained in a xenon matrix containing an electron scavenger (Freon-113). The mechanism of the radiation-induced degradation of alkane molecules and the fate of the primary cations in rigid inert media are discussed.

  15. Co(II)-doped MOF-5 nano/microcrystals: Solvatochromic behaviour, sensing solvent molecules and gas sorption property

    SciTech Connect

    Yang, Ji-Min; Liu, Qing; Sun, Wei-Yin

    2014-10-15

    Co(II)-doped MOF-5 nano/microcrystals with controllable morphology and size were successfully obtained by solvothermal method. The products were characterized by powder X-ray diffraction (PXRD), energy dispersive spectrometry (EDS), field emission scanning electron microscopy (FESEM), thermogravimetric analysis (TGA), inductively coupled plasma optical emission spectrometer (ICP-OES), elemental analysis, UV–vis and infrared (IR) spectroscopy. The factors influencing the crystal morphology and size were investigated. The gas sorption measurements reveal that highly crystalline particles have large Langmuir surface area. It was found that the Co(II)-doped MOF-5 shows enhanced hydrostability and the sorption profiles of the Co(II)-doped MOF-5 nano/microcrystals are dependent on the morphology and size of the particles. Porous Co(II)-doped MOF-5 is stable upon the removal of guest molecules and exhibits different colour with accommodating different solvent molecule, which means that it can act as solvatochromic sensing materials for recognition of solvent molecules. - Graphical abstract: Co(II)-doped MOF-5 nano/microcrystals with different shapes and sizes were synthesized by a facile hydrothermal method, which not only enhance gas sorption properties and structural stability of MOFs towards moisture, but also act as new sensing materials for sensing small molecules. - Highlights: • Co(II)-doped MOF-5 nano/microcrystals with controllable morphology and size were obtained. • Co(II)-doped MOF-5 nano/microcrystals enhance the structural stability towards moisture. • Co(II)-doped MOF-5 can act as new sensing material for sensing small molecules.

  16. A quantum gas of polar KRb molecules in an optical lattice

    NASA Astrophysics Data System (ADS)

    Covey, Jacob; Miecnikowski, Matthew; Moses, Steven; Fu, Zhengkun; Jin, Deborah; Ye, Jun

    2016-05-01

    Ultracold polar molecules provide new opportunities for investigation of strongly correlated many-body spin systems such as many-body localization and quantum magnetism. In an effort to access such phenomena, we load polar KRb molecules into a three-dimensional optical lattice. In this system, we observed many-body spin dynamics between molecules pinned in a deep lattice, even though the filling fraction of the molecules was only 5%. We have recently performed a thorough investigation of the molecule creation process in an optical lattice, and consequently improved our filling fraction to 30% by preparing and overlapping Mott and band insulators of the initial atomic gases. More recently, we switched to a second generation KRb apparatus that will allow application of large, stable electric fields as well as high-resolution addressing and detection of polar molecules in optical lattices. We plan to use these capabilities to study non-equilibrium spin dynamics in an optical lattice with nearly single site resolution. I will present the status and direction of the second generation apparatus.

  17. Investigating the nature of noble gas-copper bonds by the quantum theory of atoms in molecules.

    PubMed

    Rodrigues, Eduardo F F; de Sá, Eduardo L; Haiduke, Roberto L A

    2010-04-22

    We investigated noble gas-copper bonds in linear complexes represented by the NgCuX general formula in which Ng and X stand for a noble gas (neon, argon, krypton, or xenon) and a halogen (fluorine, chlorine or bromine), respectively, by coupled cluster methods and modified cc-pVQZ basis sets. The quantum theory of atoms in molecules (QTAIM) shows a linear relation between the dissociation energy of noble gas-copper bonds and the amount of electronic charge transferred mainly from the noble gas to copper during complexation. Large changes in the QTAIM quadrupole moments of copper and noble gases resulting from this bonding and a comparison between NgCuX and NgNaCl systems indicate that these noble gas-copper bonds should be better interpreted as predominantly covalent. Finally, QTAIM atomic dipoles of noble gases in NgNaCl systems agree satisfactorily with atomic dipoles given by a simple model for these NgNa van der Waals bonds.

  18. The PPII-to-α-helix transition of poly-l-lysine in methanol/water solvent mixtures accompanied by fibrillar self-aggregation: An influence of fluphenazine molecules.

    PubMed

    Cieślik-Boczula, Katarzyna

    2017-08-01

    Fourier-transform infrared, vibrational circular dichroism spectroscopy and transmission electron microscopy are used to follow the structural changes of pure and fluphenazine (FPh)-mixed poly-l-lysine (PLL) triggered by variations of the methanol to water ratio in solvent mixtures. FPh molecules are used as an effective psychotic drug but with a strong Parkinson's-related side effect. To answer the question whether FPh molecules can modify the fibril development, the PLL polypeptide was used as a model of α-helix- and PPII-rich fibrils. It was stated that the presence of FPh molecules did not inhibit the creation of both types of PLL fibrils with clustering features. The methanol-poor aqueous solutions promote the formation of extended polyproline II (PPII) helices; however, the methanol-rich aqueous solutions induce the development of α-helices of both pure and FPh-mixed PLL. Unpredicted and interesting features of PLL fibrillogenesis are evidenced by the formation of uncommon fibrillar aggregates, which are developed in methanol/water solvents from PLL molecules rich in either α-helix or PPII structures. Possibility of PLL molecules to form β-sheet-, α-helix- and PPII-rich fibrils demonstrating that fibrillogenesis is a common phenomenon, and fibrillar aggregates can be based on all of the basic protein secondary structures. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Characterization of a DAPI-RIT-DAPI system for gas-phase ion/molecule and ion/ion reactions.

    PubMed

    Lin, Ziqing; Tan, Lei; Garimella, Sandilya; Li, Linfan; Chen, Tsung-Chi; Xu, Wei; Xia, Yu; Ouyang, Zheng

    2014-01-01

    The discontinuous atmospheric pressure interface (DAPI) has been developed as a facile means for efficiently introducing ions generated at atmospheric pressure to an ion trap in vacuum [e.g., a rectilinear ion trap (RIT)] for mass analysis. Introduction of multiple beams of ions or neutral species through two DAPIs into a single RIT has been previously demonstrated. In this study, a home-built instrument with a DAPI-RIT-DAPI configuration has been characterized for the study of gas-phase ion/molecule and ion/ion reactions. The reaction species, including ions or neutrals, can be introduced from both ends of the RIT through the two DAPIs without complicated ion optics or differential pumping stages. The primary reactant ions were isolated prior to reaction and the product ions were mass analyzed after controlled reaction time period. Ion/molecule reactions involving peptide radical ions and proton-transfer ion/ion reactions have been carried out using this instrument. The gas dynamic effect due to the DAPI operation on internal energy deposition and the reactivity of peptide radical ions has been characterized. The DAPI-RIT-DAPI system also has a unique feature for allowing the ion reactions to be carried out at significantly elevated pressures (in 10(-1) Torr range), which has been found to be helpful to speed up the reactions. The viability and flexibility of the DAPI-RIT-DAPI system for the study of gas-phase ion reactions have been demonstrated.

  20. Characterization of a DAPI-RIT-DAPI System for Gas-Phase Ion/Molecule and Ion/Ion Reactions

    NASA Astrophysics Data System (ADS)

    Lin, Ziqing; Tan, Lei; Garimella, Sandilya; Li, Linfan; Chen, Tsung-Chi; Xu, Wei; Xia, Yu; Ouyang, Zheng

    2014-01-01

    The discontinuous atmospheric pressure interface (DAPI) has been developed as a facile means for efficiently introducing ions generated at atmospheric pressure to an ion trap in vacuum [e.g., a rectilinear ion trap (RIT)] for mass analysis. Introduction of multiple beams of ions or neutral species through two DAPIs into a single RIT has been previously demonstrated. In this study, a home-built instrument with a DAPI-RIT-DAPI configuration has been characterized for the study of gas-phase ion/molecule and ion/ion reactions. The reaction species, including ions or neutrals, can be introduced from both ends of the RIT through the two DAPIs without complicated ion optics or differential pumping stages. The primary reactant ions were isolated prior to reaction and the product ions were mass analyzed after controlled reaction time period. Ion/molecule reactions involving peptide radical ions and proton-transfer ion/ion reactions have been carried out using this instrument. The gas dynamic effect due to the DAPI operation on internal energy deposition and the reactivity of peptide radical ions has been characterized. The DAPI-RIT-DAPI system also has a unique feature for allowing the ion reactions to be carried out at significantly elevated pressures (in 10-1 Torr range), which has been found to be helpful to speed up the reactions. The viability and flexibility of the DAPI-RIT-DAPI system for the study of gas-phase ion reactions have been demonstrated.

  1. Supramolecular Low-Molecular-Weight Hydrogelator Stabilization of SERS-Active Aggregated Nanoparticles for Solution and Gas Sensing.

    PubMed

    Canrinus, Tjalling R; Lee, Wendy W Y; Feringa, Ben L; Bell, Steven E J; Browne, Wesley R

    2017-09-05

    The potential of surface-enhanced Raman scattering (SERS) spectroscopy in both laboratory and field analyses depends on the reliable formation of so-called SERS hot spots, such as those formed during gold or silver nanoparticle aggregation. Unfortunately such aggregates are not stable in solution because they typically grow until they precipitate. Here we describe the use of low-molecular-weight hydrogels formed through pH-triggered self-assembly that occurs at a rate that well matches the rates of aggregation of Au or Ag colloids, allowing them to be trapped at the SERS-active point in the aggregation process. We show that the colloid-containing gels give SERS signals similar to the parent colloid but are stable over several months. Moreover, lyophilized gels can be stored as dry powders for subsequent use in the analyses of gases and dissolved analytes by contact with either solutions or vapors. The present system shows how the combination of pH-switchable low-molecular-weight gelators and pH-induced colloid aggregation can be combined to make a highly stable, low-cost SERS platform for the detection of volatile organic compounds and the microvolume analysis of solutions.

  2. An investigation of the interaction of intense laser radiation with molecules of sulfur hexafluoride through the buffer gas technique

    NASA Astrophysics Data System (ADS)

    Eletskii, A. V.; Klimov, V. D.; Udalova, T. A.

    1981-02-01

    Measurements of the coefficient of the absorption of intense (approximately 10 to the 7th W/sq cm) radiation from a CO2 laser by SF6 molecules in the presence of noble gases and at pressures up to 40 bars are presented. The dependence of the coefficient of absorption on the pressure and type of buffer gas, as well as on the wavelength and intensity of the incident radiation, makes it possible to follow the formation of the vibrational state distribution function of the molecules. The character of the distribution function depends on the competition between vibrational relaxation processes and laser radiation absorption. At high pressures, that is, at helium pressures greater than approximately 20-40 bars, a two-level scheme for the interaction of intense laser radiation with SF6 is implemented experimentally for the first time. Here, molecules excited by light to the v = 1 state relax instantaneously upon collision. The dependence of the rate constant for the destruction of SF6 molecular states on the number of the vibrational level v upon collision with helium atoms can be evaluated from the experimental data. Taken as a whole, the data confirm the assumption of the linear, single-photon nature of the interaction of laser radiation with SF6 molecules.

  3. Quantum Gas of Polar Molecules Ensembles at Ultralow Temperatures: f-wave Superfluids

    NASA Astrophysics Data System (ADS)

    Boudjemâa, Abdelâali

    2017-10-01

    We investigate novel f-wave superfluids of fermionic polar molecules in a two-dimensional bilayer system with dipole moments polarized perpendicular to the layers and in opposite directions in different layers. The solution of the BCS gap equation reveals that these unconventional superfluids emerge at temperatures on the level of femtokelvin which opens up new possibilities to explore the topological f+i f phase, quantum interferometry and Majorana fermions in experiments with ultracold polar molecules. The experimental realization of such interesting novel f-wave pairings is discussed.

  4. The role of multiparticle correlations and Cooper pairing in the formation of molecules in an ultracold gas of Fermi atoms with a negative scattering length

    SciTech Connect

    Babichenko, V. S. Kagan, Yu.

    2012-11-15

    The influence of multiparticle correlation effects and Cooper pairing in an ultracold Fermi gas with a negative scattering length on the formation rate of molecules is investigated. Cooper pairing is shown to cause the formation rate of molecules to increase, as distinct from the influence of Bose-Einstein condensation in a Bose gas on this rate. This trend is retained in the entire range of temperatures below the critical one.

  5. Drag force and transport property of a small cylinder in free molecule flow: A gas-kinetic theory analysis.

    PubMed

    Liu, Changran; Li, Zhigang; Wang, Hai

    2016-08-01

    Analytical expressions are derived for aerodynamic drag force on small cylinders in the free molecule flow using the gas-kinetic theory. The derivation considers the effect of intermolecular interactions between the cylinder and gas media. Two limiting collision models, specular and diffuse scattering, are investigated in two limiting cylinder orientations with respect to the drift velocity. The earlier solution of Dahneke [B. E. Dahneke, J. Aerosol Sci. 4, 147 (1973)10.1016/0021-8502(73)90066-9] is shown to be a special case of the current expressions in the rigid-body limit of collision. Drag force expressions are obtained for cylinders that undergo Brownian rotation and for those that align with the drift velocity. The validity of the theoretical expressions is tested against experimental mobility data available for carbon nanotubes.

  6. Drag force and transport property of a small cylinder in free molecule flow: A gas-kinetic theory analysis

    NASA Astrophysics Data System (ADS)

    Liu, Changran; Li, Zhigang; Wang, Hai

    2016-08-01

    Analytical expressions are derived for aerodynamic drag force on small cylinders in the free molecule flow using the gas-kinetic theory. The derivation considers the effect of intermolecular interactions between the cylinder and gas media. Two limiting collision models, specular and diffuse scattering, are investigated in two limiting cylinder orientations with respect to the drift velocity. The earlier solution of Dahneke [B. E. Dahneke, J. Aerosol Sci. 4, 147 (1973), 10.1016/0021-8502(73)90066-9] is shown to be a special case of the current expressions in the rigid-body limit of collision. Drag force expressions are obtained for cylinders that undergo Brownian rotation and for those that align with the drift velocity. The validity of the theoretical expressions is tested against experimental mobility data available for carbon nanotubes.

  7. Oxygen K-edge absorption spectra of small molecules in the gas phase

    SciTech Connect

    Yang, B.X.; Kirz, J.; Sham, T.K.

    1986-01-01

    The absorption spectra of O/sub 2/, CO, CO/sub 2/ and OCS have been recorded in a transmission mode in the energy region from 500 to 950 eV. Recent observation of EXAFS in these molecules is confirmed in this study. 7 refs., 3 figs.

  8. Creation of a strongly dipolar gas of ultracold ground-state 23 Na87 Rb molecules

    NASA Astrophysics Data System (ADS)

    Guo, Mingyang; Zhu, Bing; Lu, Bo; Ye, Xin; Wang, Fudong; Wang, Dajun; Vexiau, Romain; Bouloufa-Maafa, Nadia; Quéméner, Goulven; Dulieu, Olivier

    2016-05-01

    We report on successful creation of an ultracold sample of ground-state 23 Na87 Rb molecules with a large effective electric dipole moment. Through a carefully designed two-photon Raman process, we have successfully transferred the magneto-associated Feshbach molecules to the singlet ground state with high efficiency, obtaining up to 8000 23 Na87 Rb molecules with peak number density over 1011 cm-3 in their absolute ground-state level. With an external electric field, we have induced an effective dipole moment over 1 Debye, making 23 Na87 Rb the most dipolar ultracold particle ever achieved. Contrary to the expectation, we observed a rather fast population loss even for 23 Na87 Rb in the absolute ground state with the bi-molecular exchange reaction energetically forbidden. The origin for the short lifetime and possible ways of mitigating it are currently under investigation. Our achievements pave the way toward investigation of ultracold bosonic molecules with strong dipolar interactions. This work is supported by the Hong Kong RGC CUHK404712 and the ANR/RGC Joint Research Scheme ACUHK403/13.

  9. Ultrasensitive ultraviolet-visible 20 fs absorption spectroscopy of low vapor pressure molecules in the gas phase.

    PubMed

    Schriever, C; Lochbrunner, S; Riedle, E; Nesbitt, D J

    2008-01-01

    We describe an ultrasensitive pump-probe spectrometer for transient absorption measurements in the gas phase and in solution. The tunable UV pump and the visible (450-740 nm) probe pulses are generated by two independently tunable noncollinear optical parametric amplifiers, providing a temporal resolution of 20 fs. A homebuilt low gain photodetector is used to accommodate strong probe pulses with a shot noise significantly lower than the overall measurement noise. A matched digitizing scheme for single shot analysis of the light pulses at kilohertz repetition rates that minimizes the electronic noise contributions to the transient absorption signal is developed. The data processing scheme is optimized to yield best suppression of the laser excess noise and thereby transient absorbance changes down to 1.1 x 10(-6) can be resolved. A collinear focusing geometry optimized for a 50 mm interaction length combined with a heatable gas cell allows us to perform measurements on substances with low vapor pressures, e.g., on medium sized molecules which are crystalline at room temperature. As an application example highlighting the capability of this instrument, we present the direct time-domain observation of the ultrafast excited state intramolecular proton transfer of 2-(2(')-hydroxyphenyl)benzothiazole in the gas phase. We are able to compare the resulting dynamics in the gas phase and in solution with a temporal precision of better than 5 fs.

  10. Ultrasensitive ultraviolet-visible 20 fs absorption spectroscopy of low vapor pressure molecules in the gas phase

    NASA Astrophysics Data System (ADS)

    Schriever, C.; Lochbrunner, S.; Riedle, E.; Nesbitt, D. J.

    2008-01-01

    We describe an ultrasensitive pump-probe spectrometer for transient absorption measurements in the gas phase and in solution. The tunable UV pump and the visible (450-740nm) probe pulses are generated by two independently tunable noncollinear optical parametric amplifiers, providing a temporal resolution of 20fs. A homebuilt low gain photodetector is used to accommodate strong probe pulses with a shot noise significantly lower than the overall measurement noise. A matched digitizing scheme for single shot analysis of the light pulses at kilohertz repetition rates that minimizes the electronic noise contributions to the transient absorption signal is developed. The data processing scheme is optimized to yield best suppression of the laser excess noise and thereby transient absorbance changes down to 1.1×10-6 can be resolved. A collinear focusing geometry optimized for a 50mm interaction length combined with a heatable gas cell allows us to perform measurements on substances with low vapor pressures, e.g., on medium sized molecules which are crystalline at room temperature. As an application example highlighting the capability of this instrument, we present the direct time-domain observation of the ultrafast excited state intramolecular proton transfer of 2-(2'-hydroxyphenyl)benzothiazole in the gas phase. We are able to compare the resulting dynamics in the gas phase and in solution with a temporal precision of better than 5fs.

  11. Radiation and Laser Potential of Homo and Heteronuclear Rare-Gas Diatomic Molecules.

    DTIC Science & Technology

    1982-12-01

    SUPPLEMENTARY NOTES " .. . . , 19 KEy WOODS (Continue on reverse side if necessary and identify by block number) Ll Vacuum Ultraviolet Spectroscopy Rare-Gas...absorption we used the same "C. H. Chen, P. E. Siska, and Y. T. Lee, J. Chem. Phys. terminology. See G. Herzberg, Spectrs of Diatomi Mole- 5, 601

  12. Multispectral actinometry of water and water-derivative molecules in moist, inert gas discharge plasmas

    NASA Astrophysics Data System (ADS)

    Bernatskiy, A. V.; Ochkin, V. N.; Kochetov, I. V.

    2016-10-01

    A new version of optical actinometry (OA) is used to determine the concentrations of water molecules and their fragments in hollow cathode discharge plasma in moist inert gases. Use is made of two actinometer particles, namely, the atoms Xe and Ar, for concurrent measurements of the concentrations of the H2O molecule and its fragments O, H, and OH. A self-consistent method is suggested for the determination of particle concentrations with due regard for the quenching of the emitting states. The temporal behavior of particles during discharge glow is studied. Noted are fast variations (lasting from a few to a few tens of s) in the concentrations of all the particles, followed by their stabilization (within a few to a few tens of mins). The scheme of the processes responsible for the observed dynamics of the plasma composition is discussed.

  13. Half-quantum vortex molecules in a binary dipolar Bose gas.

    PubMed

    Shirley, Wilbur E; Anderson, Brandon M; Clark, Charles W; Wilson, Ryan M

    2014-10-17

    We study the ground state phases of a rotating two-component, or binary, Bose-Einstein condensate, wherein one component possesses a large permanent magnetic dipole moment. A variety of nontrivial phases emerge in this system, including a half-quantum vortex (HQV) chain phase and a HQV molecule phase, where HQVs bind at short distances. We attribute these phases to the development of a minimum in the HQV interaction potential, which emerges without coherent coupling or attractive interactions between the components. Thus, we show that the presence of dipolar interactions in this system provides a unique mechanism for the formation of HQV molecules and results in a rich ground state phase diagram.

  14. Strongly aligned gas-phase molecules at free-electron lasers

    SciTech Connect

    Kierspel, Thomas; Wiese, Joss; Mullins, Terry; Robinson, Joseph; Aquila, Andy; Barty, Anton; Bean, Richard; Boll, Rebecca; Boutet, Sebastien; Bucksbaum, Philip; Chapman, Henry N.; Christensen, Lauge; Fry, Alan; Hunter, Mark; Koglin, Jason E.; Liang, Mengning; Mariani, Valerio; Morgan, Andrew; Natan, Adi; Petrovic, Vladimir; Rolles, Daniel; Rudenko, Artem; Schnorr, Kirsten; Stapelfeldt, Henrik; Stern, Stephan; Thogersen, Jan; Yoon, Chun Hong; Wang, Fenglin; Trippel, Sebastian; Kupper, Jochen

    2015-09-16

    Here, we demonstrate a novel experimental implementation to strongly align molecules at full repetition rates of free-electron lasers. We utilized the available in-house laser system at the coherent x-ray imaging beamline at the linac coherent light source. Chirped laser pulses, i.e., the direct output from the regenerative amplifier of the Ti:Sa chirped pulse amplification laser system, were used to strongly align 2, 5-diiodothiophene molecules in a molecular beam. The alignment laser pulses had pulse energies of a few mJ and a pulse duration of 94 ps. A degree of alignment of $\\langle {\\mathrm{cos}}^{2}{\\theta }_{2{\\rm{D}}}\\rangle =0.85$ was measured, limited by the intrinsic temperature of the molecular beam rather than by the available laser system. With the general availability of synchronized chirped-pulse-amplified near-infrared laser systems at short-wavelength laser facilities, our approach allows for the universal preparation of molecules tightly fixed in space for experiments with x-ray pulses.

  15. Strongly aligned gas-phase molecules at free-electron lasers

    DOE PAGES

    Kierspel, Thomas; Wiese, Joss; Mullins, Terry; ...

    2015-09-16

    Here, we demonstrate a novel experimental implementation to strongly align molecules at full repetition rates of free-electron lasers. We utilized the available in-house laser system at the coherent x-ray imaging beamline at the linac coherent light source. Chirped laser pulses, i.e., the direct output from the regenerative amplifier of the Ti:Sa chirped pulse amplification laser system, were used to strongly align 2, 5-diiodothiophene molecules in a molecular beam. The alignment laser pulses had pulse energies of a few mJ and a pulse duration of 94 ps. A degree of alignment ofmore » $$\\langle {\\mathrm{cos}}^{2}{\\theta }_{2{\\rm{D}}}\\rangle =0.85$$ was measured, limited by the intrinsic temperature of the molecular beam rather than by the available laser system. With the general availability of synchronized chirped-pulse-amplified near-infrared laser systems at short-wavelength laser facilities, our approach allows for the universal preparation of molecules tightly fixed in space for experiments with x-ray pulses.« less

  16. Beams of fast neutral atoms and molecules in low-pressure gas-discharge plasma

    SciTech Connect

    Metel, A. S.

    2012-03-15

    Fast neutral atom and molecule beams have been studied, the beams being produced in a vacuum chamber at nitrogen, argon, or helium pressure of 0.1-10 Pa due to charge-exchange collisions of ions accelerated in the sheath between the glow discharge plasma and a negative grid immersed therein. From a flat grid, two broad beams of molecules with continuous distribution of their energy from zero up to e(U + U{sub c}) (where U is voltage between the grid and the vacuum chamber and U{sub c} is cathode fall of the discharge) are propagating in opposite directions. The beam propagating from the concave surface of a 0.2-m-diameter grid is focused within a 10-mm-diameter spot on the target surface. When a 0.2-m-diameter 0.2-m-high cylindrical grid covered by end disks and composed of parallel 1.5-mm-diameter knitting needles spaced by 4.5 mm is immersed in the plasma, the accelerated ions pass through the gaps between the needles, turn inside the grid into fast atoms or molecules, and escape from the grid through the gaps on its opposite side. The Doppler shift of spectral lines allows for measuring the fast atom energy, which corresponds to the potential difference between the plasma inside the chamber and the plasma produced as a result of charge-exchange collisions inside the cylindrical grid.

  17. Quantum Engineering of a Low-Entropy Gas of Heteronuclear Bosonic Molecules in an Optical Lattice

    NASA Astrophysics Data System (ADS)

    Reichsöllner, Lukas; Schindewolf, Andreas; Takekoshi, Tetsu; Grimm, Rudolf; Nägerl, Hanns-Christoph

    2017-02-01

    We demonstrate a generally applicable technique for mixing two-species quantum degenerate bosonic samples in the presence of an optical lattice, and we employ it to produce low-entropy samples of ultracold Rb 87 Cs 133 Feshbach molecules with a lattice filling fraction exceeding 30%. Starting from two spatially separated Bose-Einstein condensates of Rb and Cs atoms, Rb-Cs atom pairs are efficiently produced by using the superfluid-to-Mott insulator quantum phase transition twice, first for the Cs sample, then for the Rb sample, after nulling the Rb-Cs interaction at a Feshbach resonance's zero crossing. We form molecules out of atom pairs and characterize the mixing process in terms of sample overlap and mixing speed. The dense and ultracold sample of more than 5000 RbCs molecules is an ideal starting point for experiments in the context of quantum many-body physics with long-range dipolar interactions.

  18. Dipolar Effects in an Ultracold Gas of LiCs Molecules

    NASA Astrophysics Data System (ADS)

    Weidemueller, Matthias

    2011-05-01

    Recently, there has been important progress in the investigation of ultracold polar molecules in the absolute ground state, thus opening intriguing perspectives for strongly correlated quantum systems under the influence of long-range dipolar forces. We have studied the formation of LiCs molecules via photoassociation (PA) in a double-species magneto-optical trap. The LiCs dimer is a particularly promising candidate for observing dipolar effects, as it possesses the largest dipole moment of all alkali dimers (5.5 Debye in the ground state). Ultracold LiCs molecules in the absolute rovibrational ground state are formed by a single photo-association step. The dipole moment of ground state levels is determined by Stark spectroscopy and was found to be in excellent agreement with the theoretical predictions. Vibrational redistribution due to spontaneous emission and blackbody radiation is observed and compared a rate-equation model.In collaboration with Johannes Deiglmayr, Marc Repp, University of Heidelberg; Roland Wester, University of Innsbruck; and Olivier Dulieu, Laboratoire Aime Cotton. Work was supported by DFG and ESF in the framework of the Eurocores EuroQUAM as well as the Heidelberg Center for Quantum Dynamics.

  19. Photophysics of sunscreen molecules in the gas phase: a stepwise approach towards understanding and developing next-generation sunscreens

    NASA Astrophysics Data System (ADS)

    Rodrigues, Natércia D. N.; Staniforth, Michael; Stavros, Vasilios G.

    2016-11-01

    The relationship between exposure to ultraviolet (UV) radiation and skin cancer urges the need for extra photoprotection, which is presently provided by widespread commercially available sunscreen lotions. Apart from having a large absorption cross section in the UVA and UVB regions of the electromagnetic spectrum, the chemical absorbers in these photoprotective products should also be able to dissipate the excess energy in a safe way, i.e. without releasing photoproducts or inducing any further, harmful, photochemistry. While sunscreens are tested for both their photoprotective capability and dermatological compatibility, phenomena occurring at the molecular level upon absorption of UV radiation are largely overlooked. To date, there is only a limited amount of information regarding the photochemistry and photophysics of these sunscreen molecules. However, a thorough understanding of the intrinsic mechanisms by which popular sunscreen molecular constituents dissipate excess energy has the potential to aid in the design of more efficient, safer sunscreens. In this review, we explore the potential of using gas-phase frequency- and time-resolved spectroscopies in an effort to better understand the photoinduced excited-state dynamics, or photodynamics, of sunscreen molecules. Complementary computational studies are also briefly discussed. Finally, the future outlook of expanding these gas-phase studies into the solution phase is considered.

  20. Photophysics of sunscreen molecules in the gas phase: a stepwise approach towards understanding and developing next-generation sunscreens

    PubMed Central

    Rodrigues, Natércia D. N.; Staniforth, Michael

    2016-01-01

    The relationship between exposure to ultraviolet (UV) radiation and skin cancer urges the need for extra photoprotection, which is presently provided by widespread commercially available sunscreen lotions. Apart from having a large absorption cross section in the UVA and UVB regions of the electromagnetic spectrum, the chemical absorbers in these photoprotective products should also be able to dissipate the excess energy in a safe way, i.e. without releasing photoproducts or inducing any further, harmful, photochemistry. While sunscreens are tested for both their photoprotective capability and dermatological compatibility, phenomena occurring at the molecular level upon absorption of UV radiation are largely overlooked. To date, there is only a limited amount of information regarding the photochemistry and photophysics of these sunscreen molecules. However, a thorough understanding of the intrinsic mechanisms by which popular sunscreen molecular constituents dissipate excess energy has the potential to aid in the design of more efficient, safer sunscreens. In this review, we explore the potential of using gas-phase frequency- and time-resolved spectroscopies in an effort to better understand the photoinduced excited-state dynamics, or photodynamics, of sunscreen molecules. Complementary computational studies are also briefly discussed. Finally, the future outlook of expanding these gas-phase studies into the solution phase is considered. PMID:27956888

  1. Generation, detection and characterization of gas-phase transition metal aggregates and compounds. Final technical report, September 15, 1991--July 14, 1994

    SciTech Connect

    Steimle, T.C.

    1994-11-12

    The goal of this research project has been to identify and characterize small gas-phase metal containing molecules and relate these properties to proposed reaction mechanisms. Of particular emphasis has been the elucidation of the mechanism for activation of C-H, N-H, S-H, and C-C bonds in CH{sub 4}, HCCH, H{sub 2}S and NH{sub 3} by platinum, titanium, molybdenum, and niobium.

  2. Neutralization of solvated protons and formation of noble-gas hydride molecules: Matrix-isolation indications of tunneling mechanisms?

    SciTech Connect

    Khriachtchev, Leonid; Lignell, Antti; Raesaenen, Markku

    2005-08-08

    The (NgHNg){sup +} cations (Ng=Ar and Kr) produced via the photolysis of HF/Ar, HF/Kr, and HBr/Kr solid mixtures are studied, with emphasis on their decay mechanisms. The present experiments provide a large variety of parameters connected to this decay phenomenon, which allows us to reconsider various models for the decay of the (NgHNg){sup +} cations in noble-gas matrices. As a result, we propose that this phenomenon could be explained by the neutralization of the solvated protons by electrons. The mechanism of this neutralization reaction probably involves tunneling of an electron from an electronegative fragment or another trap to the (NgHNg){sup +} cation. The proposed electron-tunneling mechanism should be considered as a possible alternative to the literature models based on tunneling-assisted or radiation-induced diffusion of protons in noble-gas solids. As a novel experimental observation of this work, the efficient formation of HArF molecules occurs at 8 K in a photolyzed HF/Ar matrix. It is probable that the low-temperature formation of HArF involves local tunneling of the H atom to the Ar-F center, which in turn supports the locality of HF photolysis in solid Ar. In this model, the decay of (ArHAr){sup +} ions and the formation of HArF molecules observed at low temperatures are generally unconnected processes; however, the decaying (ArHAr){sup +} ions may contribute to some extent to the formation of HArF molecules.

  3. Turing Patterning Using Gene Circuits with Gas-Induced Degradation of Quorum Sensing Molecules

    PubMed Central

    Hasty, Jeff; Tsimring, Lev

    2016-01-01

    The Turing instability was proposed more than six decades ago as a mechanism leading to spatial patterning, but it has yet to be exploited in a synthetic biology setting. Here we characterize the Turing instability in a specific gene circuit that can be implemented in vitro or in populations of clonal cells producing short-range activator N-Acyl homoserine lactone (AHL) and long-range inhibitor hydrogen peroxide (H2O2) gas. Slowing the production rate of the AHL-degrading enzyme, AiiA, generates stable fixed states, limit cycle oscillations and Turing patterns. Further tuning of signaling parameters determines local robustness and controls the range of unstable wavenumbers in the patterning regime. These findings provide a roadmap for optimizing spatial patterns of gene expression based on familiar quorum and gas sensitive E. coli promoters. The circuit design and predictions may be useful for (re)programming spatial dynamics in synthetic and natural gene expression systems. PMID:27148743

  4. Experimental and Numerical Investigation of Guest Molecule Exchange Kinetics based on the 2012 Ignik Sikumi Gas Hydrate Field Trial

    NASA Astrophysics Data System (ADS)

    Ruprecht Yonkofski, C. M.; Horner, J.; White, M. D.

    2015-12-01

    In 2012 the U.S. DOE/NETL, ConocoPhillips Company, and Japan Oil, Gas and Metals National Corporation jointly sponsored the first field trial of injecting a mixture of N2-CO2 into a CH4-hydrate bearing formation beneath the permafrost on the Alaska North Slope. Known as the Ignik Sikumi #1 Gas Hydrate Field Trial, this experiment involved three stages: 1) the injection of a N2-CO2 mixture into a targeted hydrate-bearing layer, 2) a 4-day pressurized soaking period, and 3) a sustained depressurization and fluid production period. Data collected during the three stages of the field trial were made available after a thorough quality check. The Ignik Sikumi #1 data set is extensive, but contains no direct evidence of the guest-molecule exchange process. This study uses numerical simulation to provide an interpretation of the CH4/CO2/N2 guest molecule exchange process that occurred at Ignik Sikumi #1. Simulations were further informed by experimental observations. The goal of the scoping experiments was to understand kinetic exchange rates and develop parameters for use in Iġnik Sikumi history match simulations. The experimental procedure involves two main stages: 1) the formation of CH4 hydrate in a consolidated sand column at 750 psi and 2°C and 2) flow-through of a 77.5/22.5 N2/CO2 molar ratio gas mixture across the column. Experiments were run both above and below the hydrate stability zone in order to observe exchange behavior across varying conditions. The numerical simulator, STOMP-HYDT-KE, was then used to match experimental results, specifically fitting kinetic behavior. Once this behavior is understood, it can be applied to field scale models based on Ignik Sikumi #1.

  5. Thermochemical Data on Gas-Phase Ion-Molecule Association and Clustering Reactions

    SciTech Connect

    Keesee, R.G.; Castleman, A.W. Jr.

    1986-07-01

    A comprehensive tabulation of the standard enthalpy change, ..delta..H/sup 0/, entropy change, ..delta..S/sup 0/, and free energy change, ..delta..G/sup 0/, for the formation of ion clusters from ion-molecule association reactions is given. The experimental methods which are used to derive the data are briefly discussed. For some experiments, dissociation energies of ion clusters are reported and listed under the category of ..delta..H/sup 0/. The relationship between ..delta..H/sup 0/ and dissociation energy is discussed in the text.

  6. Gas phase chemical kinetics at high temperature of carbonaceous molecules: application to circumstellar envelopes

    NASA Astrophysics Data System (ADS)

    Biennier, L.; Gardez, A.; Saidani, G.; Georges, R.; Rowe, B.; Reddy, K. P. J.

    2011-05-01

    Circumstellar shells of evolved stars are a theater of extremely rich physical and chemical processes. More than seventy molecules of varied nature have been identified in the envelopes through their spectral fingerprints in the microwave or far infrared regions. Many of them are carbon chain molecules and radicals and a significant number are unique to the circumstellar medium. However, observational data remain scarce and more than half of the detected species have been observed in only one object, the nearby carbon star IRC + 10216. Chemical kinetic models are needed to describe the formation of molecules in evolved circumstellar outflows. Upcoming terrestrial telescopes such as ALMA will increase the spatial resolution by several orders of magnitude and provide a wealth of data. The determination of relevant laboratory kinetics data is critical to keep up with the development of the observations and of the refinement of chemical models. Today, the majority of reactions studied in the laboratory are the ones involved in combustion and concerning light hydrocarbons. Our objective is to provide the scientific community with rate coefficients of reactions between abundant species in these warm environments. Cyanopolyynes from HC_2N to HC_9N have all been detected in carbon rich circumstellar envelopes in up to 10 sources for HC_3N. Neutral-neutral reactions of the CN radical with unsaturated hydrocarbons could be a dominant route in the formation of cyanopolyynes, even at low temperatures. Our approach aims to bridge the temperature gap between resistively heated flow tubes and shock tubes. The present kinetic measurements are obtained using a new reactor combining a high enthalpy source (Moudens et al. 2011) with a flow tube and a pulsed laser photolysis and laser induced fluorescence system to probe the undergoing chemical reactions. The high enthalpy flow tube has been used to measure the rate constant of the reaction of the CN radical with propane, propene

  7. THE SINTERING REGION OF ICY DUST AGGREGATES IN A PROTOPLANETARY NEBULA

    SciTech Connect

    Sirono, Sin-iti

    2011-07-10

    Icy grain aggregates are formed in the outer region of a protoplanetary nebula. The infall of these aggregates to the central star is due to gas drag, and their temperature increases as the infall proceeds. The icy molecules on the grain move to the neck where the grains get connected through sublimation and condensation of the molecules. This process is called sintering. As the sintering proceeds, the mechanical strength of the neck changes considerably, strongly affecting the collisional evolution of the aggregates. The timescale required for sintering is determined in this study, based on which the region where the sintering proceeds within a prescribed timescale is obtained. It is found that the region covers a substantial fraction of the protoplanetary nebula, and the location of the region depends on the temperature distribution inside the nebula. If the aggregate is stirred up and the temperature of the aggregate increases temporally, the sintering region spreads to the whole nebula.

  8. Molecular Frame Photoemission: Probe of the Photoionization Dynamics for Molecules in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Dowek, D.; Picard, Y. J.; Billaud, P.; Elkharrat, C.; Houver, J. C.

    2009-04-01

    Molecular frame photoemission is a very sensitive probe of the photoionization (PI) dynamics of molecules. This paper reports a comparative study of non-resonant and resonant photoionization of D2 induced by VUV circularly polarized synchrotron radiation at SOLEIL at the level of the molecular frame photoelectron angular distributions (MFPADs). We use the vector correlation method which combines imaging and time-of-flight resolved electron-ion coincidence techniques, and a generalized formalism for the expression of the I(χ, θe, varphie) MFPADs, where χ is the orientation of the molecular axis with respect to the light quantization axis and (θe, varphie) the electron emission direction in the molecular frame. Selected MFPADs for a molecule aligned parallel or perpendicular to linearly polarized light, or perpendicular to the propagation axis of circularly polarized light, are presented for dissociative photoionization (DPI) of D2 at two photon excitation energies, hν = 19 eV, where direct PI is the only channel opened, and hν = 32.5 eV, i.e. in the region involving resonant excitation of Q1 and Q2 doubly excited state series. We discuss in particular the properties of the circular dichroism characterizing photoemission in the molecular frame for direct and resonant PI. In the latter case, a remarkable behavior is observed which may be attributed to the interference occurring between undistinguishable autoionization decay channels.

  9. Gas Separation Membranes Derived from High-Performance Immiscible Polymer Blends Compatibilized with Small Molecules.

    PubMed

    Panapitiya, Nimanka P; Wijenayake, Sumudu N; Nguyen, Do D; Huang, Yu; Musselman, Inga H; Balkus, Kenneth J; Ferraris, John P

    2015-08-26

    An immiscible polymer blend comprised of high-performance copolyimide 6FDA-DAM:DABA(3:2) (6FDD) and polybenzimidazole (PBI) was compatibilized using 2-methylimidazole (2-MI), a commercially available small molecule. Membranes were fabricated from blends of 6FDD:PBI (50:50) with and without 2-MI for H2/CO2 separations. The membranes demonstrated a matrix-droplet type microstructure as evident with scanning electron microscopy (SEM) imaging where 6FDD is the dispersed phase and PBI is the continuous phase. In addition, membranes with 2-MI demonstrated a uniform microstructure as observed by smaller and more uniformly dispersed 6FDD domains in contrast to 6FDD:PBI (50:50) blend membranes without 2-MI. This compatibilization effect of 2-MI was attributed to interfacial localization of 2-MI that lowers the interfacial energy similar to a surfactant. Upon the incorporation of 2-MI, the H2/CO2 selectivity improved remarkably, compared to the pure blend, and surpassed the Robeson's upper bound. To our knowledge, this is the first report of the use of a small molecule to compatibilize a high-performance immiscible polymer blend. This approach could afford a novel class of membranes in which immiscible polymer blends can be compatibilized in an economical and convenient fashion.

  10. Interactions of molecules with HCl in the gas and matrix phases

    NASA Astrophysics Data System (ADS)

    George, W. O.; Lewis, Rh.; Hussain, G.; Rees, G. J.

    1988-10-01

    The FT-IR spectra of mixtures of HCl and the following compounds have been recorded in the gaseous and matrix isolated phases: argon, ethene, ethyne, d 6-benzene, fluorobenzene, CO, CO 2, SO 2, CCl 4, CHCl 3, d 6-acetone, ethanal, HCN, acrylonitrile. The features which are measured are: firstly the changes in the integrated intensity of lines in the rotation—vibration spectrum of the fundamental HCl band as a function of non-specific interactions with other components of the mixture and secondly bands associated with specific interactions forming hydrogen bonded complexes in the gas and matrix isolated phases. The relationship between the two kinds of interactions is discussed.

  11. An index of the literature for bimolecular gas phase cation-molecule reaction kinetics

    NASA Technical Reports Server (NTRS)

    Anicich, V. G.

    2003-01-01

    This is an index to the literature for gas phase bimolecular positive ionmolecule reactions. Over 2300 references are cited. Reaction rate coefficients and product distributions of the reactions are abstracted out of the original citations where available. This index is intended to cover the literature from 1936 to 2003. This is a continuation of several surveys: the original (Huntress Astrophys. J. Suppl. Ser., 33, 495 (1977)), an expansion (Anicich and Huntress, Astrophys. J. Suppl. Ser. 62, 553 (1986)), a supplement (Anicich, Astrophys. J. Suppl. Ser. 84, 215 (1993)), and an evaluation (Anicich, V. G. J. Phys. Chem. Ref. Data 22,1469 (1993b). The Table of reactions is listed by reactant ion.

  12. An index of the literature for bimolecular gas phase cation-molecule reaction kinetics

    NASA Technical Reports Server (NTRS)

    Anicich, V. G.

    2003-01-01

    This is an index to the literature for gas phase bimolecular positive ionmolecule reactions. Over 2300 references are cited. Reaction rate coefficients and product distributions of the reactions are abstracted out of the original citations where available. This index is intended to cover the literature from 1936 to 2003. This is a continuation of several surveys: the original (Huntress Astrophys. J. Suppl. Ser., 33, 495 (1977)), an expansion (Anicich and Huntress, Astrophys. J. Suppl. Ser. 62, 553 (1986)), a supplement (Anicich, Astrophys. J. Suppl. Ser. 84, 215 (1993)), and an evaluation (Anicich, V. G. J. Phys. Chem. Ref. Data 22,1469 (1993b). The Table of reactions is listed by reactant ion.

  13. Dispersion and functionalization of nanoparticles synthesized by gas aggregation source: Opening new routes towards the fabrication of nanoparticles for bio-medicine

    PubMed Central

    Oprea, B.; Martínez, L.; Román, E.; Vanea, E.; Simon, S.; Huttel, Y.

    2015-01-01

    The need to find new nanoparticles for biomedical applications is pushing the limits of the fabrication methods. New techniques with versatilities beyond the extended chemical routes can provide new insight in the field. In particular gas aggregation sources offer the possibility to fabricate nanoparticles with controlled size, composition and structure out of thermodynamics. In this context, the milestone is the optimization of the dispersion and functionalization processes of nanoparticles once fabricated by these routes as they are generated in the gas phase and deposited on substrates in vacuum or ultra-high vacuum conditions. In the present work we propose a fabrication route in ultra-high vacuum that is compatible with the subsequent dispersion and functionalization of nanoparticles in aqueous media and, that is more remarkable, in one single step. In particular, we will present the fabrication of nanoparticles with a sputter gas aggregation source, using a Fe50B50 target, and their further dispersion and functionalization with polyethileneglycol (PEG). A characterization of these nanoparticles is carried out before and after PEG functionalization. During functionalization, significant boron dissolution occurs, which facilitates nanoparticle dispersion in the aqueous solution. The use of different complementary techniques allows us to prove the PEG attachment onto the surface of the nanoparticles creating a shell to make them biocompatible. The result is the formation of nanoparticles with a structure mainly composed by a metallic Fe core and an iron oxide shell, surrounded by a second PEG shell dispersed in aqueous solution. Relaxivitiy measurements of these PEG functionalized nanoparticles assessed their effectiveness as contrast agents for Magnetic Resonance Imaging (MRI) analysis. Therefore, this new fabrication route is a reliable alternative for the synthesis of nanoparticles for biomedicine. PMID:26640032

  14. Femtosecond x-ray photoelectron diffraction on gas-phase dibromobenzene molecules

    NASA Astrophysics Data System (ADS)

    Rolles, D.; Boll, R.; Adolph, M.; Aquila, A.; Bostedt, C.; Bozek, J. D.; Chapman, H. N.; Coffee, R.; Coppola, N.; Decleva, P.; Delmas, T.; Epp, S. W.; Erk, B.; Filsinger, F.; Foucar, L.; Gumprecht, L.; Hömke, A.; Gorkhover, T.; Holmegaard, L.; Johnsson, P.; Kaiser, Ch; Krasniqi, F.; Kühnel, K.-U.; Maurer, J.; Messerschmidt, M.; Moshammer, R.; Quevedo, W.; Rajkovic, I.; Rouzée, A.; Rudek, B.; Schlichting, I.; Schmidt, C.; Schorb, S.; Schröter, C. D.; Schulz, J.; Stapelfeldt, H.; Stener, M.; Stern, S.; Techert, S.; Thøgersen, J.; Vrakking, M. J. J.; Rudenko, A.; Küpper, J.; Ullrich, J.

    2014-06-01

    We present time-resolved femtosecond photoelectron momentum images and angular distributions of dissociating, laser-aligned 1,4-dibromobenzene (C6H4Br2) molecules measured in a near-infrared pump, soft-x-ray probe experiment performed at an x-ray free-electron laser. The observed alignment dependence of the bromine 2p photoelectron angular distributions is compared to density functional theory calculations and interpreted in terms of photoelectron diffraction. While no clear time-dependent effects are observed in the angular distribution of the Br(2p) photoelectrons, other, low-energy electrons show a pronounced dependence on the time delay between the near-infrared laser and the x-ray pulse.

  15. Molecular structure and the EPR calculation of the gas phase succinonitrile molecule

    NASA Astrophysics Data System (ADS)

    Kepceoǧlu, A.; Kılıç, H. Ş.; Dereli, Ö.

    2017-02-01

    Succinonitrile (i.e. butanedinitrile) is a colorless nitrile compound that can be used in the gel polymer batteries as a solid-state solvent electrolytes and has a plastic crystal structure. Prior to the molecular structure calculation of the succinonitrile molecule, the conformer analysis were calculated by using semi empirical method PM3 core type Hamiltonian and eight different conformer structures were determined. Molecular structure with energy related properties of these conformers having the lowest energy was calculated by using DFT (B3LYP) methods with 6-311++G(d,p) basis set. Possible radicals, can be formed experimentally, were modeled in this study. EPR parameters of these model radicals were calculated and then compared with that obtained experimentally.

  16. Gas-phase Reactions of Polycyclic Aromatic Hydrocarbon Anions with Molecules of Interstellar Relevance

    NASA Astrophysics Data System (ADS)

    Demarais, Nicholas J.; Yang, Zhibo; Martinez, Oscar; Wehres, Nadine; Snow, Theodore P.; Bierbaum, Veronica M.

    2012-02-01

    We have studied reactions of small dehydrogenated polycyclic aromatic hydrocarbon anions with neutral species of interstellar relevance. Reaction rate constants are measured at 300 K for the reactions of phenide (C6H- 5), naphthalenide (C10H- 7), and anthracenide (C14H- 9) with atomic H, H2, and D2 using a flowing afterglow-selected ion flow tube instrument. Reaction rate constants of phenide with neutral molecules (CO, O2, CO2, N2O, C2H2, CH3OH, CH3CN, (CH3)2CO, CH3CHO, CH3Cl, and (CH3CH2)2O) are also measured under the same conditions. Experimental measurements are accompanied by ab initio calculations to provide insight into reaction pathways and enthalpies. Our measured reaction rate constants should prove useful in the modeling of astrophysical environments, particularly when applied to dense regions of the interstellar and circumstellar medium.

  17. Post-translational modification in the gas phase: mechanism of cysteine S-nitrosylation via ion-molecule reactions

    PubMed Central

    Osburn, Sandra; O'Hair, Richard A.J.; Black, Stephen M.; Ryzhov, Victor

    2013-01-01

    The gas-phase mechanism of S-nitrosylation of thiols was studied in a quadrupole ion trap mass spectrometer. This was done via ion-molecule reactions of protonated cysteine and many of its derivatives and other thiol ions with neutral tert-butyl nitrite or nitrous acid. Our results showed that the presence of the carboxylic acid functional group, –COOH, in the vicinity of the thiol group is essential for the gas-phase nitrosylation of thiols. When the carboxyl proton is replaced by a methyl group (cysteine methyl ester) no nitrosylation was observed. Other thiols lacking a carboxylic acid functional group displayed no S-nitrosylation, strongly suggesting that the carboxyl hydrogen plays a key role in the nitrosylation process. These results are in excellent agreement with a solution-phase mechanism proposed by Stamler et al. (J. S. Stamler, E. J. Toone, S. A. Lipton, N. J. Sucher. Neuron 1997, 18, 691–696) who suggested a catalytic role for the carboxylic acid group adjacent to cysteine residues and with later additions by Ascenzi et al. (P. Ascenzi, M. Colasanti, T. Persichini, M. Muolo, F. Polticelli, G. Venturini, D. Bordo, M. Bolognesi. Biol. Chem. 2000, 381, 623–627) who postulated that the presence of the carboxyl in the cysteine microenvironment in proteins is crucial for S-nitrosylation. A concerted mechanism for the gas-phase S-nitrosylation was proposed based on our results and was further studied using theoretical calculations. Our calculations showed that this proposed pathway is exothermic by 44.0 kJ mol−1. This is one of the few recent examples when a gas-phase mechanism matches one in solution. PMID:22006383

  18. Normal Auger spectra of iodine in gas phase alkali iodide molecules

    NASA Astrophysics Data System (ADS)

    Hu, Zhengfa; Caló, Antonio; Kukk, Edwin; Aksela, Helena; Aksela, Seppo

    2005-06-01

    Molecular normal Auger electron spectra following the iodine 4d ionization in gas-phase alkali iodides were investigated both experimentally and theoretically. The Auger electron spectra for LiI, NaI and KI were recorded using electron impact, and for RbI by using photo-excitation. These Auger spectra were analyzed in detail and compared to the referenced normal Auger spectra of HI [L. Karlsson, S. Svensson, P. Baltzer, M. Carlsson-Göthe, M.P. Keane, A. Naves de Brito, N. Correia, B. Wannberg, J. Phys. B 22 (1989) 3001]. An energy shift toward higher kinetic energy and a narrowing in linewidth are observed in the Auger spectra series revealing the effect of the changing environment from covalently bonded HI to ionic alkali iodide compounds. The experimental results are also compared with the theoretical ab initio calculations and with the Auger spectra of I -, computed with the multiconfiguration Hartree-Fock (MCHF) method.

  19. Nuclear dynamics and spectator effects in resonant inelastic soft x-ray scattering of gas-phase water molecules

    SciTech Connect

    Weinhardt, Lothar; Benkert, Andreas; Meyer, Frank; Blum, Monika; Wilks, Regan G.; Yang, Wanli; Baer, Marcus; Reinert, Friedrich; and others

    2012-04-14

    The electronic structure of gas-phase H{sub 2}O and D{sub 2}O molecules has been investigated using resonant inelastic soft x-ray scattering (RIXS). We observe spectator shifts for all valence orbitals when exciting into the lowest three absorption resonances. Strong changes of the relative valence orbital emission intensities are found when exciting into the different absorption resonances, which can be related to the angular anisotropy of the RIXS process. Furthermore, excitation into the 4a{sub 1} resonance leads to nuclear dynamics on the time scale of the RIXS process; we find evidence for vibrational coupling and molecular dissociation in both, the spectator and the participant emission.

  20. Far-infrared permanent and induced dipole absorption of diatomic molecules in rare-gas fluids. I. Spectral theory

    NASA Astrophysics Data System (ADS)

    Roco, J. M. M.; Hernández, A. Calvo; Velasco, S.

    1995-12-01

    We present a spectral theory for the far-infrared absorption spectrum of a very diluted solution of diatomic molecules in a rare-gas fluid, that includes permanent and induced contributions. The absorption coefficient is given as the convolution of a translational spectrum and a rotational spectrum. The former is described in terms of time correlation functions associated to the induced dipole moment. The latter is discussed on the basis of a model consisting of a quantum rigid rotor interacting with a thermal bath, making use of time correlation functions associated to the different anisotropic orders of the solute-solvent intermolecular potential. Non-Markovian and line mixing effects are taken into account. Explicit expressions for the five leading contributions of the induced dipole moment are given.

  1. Dissociation degree of nitrogen molecule in low-pressure microwave-discharge nitrogen plasma with various rare-gas admixtures

    NASA Astrophysics Data System (ADS)

    Kuwano, Kei; Nezu, Atsushi; Matsuura, Haruaki; Akatsuka, Hiroshi

    2016-08-01

    The dissociation degree of nitrogen molecules is examined in a microwave discharge nitrogen-rare gas mixture plasma with a total discharge pressure of 1 Torr, by actinometry measurement. Although the spectral line from the excited nitrogen atoms is overlapped by the band spectrum of the N2 first positive system (1PS), the subtraction of the 1PS spectrum fitted theoretically can successfully extract the atomic nitrogen line, which enables actinometry measurement. The nitrogen dissociation degree decreases with increasing mixture ratio of Ar to Kr, whereas it increases with He, which is attributed to the variations in the electron temperature and density. When we dilute the nitrogen with neon, however, we find an anomalous increase in the nitrogen dissociation degree by several orders of magnitude even at a downstream region in the discharge tube. The reason for the dissociation enhancement upon adding neon is discussed in terms of atomic and molecular processes in the plasma.

  2. In-situ Evaluation of Soil Organic Molecules: Functional Group Chemistry Aggregate Structures, Metal & Surface Complexation Using Soft X-Ray

    SciTech Connect

    Myneni, Satish, C

    2008-11-30

    Organic molecules are common in all Earth surface environments, and their composition and chemistry play an important role in a variety of biogeochemical reactions, such as mineral weathering, nutrient cycling and the solubility and transport of contaminants. However, most of what we know about the chemistry of these molecules comes from spectroscopy and microscopy studies of organic molecules extracted from different natural systems using either inorganic or organic solvents. Although all these methods gave us clues about the composition of these molecules, their composition and structure change with the extraction and the type of ex-situ analysis, their true behavior is less well understood. The goal of this project is to develop synchrotron instrumentation for studying natural organics, and to apply these recently developed synchrotron X-ray spectroscopy and microscopy techniques for understanding the: (1) functional group composition of naturally occurring organic molecules; (2) macromolecular structures of organic molecules; and (3) the nature of interactions of organic molecules with mineral surfaces in different environmental conditions.

  3. Use of inverse gas chromatography to characterize cotton fabrics and their interactions with fragrance molecules at controlled relative humidity.

    PubMed

    Cantergiani, Ennio; Benczédi, Daniel

    2002-09-06

    The present work focused on the surface characterization and fragrance interactions of a common cotton towel at different relative humidities (RHs) using inverse gas chromatography (IGC) and dynamic vapour sorption. The sigmoidal water sorption isotherms showed a maximum of 16% (w/w) water uptake with limited swelling at 100% RH. This means that water interacts strongly with cotton and might change its initial physico-chemical properties. The same cotton towel was then packed in a glass column and characterized by IGC at different relative humidities, calculating the dispersive and specific surface energy components. The dispersive component of the surface energy decreases slightly as a function of relative humidity (42 mJ/m2 at 0% RH to 36 mJ/m2 at 80% RH) which would be expected from swelling of the humidified cotton. The Gutmann's donor constant Kd increased from 0.28 kJ/mol at 0% RH to 0.42 kJ/mol at 80% RH, indicating that a greater hydrophilic surface exists at 80% RH, which is also as expected. Water, undecane and four fragrance molecules (dimetol, benzyl acetate, decanal and phenylethanol) were used to investigate cotton-fragrance interactions between 0 and 80% RH. The adsorption enthalpies and the Henry's constants were calculated and are discussed. The higher values for the adsorption enthalpies of polar molecules such as dimetol and phenylethanol suggest the presence of hydrogen bonds as the main adsorption mechanism. The Henry's constant of dimetol was also determined by headspace gas chromatography measurements at 20% RH, giving a similar value (230 nmol/Pa g by IGC and 130 nmol/Pa g by headspace GC), supporting the usefulness of IGC for such determinations. This work confirms the usefulness of chromatographic methods to investigate biopolymers such as textiles, starches and hairs.

  4. Fabrication of zeolitic imidazolate framework-8-methacrylate monolith composite capillary columns for fast gas chromatographic separation of small molecules.

    PubMed

    Yusuf, Kareem; Badjah-Hadj-Ahmed, Ahmed Yacine; Aqel, Ahmad; ALOthman, Zeid Abdullah

    2015-08-07

    A composite zeolitic imidazolate framework-8 (ZIF-8) with a butyl methacrylate-co-ethylene dimethacrylate (BuMA-co-EDMA) monolithic capillary column (33.5cm long×250μm i.d.) was fabricated to enhance the separation efficiency of methacrylate monoliths toward small molecules using conventional low-pressure gas chromatography in comparison with a neat butyl methacrylate-co-ethylene dimethacrylate (BuMA-co-EDMA) monolithic capillary column (33.5cm long×250μm i.d.). The addition of 10mgmL(-1) ZIF-8 micro-particles increased the BET surface area of BuMA-co-EDMA by 3.4-fold. A fast separation of five linear alkanes in 36s with high resolution (Rs≥1.3) was performed using temperature program. Isothermal separation of the same sample also showed a high efficiency (3315platesm(-1) for octane) at 0.89min. Moreover, the column was able to separate skeletal isomers, such as iso-octane/octane and 2-methyl octane/nonane. In addition, an iso-butane/iso-butylene gas mixture was separated at ambient temperature. Comparison with an open tubular TR-5MS column (30m long×250μm i.d.) revealed the superiority of the composite column in separating the five-membered linear alkane mixture with 4-5 times increase in efficiency and a total separation time of 0.89min instead of 4.67min. A paint thinner sample was fully separated using the composite column in 2.43min with a good resolution (Rs≥0.89). The perfect combination between the polymeric monolith, with its high permeability, and ZIF-8, with its high surface area and flexible 0.34nm pore openings, led to the fast separation of small molecules with high efficiency and opened a new horizon in GC applications.

  5. Gas phase ion/molecule reactions in phosphine/germane mixtures studied by ion trapping

    NASA Astrophysics Data System (ADS)

    Benzi, P.; Operti, L.; Rabezzana, R.; Splendore, M.; Volpe, P.

    1996-01-01

    Gaseous mixtures of phosphine and germane have been investigated by ion trap mass spectrometry. Reaction pathways together with rate constants of the main reactions are reported. The mechanisms of ion/molecule reactions have been elucidated by single and multiple isolation steps. The GeHn+ (n = 1-3) ions react with phosphine to give GePHn+ (n = 2-4) ions. The GePH4+ ion further reacts with GeH4 to yield Ge2PH6+. The GePHn+ (n = 2-4) mixed ionic family also originates from the P+ phosphine primary ion, as well as from the P2Hn+ (n = 0-3) secondary ions of phosphine reacting with neutral germane and from Ge2H2+ reacting with phosphine. The main reaction pathways of the PHn+ (n = 0-2) ions with GeH4 lead to the formation of the GeH2+ and GeH3+ ionic species. Protonation of phosphine from different ionic precursors is a very common process and yields the stable phosphonium ion, PH4+. Trends in total abundances of secondary GePHn+ (n = 2-4) ions as function of reaction time for different PH3/GeH4 pressure ratios show that excess of germane slightly affects the nucleation of mixed Ge-P ions.

  6. GAS-PHASE REACTIONS OF POLYCYCLIC AROMATIC HYDROCARBON ANIONS WITH MOLECULES OF INTERSTELLAR RELEVANCE

    SciTech Connect

    Demarais, Nicholas J.; Yang Zhibo; Martinez, Oscar; Wehres, Nadine; Bierbaum, Veronica M.; Snow, Theodore P. E-mail: Zhibo.Yang@Colorado.edu E-mail: Nadine.Wehres@Colorado.edu E-mail: Theodore.Snow@Colorado.edu

    2012-02-10

    We have studied reactions of small dehydrogenated polycyclic aromatic hydrocarbon anions with neutral species of interstellar relevance. Reaction rate constants are measured at 300 K for the reactions of phenide (C{sub 6}H{sup -}{sub 5}), naphthalenide (C{sub 10}H{sup -}{sub 7}), and anthracenide (C{sub 14}H{sup -}{sub 9}) with atomic H, H{sub 2}, and D{sub 2} using a flowing afterglow-selected ion flow tube instrument. Reaction rate constants of phenide with neutral molecules (CO, O{sub 2}, CO{sub 2}, N{sub 2}O, C{sub 2}H{sub 2}, CH{sub 3}OH, CH{sub 3}CN, (CH{sub 3}){sub 2}CO, CH{sub 3}CHO, CH{sub 3}Cl, and (CH{sub 3}CH{sub 2}){sub 2}O) are also measured under the same conditions. Experimental measurements are accompanied by ab initio calculations to provide insight into reaction pathways and enthalpies. Our measured reaction rate constants should prove useful in the modeling of astrophysical environments, particularly when applied to dense regions of the interstellar and circumstellar medium.

  7. Electronegativity effects and single covalent bond lengths of molecules in the gas phase.

    PubMed

    Lang, Peter F; Smith, Barry C

    2014-06-07

    This paper discusses in detail the calculation of internuclear distances of heteronuclear single bond covalent molecules in the gaseous state. It reviews briefly the effect of electronegativity in covalent bond length. A set of single bond covalent radii and electronegativity values are proposed. Covalent bond lengths calculated by an adapted form of a simple expression (which calculated internuclear separation of different Group 1 and Group 2 crystalline salts to a remarkable degree of accuracy) show very good agreement with observed values. A small number of bond lengths with double bonds as well as bond lengths in the crystalline state are calculated using the same expression and when compared with observed values also give good agreement. This work shows that covalent radii are not additive and that radii in the crystalline state are different from those in the gaseous state. The results also show that electronegativity is a major influence on covalent bond lengths and the set of electronegativity scale and covalent radii proposed in this work can be used to calculate covalent bond lengths in different environments that have not yet been experimentally measured.

  8. On the effect of spatial aggregation of source regions on the stability of greenhouse gas emission estimates calculated by an inverse Lagrangian box model

    NASA Astrophysics Data System (ADS)

    Pieterse, G.; Vermeulen, A.

    2005-12-01

    Estimation of emission rates from atmospheric concentration observations has proven to remain a big challenge. In this paper, a new approach is chosen for the source strength estimation algorithm based on Source Receptor Matrices (SRM's) as derived for the COMET trajectory model for methane (Vermeulen et al., 2001). In the new approach, source regions are identified automatically by calculation of the Potential Source Region Contribution (PSRC) to measurements performed at multiple sites and spatial aggregation of these regions to achieve uniform PSRC in the aggregated Source-Receptor Matrix (aSRM). The emission strengths are then estimated using Singular Value Decomposition (SVD) of the aSRM. The SVD procedure also yields a Covariance Matrix (CM), which describes the statistical accuracies and mutual dependencies of the solutions. A recursive algorithm is implemented to further accumulate source regions in order to improve covariance and accuracy for the source strength estimates. The aSRM of Europe was constructed using the influence functions for the year 2002 for the locations of the CHIOTTO Tall Tower sites. Measurement data was not available for all sites. The results indicate that the new approach will enable accurate and stable methane budget calculations for the monitored region. As expected, the spatial distribution of the aggregated source regions will not be uniform, because the individual sources are not represented uniformly in the measured signals. Currently, the method is also evaluated for estimation of other greenhouse gas budgets of Europe, like CO2, SF6 and N2O. In principle, the aSRM method can be applied to SRM's of any transport model and component, provided that the forward performance of the model is adequate and that matching observations exist.

  9. Evaluation of Chemical Interactions between Small Molecules in the Gas Phase Using Chemical Force Microscopy.

    PubMed

    Lee, Jieun; Ju, Soomi; Kim, In Tae; Jung, Sun-Hwa; Min, Sun-Joon; Kim, Chulki; Sim, Sang Jun; Kim, Sang Kyung

    2015-12-04

    Chemical force microscopy analyzes the interactions between various chemical/biochemical moieties in situ. In this work we examined force-distance curves and lateral force to measure the interaction between modified AFM tips and differently functionalized molecular monolayers. Especially for the measurements in gas phase, we investigated the effect of humidity on the analysis of force-distance curves and the images in lateral force mode. Flat chemical patterns composed of different functional groups were made through micro-contact printing and lateral force mode provided more resolved analysis of the chemical patterns. From the images of 1-octadecanethiol/11-mercapto-1-undecanoic acid patterns, the amine group functionalized tip brought out higher contrast of the patterns than an intact silicon nitride tip owing to the additional chemical interaction between carboxyl and amine groups. For more complex chemical interactions, relative chemical affinities toward specific peptides were assessed on the pattern of 1-octadecanethiol/phenyl-terminated alkanethiol. The lateral image of chemical force microscopy reflected specific preference of a peptide to phenyl group as well as the hydrophobic interaction.

  10. Evaluation of Chemical Interactions between Small Molecules in the Gas Phase Using Chemical Force Microscopy

    PubMed Central

    Lee, Jieun; Ju, Soomi; Kim, In Tae; Jung, Sun-Hwa; Min, Sun-Joon; Kim, Chulki; Sim, Sang Jun; Kim, Sang Kyung

    2015-01-01

    Chemical force microscopy analyzes the interactions between various chemical/biochemical moieties in situ. In this work we examined force-distance curves and lateral force to measure the interaction between modified AFM tips and differently functionalized molecular monolayers. Especially for the measurements in gas phase, we investigated the effect of humidity on the analysis of force-distance curves and the images in lateral force mode. Flat chemical patterns composed of different functional groups were made through micro-contact printing and lateral force mode provided more resolved analysis of the chemical patterns. From the images of 1-octadecanethiol/11-mercapto-1-undecanoic acid patterns, the amine group functionalized tip brought out higher contrast of the patterns than an intact silicon nitride tip owing to the additional chemical interaction between carboxyl and amine groups. For more complex chemical interactions, relative chemical affinities toward specific peptides were assessed on the pattern of 1-octadecanethiol/phenyl-terminated alkanethiol. The lateral image of chemical force microscopy reflected specific preference of a peptide to phenyl group as well as the hydrophobic interaction. PMID:26690165

  11. Interaction energy and itinerant ferromagnetism in a strongly interacting Fermi gas in the absence of molecule formation

    SciTech Connect

    He, Lianyi

    2014-11-26

    In this study, we investigate the interaction energy and the possibility of itinerant ferromagnetism in a strongly interacting Fermi gas at zero temperature in the absence of molecule formation. The interaction energy is obtained by summing the perturbative contributions of Galitskii-Feynman type to all orders in the gas parameter. It can be expressed by a simple phase-space integral of an in-medium scattering phase shift. In both three and two dimensions (3D and 2D), the interaction energy shows a maximum before reaching the resonance from the Bose-Einstein condensate side, which provides a possible explanation of the experimental measurements of the interaction energy. This phenomenon can be theoretically explained by the qualitative change of the nature of the binary interaction in the medium. The appearance of an energy maximum has significant effects on the itinerant ferromagnetism. In 3D, the ferromagnetic transition is reentrant and itinerant ferromagnetism exists in a narrow window around the energy maximum. In 2D, the present theoretical approach suggests that itinerant ferromagnetism does not exist, which reflects the fact that the energy maximum becomes much lower than the energy of the fully polarized state.

  12. Interaction energy and itinerant ferromagnetism in a strongly interacting Fermi gas in the absence of molecule formation

    DOE PAGES

    He, Lianyi

    2014-11-26

    In this study, we investigate the interaction energy and the possibility of itinerant ferromagnetism in a strongly interacting Fermi gas at zero temperature in the absence of molecule formation. The interaction energy is obtained by summing the perturbative contributions of Galitskii-Feynman type to all orders in the gas parameter. It can be expressed by a simple phase-space integral of an in-medium scattering phase shift. In both three and two dimensions (3D and 2D), the interaction energy shows a maximum before reaching the resonance from the Bose-Einstein condensate side, which provides a possible explanation of the experimental measurements of the interactionmore » energy. This phenomenon can be theoretically explained by the qualitative change of the nature of the binary interaction in the medium. The appearance of an energy maximum has significant effects on the itinerant ferromagnetism. In 3D, the ferromagnetic transition is reentrant and itinerant ferromagnetism exists in a narrow window around the energy maximum. In 2D, the present theoretical approach suggests that itinerant ferromagnetism does not exist, which reflects the fact that the energy maximum becomes much lower than the energy of the fully polarized state.« less

  13. Absorption into fluorescence. A method to sense biologically relevant gas molecules

    NASA Astrophysics Data System (ADS)

    Strianese, Maria; Varriale, Antonio; Staiano, Maria; Pellecchia, Claudio; D'Auria, Sabato

    2011-01-01

    In this work we present an innovative optical sensing methodology based on the use of biomolecules as molecular gating nano-systems. Here, as an example, we report on the detection ofanalytes related to climate change. In particular, we focused our attention on the detection ofnitric oxide (NO) and oxygen (O2). Our methodology builds on the possibility of modulating the excitation intensity of a fluorescent probe used as a transducer and a sensor molecule whose absorption is strongly affected by the binding of an analyte of interest used as a filter. The two simple conditions that have to be fulfilled for the method to work are: (a) the absorption spectrum of the sensor placed inside the cuvette, and acting as the recognition element for the analyte of interest, should strongly change upon the binding of the analyte and (b) the fluorescence dye transducer should exhibit an excitation band which overlaps with one or more absorption bands of the sensor. The absorption band of the sensor affected by the binding of the specific analyte should overlap with the excitation band of the transducer. The high sensitivity of fluorescence detection combined with the use of proteins as highly selective sensors makes this method a powerful basis for the development of a new generation of analytical assays. Proof-of-principle results showing that cytochrome c peroxidase (CcP) for NO detection and myoglobin (Mb) for O2 detection can be successfully used by exploiting our new methodology are reported. The proposed technology can be easily expanded to the determination of different target analytes.

  14. Absorption into fluorescence. A method to sense biologically relevant gas molecules.

    PubMed

    Strianese, Maria; Varriale, Antonio; Staiano, Maria; Pellecchia, Claudio; D'Auria, Sabato

    2011-01-01

    In this work we present an innovative optical sensing methodology based on the use of biomolecules as molecular gating nano-systems. Here, as an example, we report on the detection of analytes related to climate change. In particular, we focused our attention on the detection of nitric oxide (NO) and oxygen (O2). Our methodology builds on the possibility of modulating the excitation intensity of a fluorescent probe used as a transducer and a sensor molecule whose absorption is strongly affected by the binding of an analyte of interest used as a filter. The two simple conditions that have to be fulfilled for the method to work are: (a) the absorption spectrum of the sensor placed inside the cuvette, and acting as the recognition element for the analyte of interest, should strongly change upon the binding of the analyte and (b) the fluorescence dye transducer should exhibit an excitation band which overlaps with one or more absorption bands of the sensor. The absorption band of the sensor affected by the binding of the specific analyte should overlap with the excitation band of the transducer. The high sensitivity of fluorescence detection combined with the use of proteins as highly selective sensors makes this method a powerful basis for the development of a new generation of analytical assays. Proof-of-principle results showing that cytochrome c peroxidase (CcP) for NO detection and myoglobin (Mb) for O2 detection can be successfully used by exploiting our new methodology are reported. The proposed technology can be easily expanded to the determination of different target analytes.

  15. Charged Dust Aggregate Interactions

    NASA Astrophysics Data System (ADS)

    Matthews, Lorin; Hyde, Truell

    2015-11-01

    A proper understanding of the behavior of dust particle aggregates immersed in a complex plasma first requires a knowledge of the basic properties of the system. Among the most important of these are the net electrostatic charge and higher multipole moments on the dust aggregate as well as the manner in which the aggregate interacts with the local electrostatic fields. The formation of elongated, fractal-like aggregates levitating in the sheath electric field of a weakly ionized RF generated plasma discharge has recently been observed experimentally. The resulting data has shown that as aggregates approach one another, they can both accelerate and rotate. At equilibrium, aggregates are observed to levitate with regular spacing, rotating about their long axis aligned parallel to the sheath electric field. Since gas drag tends to slow any such rotation, energy must be constantly fed into the system in order to sustain it. A numerical model designed to analyze this motion provides both the electrostatic charge and higher multipole moments of the aggregate while including the forces due to thermophoresis, neutral gas drag, and the ion wakefield. This model will be used to investigate the ambient conditions leading to the observed interactions. This research is funded by NSF Grant 1414523.

  16. Molecular aggregation of humic substances

    USGS Publications Warehouse

    Wershaw, R. L.

    1999-01-01

    Humic substances (HS) form molecular aggregates in solution and on mineral surfaces. Elucidation of the mechanism of formation of these aggregates is important for an understanding of the interactions of HS in soils arid natural waters. The HS are formed mainly by enzymatic depolymerization and oxidation of plant biopolymers. These reactions transform the aromatic and lipid plant components into amphiphilic molecules, that is, molecules that consist of separate hydrophobic (nonpolar) and hydrophilic (polar) parts. The nonpolar parts of the molecules are composed of relatively unaltered segments of plant polymers and the polar parts of carboxylic acid groups. These amphiphiles form membrane-like aggregates on mineral surfaces and micelle-like aggregates in solution. The exterior surfaces of these aggregates are hydrophilic, and the interiors constitute separate hydrophobic liquid-like phases.

  17. Peptide bond formation in gas-phase ion/molecule reactions of amino acids: a novel proposal for the synthesis of prebiotic oligopeptides.

    PubMed

    Wincel, H; Fokkens, R H; Nibbering, N M

    2000-01-01

    There is a general fascination with regard to the origin of life on Earth. There is an intriguing possibility that prebiotic precursors of life occurred in the interstellar space and were then transported to the early Earth by comets, asteroids and meteorites. It is probable that some part of the prebiotic molecules may have been generated by gas-phase ion/molecule reactions. Here we show experimentally that gaseous ion/molecule reactions of the amino acids, Glu and Met, may promote the synthesis of protonated dipeptides such as (Glu-Glu)H(+) and (Glu-Met)H(+) and their chemical growth to larger protonated peptides. Copyright 2000 John Wiley & Sons, Ltd.

  18. Four molecules of the 33 kDa haemagglutinin component of the Clostridium botulinum serotype C and D toxin complexes are required to aggregate erythrocytes.

    PubMed

    Mutoh, Shingo; Suzuki, Tomonori; Hasegawa, Kimiko; Nakazawa, Yozo; Kouguchi, Hirokazu; Sagane, Yoshimasa; Niwa, Koichi; Watanabe, Toshihiro; Ohyama, Tohru

    2005-12-01

    Normally, large-sized botulinum toxin complexes (L-TC) of serotype C and D are composed of a single neurotoxin, a single non-toxic non-haemagglutinin, two HA-70 molecules, four HA-33 molecules and four HA-17 molecules that assemble to form a 650 kDa L-TC. The 540 and 610 kDa TC species (designated here as L-TC2 and L-TC3, respectively) were purified in addition to the 650 kDa L-TC from the culture supernatants of serotype D strains (D-4947 and D-CB16) and serotype C strains (C-6814 and C-Yoichi). The 650 kDa L-TC from D-4947, D-CB16 and C-6814 showed haemagglutination and erythrocyte-binding activity, but their L-TC2 and L-TC3 species had only binding activity. In contrast, every TC species from C-Yoichi having the C-terminally truncated variant of HA-33 exhibited neither haemagglutination activity nor erythrocyte-binding activity. Four strain-specific HA-33/HA-17 complexes were isolated from the 650 kDa L-TC of each strain. The 650 kDa HA-hybrid L-TCs were reconstituted by various combinations of isolated HA-33/HA-17 complexes and haemagglutination-negative L-TC2 or L-TC3 from each strain. HA-hybrid 650 kDa L-TC, including at least one HA-33/HA-17 complex derived from C-Yoichi, lost haemagglutination activity, leading to the conclusion that the binding of four HA-33 molecules is required for haemagglutination activity of botulinum L-TC. The results of the modelling approach indicated that the structure of a variant C-Yoichi HA-33 molecule reveals clear deformation of the beta-trefoil domain responsible for the carbohydrate recognition site.

  19. Effect of Solvent Molecule in Pore for Flexible Porous Coordination Polymer upon Gas Adsorption and Iodine Encapsulation.

    PubMed

    Arıcı, Mürsel; Yeşilel, Okan Zafer; Taş, Murat; Demiral, Hakan

    2015-12-07

    Four new Zn(II)-coordination polymers, namely, [Zn2(μ6-ao2btc)(μ-obix)2]n (1), [Zn2(μ4-ao2btc)(μ-obix)2]n (2), [Zn2(μ4-ao2btc)(μ-mbix)2]n (3), and {[Zn2(μ4-ao2btc)(μ-pbix)2] · 2DMF · 8H2O}n (4), where ao2btc = dioxygenated form of 3,3',5,5'-azobenzenetetracarboxylate and obix, mbix, and pbix = 1,2-, 1,3-, and 1,4-bis(imidazol-1-ylmethyl)benzene, have been synthesized with azobenzenetetracarboxylic acid and isomeric bis(imidazole) ligands and characterized by elemental analyses, IR spectra, single-crystal X-ray diffraction, powder X-ray diffraction, and thermal analyses. X-ray results showed that 1, 2, and 4 had two-dimensional structures with 3,4L13 topology, while 3 was a three-dimensional coordination polymer with bbf topology. For 4, two types of activation strategies, solvent exchange + heating (which produced 4a) and direct heating (which produced 4b), were used to investigate the effect of a guest molecule in a flexible framework. Gas adsorption and iodine encapsulation properties of activated complexes were studied. The CO2 uptake capacities for 4a and 4b were 3.62% and 9.50%, respectively, and Langmuir surface areas calculated from CO2 isotherms were 167.4 and 350.7 m(2)/g, respectively. Moreover, 4b exhibited 19.65% and 15.27% iodine uptake in vapor phase and cyclohexane solution, respectively, which corresponded to 1.47 and 0.97 molecules of iodine/formula unit, respectively. Moreover, photoluminescence properties of the complexes were studied.

  20. Effects of London dispersion correction in density functional theory on the structures of organic molecules in the gas phase.

    PubMed

    Grimme, Stefan; Steinmetz, Marc

    2013-10-14

    A benchmark set of 25 rotational constants measured in the gas phase for nine molecules (termed ROT25) was compiled from available experimental data. The medium-sized molecules with 18-35 atoms cover common (bio)organic structure motifs including hydrogen bonding and flexible side chains. They were each considered in a single conformation. The experimental B0 values were back-corrected to reference equilibrium rotational constants (Be) by computation of the vibrational corrections ΔBvib. Various density functional theory (DFT) methods and Hartree-Fock with and without dispersion corrections as well as MP2 type methods and semi-empirical quantum chemical approaches are investigated. The ROT25 benchmark tests their ability to describe covalent bond lengths, longer inter-atomic distances, and the relative orientation of functional groups (intramolecular non-covalent interactions). In general, dispersion corrections to DFT and HF increase Be values (shrink molecular size) significantly by about 0.5-1.5% thereby in general improving agreement with the reference data. Regarding DFT methods, the overall accuracy of the optimized structures roughly follows the 'Jacobs ladder' classification scheme, i.e., it decreases in the series double-hybrid > (meta)hybrid > (meta)GGA > LDA. With B2PLYP-D3, SCS-MP2, B3LYP-D3/NL, or PW6B95-D3 methods and extended QZVP (def2-TZVP) AO basis sets, Be values, accurate to about 0.3-0.6 (0.5-1)% on average, can be computed routinely. The accuracy of B2PLYP-D3/QZVP with a mean deviation of only 3 MHz and a standard deviation of 0.24% is exceptional and we recommend this method when highly accurate structures are required or for problematic conformer assignments. The correlation effects for three inter-atomic distance regimes (covalent, medium-range, long) and the performance of minimal basis set (semi-empirical) methods are discussed.

  1. Hemoglobin: a gas transport molecule that is hormonally regulated in the ovarian follicle in mice and humans.

    PubMed

    Brown, Hannah M; Anastasi, Marie R; Frank, Laura A; Kind, Karen L; Richani, Dulama; Robker, Rebecca L; Russell, Darryl L; Gilchrist, Robert B; Thompson, Jeremy G

    2015-01-01

    An increasing number of nonerythroid tissues are found to express hemoglobin mRNA and protein. Hemoglobin is a well-described gas transport molecule, especially for O2, but also for NO, CO2, and CO, and also acts as a reactive oxygen species scavenger. We previously found Hba-a1 and Hbb mRNA and protein at high levels within mouse periovulatory cumulus cells, but not in cumulus following in vitro maturation. This led us to investigate the temporal and spatial regulation in follicular cells during the periovulatory period. Cumulus-oocyte complexes were collected from equine chorionic gonadotropin/human chorionic gonadotropin-treated peripubertal SV129 female mice and collected and analyzed for gene expression and protein localization at a variety of time points over the periovulatory period. A further cohort matured in vitro with different forms of hemoglobin (ferro- and ferrihemoglobin) under different O2 atmospheric conditions (2%, 5%, and 20% O2) were subsequently fertilized in vitro and cultured to the blastocyst stage. Murine mRNA transcripts for hemoglobin were regulated by stimulation of the ovulatory cascade, in both granulosa and cumulus cells, and expression of HBA1 and HBB was highly significant in human granulosa and cumulus, but erythrocyte cell marker genes were not. Several other genes involved in hemoglobin function were similarly luteinizing hormone-regulated, including genes for heme biosynthesis. Immunohistochemistry revealed a changing localization pattern of HBA-A1 protein in murine cumulus cells and oocytes following the ovulatory signal. Significantly, no positive staining for HBA-A1 protein was observed within in vitro-matured oocytes, but, if coincubated with ferro- or ferrihemoglobin, cytoplasmic HBA-A1 was observed, similar to in vivo-derived oocytes. Addition of ferro-, but not ferrihemoglobin, had a small, positive effect on blastocyst yield, but only under either 2% or 20% O2 gas atmosphere. The identification of hemoglobin within

  2. Structures and aggregation states of fluoromethyllithium and chloromethyllithium carbenoids in the gas phase and in ethereal solvent.

    PubMed

    Pratt, Lawrence M; Ramachandran, Bala; Xidos, James D; Cramer, Christopher J; Truhlar, Donald G

    2002-11-01

    Using high-level quantum mechanical calculations and various models to account for solvation effects, monomers and dimers of fluoromethyllithium and chloromethyllithium carbenoids are studied in the gas phase and in dimethyl ether solvent. A combination of explicit microsolvation and a continuum reaction field is required to account fully for the structural and energetic effects of solvation. One important effect of solvent is the stabilization of charge-separated structures in which the lithium-halogen distance is much greater than in the gas-phase structures. At the most complete level of theory the 173 K standard-state free energy of dimerization of fluoromethyllithium in dimethyl ether is predicted to be -0.9 kcal mol(-)(1), while that for chloromethyllithium in the same solvent is predicted to be 3.7 kcal mol(-)(1). This suggests that, under typical experimental conditions, dimers of chloroalkyllithiums will not be observed, while dimers of fluoroalkyllithiums may contribute to the equilibrium population at a detectable level.

  3. Radial diffusion and penetration of gas molecules and aerosol particles through laminar flow reactors, denuders, and sampling tubes.

    PubMed

    Knopf, Daniel A; Pöschl, Ulrich; Shiraiwa, Manabu

    2015-04-07

    Flow reactors, denuders, and sampling tubes are essential tools for many applications in analytical and physical chemistry and engineering. We derive a new method for determining radial diffusion effects and the penetration or transmission of gas molecules and aerosol particles through cylindrical tubes under laminar flow conditions using explicit analytical equations. In contrast to the traditional Brown method [Brown, R. L. J. Res. Natl. Bur. Stand. (U. S.) 1978, 83, 1-8] and CKD method (Cooney, D. O.; Kim, S. S.; Davis, E. J. Chem. Eng. Sci. 1974, 29, 1731-1738), the new approximation developed in this study (known as the KPS method) does not require interpolation or numerical techniques. The KPS method agrees well with the CKD method under all experimental conditions and also with the Brown method at low Sherwood numbers. At high Sherwood numbers corresponding to high uptake on the wall, flow entry effects become relevant and are considered in the KPS and CKD methods but not in the Brown method. The practical applicability of the KPS method is demonstrated by analysis of measurement data from experimental studies of rapid OH, intermediate NO3, and slow O3 uptake on various organic substrates. The KPS method also allows determination of the penetration of aerosol particles through a tube, using a single equation to cover both the limiting cases of high and low deposition described by Gormley and Kennedy (Proc. R. Ir. Acad., Sect. A. 1949, 52A, 163-169). We demonstrate that the treatment of gas and particle diffusion converges in the KPS method, thus facilitating prediction of diffusional loss and penetration of gases and particles, analysis of chemical kinetics data, and design of fluid reactors, denuders, and sampling lines.

  4. First-principles investigations of metal (V, Nb, Ta)-doped monolayer MoS2: Structural stability, electronic properties and adsorption of gas molecules

    NASA Astrophysics Data System (ADS)

    Zhu, Jia; Zhang, Hui; Tong, Yawen; Zhao, Ling; Zhang, Yongfan; Qiu, Yuzhi; Lin, Xianning

    2017-10-01

    Two-dimensional (2D) layered materials are at the forefront of research because of their unique structures and promising catalytic abilities. Here, the structural stability, electronic properties and gas adsorption of metal (V, Nb, Ta)-doped monolayer MoS2 have been investigated by density functional theory calculations. Our results show that the metal (V, Nb, Ta)-doped monolayer MoS2 is a stable catalyst under room temperature, due to the strong interaction between the doped metals (V, Nb, Ta) and S vacancy of monolayer MoS2. Compared with the gas adsorption (CO, NO2, H2O, NH3) on pristine monolayer MoS2, doped metal (V, Nb, Ta) can significantly improve the adsorption properties, chemical activity and the sensitivity of that of adsorbed gas molecules. This effect occurs due to the strong overlap between the metal nd orbitals and gas molecule orbitals, result in activation of the adsorbed gas molecules. Analysis of Bader charge shows that, more charge transfer (-0.66 e to -0.72 e) occur from metal (V, Nb, Ta)-doped monolayer MoS2 to the oxidizing gas molecules (NO2) acting as acceptors. While for the adsorption of CO molecules, the relative less electrons (about -0.24 e - -0.35 e) transfer occuring from substrate to the adsorbed gases. Whereas the direction of charge transfers is reversed for the adsorption of the reducing gas (H2O and NH3) behaving as donors, in which small electrons (0.04 e -0.09 e) transfer from adsorbed gas to metal (V, Nb, Ta)-doped monolayer MoS2. Our results suggested that metal (V, Nb, Ta)-doped monolayer MoS2 might be a good candidate for low-cost, highly active, and stable catalysts and gas sensors, providing an avenue to facilitate the design of high active MoS2-based two dimensional catalysts and gas sensors.

  5. Gas-phase geometry optimization of biological molecules as a reasonable alternative to a continuum environment description: fact, myth, or fiction?

    PubMed

    Sousa, Sérgio Filipe; Fernandes, Pedro Alexandrino; Ramos, Maria João

    2009-12-31

    Gas-phase optimization of single biological molecules and of small active-site biological models has become a standard approach in first principles computational enzymology. The important role played by the surrounding environment (solvent, enzyme, both) is normally only accounted for through higher-level single point energy calculations performed using a polarizable continuum model (PCM) and an appropriate dielectric constant with the gas-phase-optimized geometries. In this study we analyze this widely used approximation, by comparing gas-phase-optimized geometries with geometries optimized with different PCM approaches (and considering different dielectric constants) for a representative data set of 20 very important biological molecules--the 20 natural amino acids. A total of 323 chemical bonds and 469 angles present in standard amino acid residues were evaluated. The results show that the use of gas-phase-optimized geometries can in fact be quite a reasonable alternative to the use of the more computationally intensive continuum optimizations, providing a good description of bond lengths and angles for typical biological molecules, even for charged amino acids, such as Asp, Glu, Lys, and Arg. This approximation is particularly successful if the protonation state of the biological molecule could be reasonably described in vacuum, a requirement that was already necessary in first principles computational enzymology.

  6. Gas Chromatographic-Ion Trap Mass Spectrometric Analysis of Volatile Organic Compounds by Ion-Molecule Reactions Using the Electron-Deficient Reagent Ion CCl{3/+}

    NASA Astrophysics Data System (ADS)

    Wang, Cheng-Zhong; Su, Yue; Wang, Hao-Yang; Guo, Yin-Long

    2011-10-01

    When using tetrachloromethane as the reagent gas in gas chromatography-ion trap mass spectrometry equipped with hybrid ionization source, the cation CCl{3/+} was generated in high abundance and further gas-phase experiments showed that such an electron-deficient reagent ion CCl{3/+} could undergo interesting ion-molecule reactions with various volatile organic compounds, which not only present some informative gas-phase reactions, but also facilitate qualitative analysis of diverse volatile compounds by providing unique mass spectral data that are characteristic of particular chemical structures. The ion-molecule reactions of the reagent ion CCl{3/+} with different types of compounds were studied, and results showed that such reactions could give rise to structurally diagnostic ions, such as [M + CCl3 - HCl]+ for aromatic hydrocarbons, [M - OH]+ for saturated cyclic ether, ketone, and alcoholic compounds, [M - H]+ ion for monoterpenes, M·+ for sesquiterpenes, [M - CH3CO]+ for esters, as well as the further fragment ions. The mechanisms of ion-molecule reactions of aromatic hydrocarbons, aliphatic ketones and alcoholic compounds with the reagent ion CCl{3/+} were investigated and proposed according to the information provided by MS/MS experiments and theoretical calculations. Then, this method was applied to study volatile organic compounds in Dendranthema indicum var. aromaticum and 20 compounds, including monoterpenes and their oxygen-containing derivatives, aromatic hydrocarbon and sesquiterpenes were identified using such ion-molecule reactions. This study offers a perspective and an alternative tool for the analysis and identification of various volatile compounds.

  7. [Formation of Aspergillus niger-mineral aggregation and characterization of polysaccharide from aggregation].

    PubMed

    Hu, Jie; Lian, Bin; Yu, Jianping; Hu, Xing

    2011-06-01

    In order to understand the weathering on potassium-bearing mineral by Aspergillus niger, we studied the formation of A. niger-mineral aggregation and polysaccharide in the revolving and fermenting mode and their role in the process of weathering on potassium-bearing mineral. We used four different media to study the morphology of A. niger-mineral aggregation; ultraviolet-visible spectrum (UV-Vis) , fourier transform infrared spectrum (IR), gas chromatography (GC), scanning electron microscopy (SEM) and energy dispersive spectrometer (EDS) were combined to research the changes of polysaccharide and their significances in the micro-environment forming fungal-mineral aggregation. A. niger myclia intertwined, adsorbed and bonded mineral powder to form aggregation by the assistance of polysaccharide and other metabolites. After formation of the aggregation, the concentration and structure of polysaccharide were changed significantly. The changes of polysaccharide would enhance the adsorption on minerals, chelation on metal ions and adsorption on water molecules, which provided a favorable micro-environment for the fungal using mineral nutrients effectively.

  8. Infrared Spectroscopy of Gas-Phase M(+)(CO2)n (M = Co, Rh, Ir) Ion-Molecule Complexes.

    PubMed

    Iskra, Andreas; Gentleman, Alexander S; Kartouzian, Aras; Kent, Michael J; Sharp, Alastair P; Mackenzie, Stuart R

    2017-01-12

    The structures of gas-phase M(+)(CO2)n (M = Co, Rh, Ir; n = 2-15) ion-molecule complexes have been investigated using a combination of infrared resonance-enhanced photodissociation (IR-REPD) spectroscopy and density functional theory. The results provide insight into fundamental metal ion-CO2 interactions, highlighting the trends with increasing ligand number and with different group 9 ions. Spectra have been recorded in the region of the CO2 asymmetric stretch around 2350 cm(-1) using the inert messenger technique and their interpretation has been aided by comparison with simulated infrared spectra of calculated low-energy isomeric structures. All vibrational bands in the smaller complexes are blue-shifted relative to the asymmetric stretch in free CO2, consistent with direct binding to the metal center dominated by charge-quadrupole interactions. For all three metal ions, a core [M(+)(CO2)2] structure is identified to which subsequent ligands are less strongly bound. No evidence is observed in this size regime for complete activation or insertion reactions.

  9. Volume shrinkage of a metal-organic framework host induced by the dispersive attraction of guest gas molecules.

    PubMed

    Joo, Jaeyong; Kim, Hyungjun; Han, Sang Soo

    2013-11-21

    Using a density functional theory calculation including van der Waals (vdW) corrections, we report that H2 adsorption in a cubic-crystalline microporous metal-organic framework (MOF-5) leads to volume shrinkage, which is in contrast to the intuition that gas adsorption in a confined system (e.g., pores in a material) increases the internal pressure and then leads to volumetric expansion. This extraordinary phenomenon is closely related to the vdW interactions between MOF and H2 along with the H2-H2 interaction, rather than the Madelung-type electrostatic interaction. At low temperatures, H2 molecules adsorbed in the MOF-5 form highly symmetrical interlinked nanocages that change from a cube-like shape to a sphere-like shape with H2 loading, helping to exert centrosymmetric forces and hydrostatic (volumetric) stresses from the collection of dispersive interactions. The generated internal negative stress is sufficient to overcome the stiffness of the MOF-5 which is a soft material with a low bulk modulus (15.54 GPa).

  10. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1995-01-01

    Part of the 1994 Industrial Minerals Review. The production, consumption, and applications of construction aggregates are reviewed. In 1994, the production of construction aggregates, which includes crushed stone and construction sand and gravel combined, increased 7.7 percent to 2.14 Gt compared with the previous year. These record production levels are mostly a result of funding for highway construction work provided by the Intermodal Surface Transportation Efficiency Act of 1991. Demand is expected to increase for construction aggregates in 1995.

  11. Dynamic terahertz spectroscopy of gas molecules mixed with unwanted aerosol under atmospheric pressure using fibre-based asynchronous-optical-sampling terahertz time-domain spectroscopy

    PubMed Central

    Hsieh, Yi-Da; Nakamura, Shota; Abdelsalam, Dahi Ghareab; Minamikawa, Takeo; Mizutani, Yasuhiro; Yamamoto, Hirotsugu; Iwata, Tetsuo; Hindle, Francis; Yasui, Takeshi

    2016-01-01

    Terahertz (THz) spectroscopy is a promising method for analysing polar gas molecules mixed with unwanted aerosols due to its ability to obtain spectral fingerprints of rotational transition and immunity to aerosol scattering. In this article, dynamic THz spectroscopy of acetonitrile (CH3CN) gas was performed in the presence of smoke under the atmospheric pressure using a fibre-based, asynchronous-optical-sampling THz time-domain spectrometer. To match THz spectral signatures of gas molecules at atmospheric pressure, the spectral resolution was optimized to 1 GHz with a measurement rate of 1 Hz. The spectral overlapping of closely packed absorption lines significantly boosted the detection limit to 200 ppm when considering all the spectral contributions of the numerous absorption lines from 0.2 THz to 1 THz. Temporal changes of the CH3CN gas concentration were monitored under the smoky condition at the atmospheric pressure during volatilization of CH3CN droplets and the following diffusion of the volatilized CH3CN gas without the influence of scattering or absorption by the smoke. This system will be a powerful tool for real-time monitoring of target gases in practical applications of gas analysis in the atmospheric pressure, such as combustion processes or fire accident. PMID:27301319

  12. Dynamic terahertz spectroscopy of gas molecules mixed with unwanted aerosol under atmospheric pressure using fibre-based asynchronous-optical-sampling terahertz time-domain spectroscopy

    NASA Astrophysics Data System (ADS)

    Hsieh, Yi-Da; Nakamura, Shota; Abdelsalam, Dahi Ghareab; Minamikawa, Takeo; Mizutani, Yasuhiro; Yamamoto, Hirotsugu; Iwata, Tetsuo; Hindle, Francis; Yasui, Takeshi

    2016-06-01

    Terahertz (THz) spectroscopy is a promising method for analysing polar gas molecules mixed with unwanted aerosols due to its ability to obtain spectral fingerprints of rotational transition and immunity to aerosol scattering. In this article, dynamic THz spectroscopy of acetonitrile (CH3CN) gas was performed in the presence of smoke under the atmospheric pressure using a fibre-based, asynchronous-optical-sampling THz time-domain spectrometer. To match THz spectral signatures of gas molecules at atmospheric pressure, the spectral resolution was optimized to 1 GHz with a measurement rate of 1 Hz. The spectral overlapping of closely packed absorption lines significantly boosted the detection limit to 200 ppm when considering all the spectral contributions of the numerous absorption lines from 0.2 THz to 1 THz. Temporal changes of the CH3CN gas concentration were monitored under the smoky condition at the atmospheric pressure during volatilization of CH3CN droplets and the following diffusion of the volatilized CH3CN gas without the influence of scattering or absorption by the smoke. This system will be a powerful tool for real-time monitoring of target gases in practical applications of gas analysis in the atmospheric pressure, such as combustion processes or fire accident.

  13. Dynamic terahertz spectroscopy of gas molecules mixed with unwanted aerosol under atmospheric pressure using fibre-based asynchronous-optical-sampling terahertz time-domain spectroscopy.

    PubMed

    Hsieh, Yi-Da; Nakamura, Shota; Abdelsalam, Dahi Ghareab; Minamikawa, Takeo; Mizutani, Yasuhiro; Yamamoto, Hirotsugu; Iwata, Tetsuo; Hindle, Francis; Yasui, Takeshi

    2016-06-15

    Terahertz (THz) spectroscopy is a promising method for analysing polar gas molecules mixed with unwanted aerosols due to its ability to obtain spectral fingerprints of rotational transition and immunity to aerosol scattering. In this article, dynamic THz spectroscopy of acetonitrile (CH3CN) gas was performed in the presence of smoke under the atmospheric pressure using a fibre-based, asynchronous-optical-sampling THz time-domain spectrometer. To match THz spectral signatures of gas molecules at atmospheric pressure, the spectral resolution was optimized to 1 GHz with a measurement rate of 1 Hz. The spectral overlapping of closely packed absorption lines significantly boosted the detection limit to 200 ppm when considering all the spectral contributions of the numerous absorption lines from 0.2 THz to 1 THz. Temporal changes of the CH3CN gas concentration were monitored under the smoky condition at the atmospheric pressure during volatilization of CH3CN droplets and the following diffusion of the volatilized CH3CN gas without the influence of scattering or absorption by the smoke. This system will be a powerful tool for real-time monitoring of target gases in practical applications of gas analysis in the atmospheric pressure, such as combustion processes or fire accident.

  14. Luminescence characteristics of Xe{sub 2}Cl excimer molecules under pumping the dense Xe-CCl{sub 4} gas mixtures with a pulsed electron beam

    SciTech Connect

    Mis'kevich, A I; Jinbo, Guo

    2013-05-31

    Temporal and spectral characteristics of the luminescence of dense Xe-CCl{sub 4} gas mixtures of different composition, excited by a 5-ns pulsed electron beam, were measured. The energy of the electrons amounted to 150 keV and the electron beam current pulse amplitude was 5 A. The gas mixtures were used containing Xe (38-700 Torr) and CCl{sub 4} (0.03-0.3 Torr). The studies were performed within the wavelength range 200-1200 nm using a MAYA-2000Pro diffraction grating spectrometer and a RIGOL DS 5022 ME fast digital oscilloscope. The luminescence lifetimes of the excimer molecules XeCl* (band with {lambda}{sub max} = 308 nm) and Xe{sub 2}Cl* (band with {lambda}{sub max} = 486 nm) were measured, as well as the constants of quenching by the components of the gas mixture for Xe{sub 2}Cl* molecules. A model of plasma-chemical processes for dense Xe-CCl{sub 4} gas mixtures with a very low content of the CCl{sub 4} donor is proposed. It is shown that in such 'poor' mixtures Xe{sub 2}Cl* molecules are mainly produced as a result of recombination of the Xe{sub 2}{sup +} and Cl{sup -} ions. (active media)

  15. Gas-phase ion-molecule reactions for resolution of atomic isobars: AMS and ICP-MS perspectives

    NASA Astrophysics Data System (ADS)

    Bandura, Dmitry R.; Baranov, Vladimir I.; Litherland, A. E.; Tanner, Scott D.

    2006-09-01

    Ion-molecule reactions that can be used for resolution of spectral overlaps of long-lived or stable (T1/2 > 100 years) atomic isobars on the long-lived radio-isotopes (100 < T1/2 < 1012 years) in mass spectrometry are considered. Results for the separations of isobaric overlaps via cation reactions with NO, N2O, O2, CO2, C2H2, CH3F studied with the Inductively Coupled Plasma Dynamic Reaction Cell(TM) Mass Spectrometer (ICP-DRC(TM)-MS) with use of stable isotopes are presented. Overview of potential and reported reactions for separation of 35 isobars is given. Potential for the following isobaric pairs separation is shown (reaction gas and the extent of separation achieved to date in parenthesis): 32Si+/32S+(NO, 5 x 104), 40K+/40Ar+(N2O, 1.9 x 103), 40K+/40Ca+(N2O, 50), 59Ni+/59Co+(N2O, 6), 79Se+/79Br+(O2, 7.2 x 103), 81Kr+/81Br+(C2H2, 1.5 x 104), 93Mo+/93Nb+(N2O, 100), 93Mo+/93Zr+(N2O, 150), 135Cs+/135Ba+(N2O, 8 x 104), 137,138La+/137,138Ba+(O2, 40), 146Sm+/146Nd+(CO2, 1.5 x 105), 176Lu+/176Hf+(NO, 2.8 x 103), 187Re+/187Os+(N2O, 2.8 x 104). Effect of instrumental parameters on reactivity is discussed. The relevance of this work to accelerator mass spectrometry is discussed briefly.

  16. Nanoarchitectonics of Molecular Aggregates: Science and Technology

    SciTech Connect

    Ramanathan, Nathan Muruganathan; Hong, Kunlun; Ji, Dr. Qingmin; Hill, Dr. Jonathan P; Ariga, Katsuhiko; Yusuke, Yonamine

    2014-01-01

    The field of making, studying and using molecular aggregates, in which the individual molecules (monomers) are arranged in a regular fashion, has come a long way. Taking control over the aggregation of small molecules and polymers in bulk, on surfaces and at interfaces pose a considerable challenge for their utilization in modern high tech applications. In this review we provide a detailed insight into recent trends in molecular aggregates from the perspectives of nanoarchitectonics.

  17. Determination of local concentration of H2O molecules and gas temperature in the process of hydrogen - oxygen gas mixture heating by means of linear and nonlinear laser spectroscopy

    NASA Astrophysics Data System (ADS)

    Kozlov, D. N.; Kobtsev, V. D.; Stel'makh, O. M.; Smirnov, Valery V.; Stepanov, E. V.

    2013-01-01

    Employing the methods of linear absorption spectroscopy and nonlinear four-wave mixing spectroscopy using laserinduced gratings we have simultaneously measured the local concentrations of H2O molecules and the gas temperature in the process of the H2 - O2 mixture heating. During the measurements of the deactivation rates of pulsed-laser excited singlet oxygen O2 (b 1Σ+g) in collisions with H2 in the range 294 - 850 K, the joint use of the two methods made it possible to determine the degree of hydrogen oxidation at a given temperature. As the mixture is heated, H2O molecules are formed by 'dark' reactions of H2 with O2 in the ground state. The experiments have shown that the measurements of tunable diode laser radiation absorption along an optical path through the inhomogeneously heated gas mixture in a cell allows high-accuracy determination of the local H2O concentration in the O2 laser excitation volume, if the gas temperature in this volume is known. When studying the collisional deactivation of O2 (b 1Σ+g) molecules, the necessary measurements of the local temperature can be implemented using laser-induced gratings, arising due to spatially periodic excitation of O2 (X3Σ-g) molecules to the b 1Σ+g state by radiation of the pump laser of the four-wave mixing spectrometer.

  18. Gas chromatographic-ion trap mass spectrometric analysis of volatile organic compounds by ion-molecule reactions using the electron-deficient reagent ion CCl3(+).

    PubMed

    Wang, Cheng-Zhong; Su, Yue; Wang, Hao-Yang; Guo, Yin-Long

    2011-10-01

    When using tetrachloromethane as the reagent gas in gas chromatography-ion trap mass spectrometry equipped with hybrid ionization source, the cation CCl(3)(+) was generated in high abundance and further gas-phase experiments showed that such an electron-deficient reagent ion CCl(3)(+) could undergo interesting ion-molecule reactions with various volatile organic compounds, which not only present some informative gas-phase reactions, but also facilitate qualitative analysis of diverse volatile compounds by providing unique mass spectral data that are characteristic of particular chemical structures. The ion-molecule reactions of the reagent ion CCl(3)(+) with different types of compounds were studied, and results showed that such reactions could give rise to structurally diagnostic ions, such as [M+CCl(3) - HCl](+) for aromatic hydrocarbons, [M - OH](+) for saturated cyclic ether, ketone, and alcoholic compounds, [M - H](+) ion for monoterpenes, M(·+) for sesquiterpenes, [M - CH(3)CO](+) for esters, as well as the further fragment ions. The mechanisms of ion-molecule reactions of aromatic hydrocarbons, aliphatic ketones and alcoholic compounds with the reagent ion CCl(3)(+) were investigated and proposed according to the information provided by MS/MS experiments and theoretical calculations. Then, this method was applied to study volatile organic compounds in Dendranthema indicum var. aromaticum and 20 compounds, including monoterpenes and their oxygen-containing derivatives, aromatic hydrocarbon and sesquiterpenes were identified using such ion-molecule reactions. This study offers a perspective and an alternative tool for the analysis and identification of various volatile compounds. © American Society for Mass Spectrometry, 2011

  19. Gas-phase infrared and ab initio study of the unstable CF3CNO molecule and its stable furoxan ring dimer.

    PubMed

    Havasi, Balázs; Pasinszki, Tibor; Westwood, Nicholas P C

    2005-05-05

    The unstable trifluoroacetonitrile N-oxide molecule, CF3CNO, has been generated in high yield in the gas phase from CF3BrC=NOH and studied for the first time by gas-phase mid-infrared spectroscopy. Cold trapping of this molecule followed by slow warming forms the stable ring dimer, bis(trifluoromethyl)furoxan, also investigated by gas-phase infrared spectroscopy. The spectroscopy provides an investigation into the vibrational character of the two molecules, the assignments supported by calculations of the harmonic vibrational frequencies using in the case of CF3CNO both ab initio (CCSD(T)) and density functional theory (B3LYP) and B3LYP for the ring dimer. The ground-state structures of both molecules were investigated at the B3LYP level of theory, with CF3CNO further investigated using coupled-cluster. The CCSD(T) method suggests a slightly bent (C(s)) structure for CF3CNO, while the B3LYP method (with basis sets ranging from 6-311G(d) to cc-pVTZ) suggests a close-to-linear or linear CCNO chain. The CCN bending potential in CF3CNO was explored at the CCSD(T)(fc)/cc-pVTZ level, with the results suggesting that CF3CNO exhibits strong quasi-symmetric top behavior with a barrier to linearity of 174 cm(-1). Since both isomerization and dimerization are feasible loss processes for this unstable molecule, the relative stability of CF3CNO with respect to the known cyanate (CF3OCN), isocyanate (CF3NCO), and fulminate (CF3ONC) isomers and the mechanism of the dimerization process to the ring furoxan and other isomers were studied with density functional theory.

  20. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1994-01-01

    Part of a special section on industrial minerals in 1993. The 1993 production of construction aggregates increased 6.3 percent over the 1992 figure, to reach 2.01 Gt. This represents the highest estimated annual production of combined crushed stone and construction sand and gravel ever recorded in the U.S. The outlook for construction aggregates and the issues facing the industry are discussed.

  1. 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 ...

  2. Synthesis of Pure and N-substituted Cyclic Hydrocarbons (e.g. Pyrimidine) via Gas-Phase Ion-Molecule Reactions

    NASA Astrophysics Data System (ADS)

    Bera, Partha P.; Peverati, Roberto; Head-Gordon, Martin; Lee, Timothy J.

    2015-08-01

    Large polyatomic carbonaceous molecules, known as polycyclic aromatic hydrocarbons, are known to exist in the outflows of carbon stars. How these large polyatomic molecules are synthesized in such exotic conditions is, thus far, unknown. Molecular ions, including positive and negative ions, are in relative abundance in the high radiation fields present under such conditions. Hence, barrierless ion-molecule interactions may play a major role in guiding molecules towards each other and initiating reactions. We study these condensation pathways to determine whether they are a viable means of forming large pure hydrocarbon molecules, and nitrogen-containing carbonaceous chains, stacks, and even cyclic compounds. By employing accurate quantum chemical methods we have investigated the processes of growth, structures, nature of bonding, mechanisms, and spectroscopic properties of the ensuing ionic products after pairing small carbon, hydrogen, and nitrogen-containing molecules. We have also studied the ion-neutral association pathways involving pure-carbon molecules e.g. acetylene, ethylene and other hydrocarbons, and their dissociation fragments in a plasma discharge as well as how nitrogen atoms are incorporated into the carbon ring during growth. Specifically, we explored the mechanisms by which the synthesis of pyrimidine will be feasible in the gas phase in conjunction with ion-mobility experiments. We have used accurate ab initio coupled cluster theory, Møller-Plesset and Z-averaged perturbation theories, density functional theory, and coupled cluster theory quantum chemical methods together with large correlation consistent basis sets in these investigations. We found that a series of hydrocarbons with a specific stoichiometric composition prefers cyclic molecule formation rather than chains. Some of the association products we investigated have large oscillator strengths for charge-transfer type electronic excitations in the near infrared and visible regions of

  3. Neutral gas temperature measurements of high-power-density fluorocarbon plasmas by fitting swan bands of C{sub 2} molecules

    SciTech Connect

    Bai Bo; Sawin, Herbert H.; Cruden, Brett A.

    2006-01-01

    The neutral gas temperature of fluorocarbon plasmas in a remote toroidal transformer-coupled source was measured to be greater than 5000 K, under the conditions of a power density greater than 15 W/cm{sup 3} and pressures above 2 torr. The rovibrational bands of C{sub 2} molecules (swan bands, d {sup 3}{pi}{sub g}{yields}a {sup 3}{pi}{sub u}) were fitted to obtain the rotational temperature that was assumed to equal the translational temperature. This rotational-translational temperature equilibrium assumption was supported by the comparison with the rotational temperature of second positive system of added N{sub 2}. For the same gas mixture, the neutral gas temperature is nearly a linear function of plasma power, since the conduction to chamber wall and convection are the major energy-loss processes, and they are both proportional to neutral gas temperature. The dependence of the neutral gas temperature on O{sub 2} flow rate and pressure can be well represented through the power dependence, under the condition of constant current operation. An Arrhenius type of dependence between the etching rate of oxide film and the neutral gas temperature is observed, maybe indicating the importance of the pyrolytic dissociation in the plasma formation process when the temperature is above 5000 K.

  4. Gas

    MedlinePlus

    ... intestine. Certain foods may cause gas. Foods that produce gas in one person may not cause gas in another. You can reduce the amount of gas you have by Drinking lots of water and non-fizzy drinks Eating more slowly so you swallow less air ...

  5. Recent advances in experimental techniques to probe fast excited-state dynamics in biological molecules in the gas phase: dynamics in nucleotides, amino acids and beyond

    PubMed Central

    Staniforth, Michael; Stavros, Vasilios G.

    2013-01-01

    In many chemical reactions, an activation barrier must be overcome before a chemical transformation can occur. As such, understanding the behaviour of molecules in energetically excited states is critical to understanding the chemical changes that these molecules undergo. Among the most prominent reactions for mankind to understand are chemical changes that occur in our own biological molecules. A notable example is the focus towards understanding the interaction of DNA with ultraviolet radiation and the subsequent chemical changes. However, the interaction of radiation with large biological structures is highly complex, and thus the photochemistry of these systems as a whole is poorly understood. Studying the gas-phase spectroscopy and ultrafast dynamics of the building blocks of these more complex biomolecules offers the tantalizing prospect of providing a scientifically intuitive bottom-up approach, beginning with the study of the subunits of large polymeric biomolecules and monitoring the evolution in photochemistry as the complexity of the molecules is increased. While highly attractive, one of the main challenges of this approach is in transferring large, and in many cases, thermally labile molecules into vacuum. This review discusses the recent advances in cutting-edge experimental methodologies, emerging as excellent candidates for progressing this bottom-up approach. PMID:24204191

  6. Ab-initio investigation of adsorption of CO and CO2 molecules on graphene: Role of intrinsic defects on gas sensing

    NASA Astrophysics Data System (ADS)

    Tit, Nacir; Said, Khadija; Mahmoud, Nadin M.; Kouser, Summayya; Yamani, Zain H.

    2017-02-01

    We determine the chemical activity of (a) carbon site of pristine graphene (pG), (b) Stone-Wales (SW) defect site, and (c) Single-vacancy of graphene (vG) site towards the adsorption of CO and CO2 molecules, through comparative analysis based on first-principles density-functional calculations incorporating van der Waals (vdW) interactions, but excluding the heat effects (i.e., at T = 0 °K). The results show that the chemisorption of both latter molecules to possibly occur only on vG. The response (sensitivity) of vG towards detecting CO molecule was confirmed by the rise of conductance with the increasing CO gas dose. The selectivity was investigated by testing the response of vG towards detecting eight different gases (i.e., CO, CO2, N2, O2, H2O, H2S, H2, and NH3). Three gases are found to exhibit physisorption (namely: N2, H2O, and H2S) and the other five gases alter chemisorption (namely: CO, CO2, O2, H2, and NH3). The chemisorption of CO molecule is distinct by being direct and not involving dissociation. This fact made defected graphene have the highest sensitivity and selectivity towards the detection of CO molecules.

  7. Recent advances in experimental techniques to probe fast excited-state dynamics in biological molecules in the gas phase: dynamics in nucleotides, amino acids and beyond.

    PubMed

    Staniforth, Michael; Stavros, Vasilios G

    2013-11-08

    In many chemical reactions, an activation barrier must be overcome before a chemical transformation can occur. As such, understanding the behaviour of molecules in energetically excited states is critical to understanding the chemical changes that these molecules undergo. Among the most prominent reactions for mankind to understand are chemical changes that occur in our own biological molecules. A notable example is the focus towards understanding the interaction of DNA with ultraviolet radiation and the subsequent chemical changes. However, the interaction of radiation with large biological structures is highly complex, and thus the photochemistry of these systems as a whole is poorly understood. Studying the gas-phase spectroscopy and ultrafast dynamics of the building blocks of these more complex biomolecules offers the tantalizing prospect of providing a scientifically intuitive bottom-up approach, beginning with the study of the subunits of large polymeric biomolecules and monitoring the evolution in photochemistry as the complexity of the molecules is increased. While highly attractive, one of the main challenges of this approach is in transferring large, and in many cases, thermally labile molecules into vacuum. This review discusses the recent advances in cutting-edge experimental methodologies, emerging as excellent candidates for progressing this bottom-up approach.

  8. Kronecker-product periodic systems of small gas-phase molecules and the search for order in atomic ensembles of any phase.

    PubMed

    Hefferlin, Ray

    2008-11-01

    The periodic law, manifested in the chart of the elements, is so fundamental in chemistry and related areas of physics that the question arises "Might periodicity among molecules also be embodied in a periodic system?" This review paper details how a particular periodic system of gas-phase diatomic molecules, allowing for the forecasting of thousands of new data, was developed. It can include ionized and even quarked-nuclei molecules and it coincides with locality (averaging) and the additivity found in some data; it has interesting vector properties, and it may be related in challenging ways to partial order. The review then explains how periodic systems for triatomic and four-atomic species are evolving along a similar path. The systems rest largely upon exhaustive comparisons of tabulated data, relate to some extent to the octet rule, and include reducible representations of the dynamic group SO(4) in higher spaces. Finally, the paper shows how periodicity can be quantified in data for larger molecules. Data for properties of homologous or substituted molecules, in any phase, are quantified with a vector index, and the index for one set can be transformed into that for another set.

  9. Stoichiometry and Physical Chemistry of Promiscuous Aggregate-Based Inhibitors

    PubMed Central

    Coan, Kristin E. D.

    2009-01-01

    Many false positives in early drug discovery owe to nonspecific inhibition by colloid-like aggregates of organic molecules. Despite their prevalence, little is known about aggregate concentration, structure, or dynamic equilibrium; the binding mechanism, stoichiometry with, and affinity for enzymes remain uncertain. To investigate the elementary question of concentration, we counted aggregate particles using flow cytometry. For seven aggregate-forming molecules, aggregates were not observed until the concentration of monomer crossed a threshold, indicating a “critical aggregation concentration” (CAC). Above the CAC, aggregate count increased linearly with added organic material, while the particles dispersed when diluted below the CAC. The concentration of monomeric organic molecule is constant above the CAC, as is the size of the aggregate particles. For two compounds that form large aggregates, nicardipine and miconazole, we measured particle numbers directly by flow cytometry, determining that the aggregate concentration just above the CAC ranged from 5 to 30 fM. By correlating inhibition of an enzyme with aggregate count for these two drugs, we determined that the stoichiometry of binding is about 10 000 enzyme molecules per aggregate particle. Using measured volumes for nicardipine and miconazole aggregate particles (2.1 × 1011 and 4.7 × 1010 Å3, respectively), computed monomer volumes, and the observation that past the CAC all additional monomer forms aggregate particles, we find that aggregates are densely packed particles. Finally, given their size and enzyme stoichiometry, all sequestered enzyme can be comfortably accommodated on the surface of the aggregate. PMID:18588298

  10. The insertion of gas molecules into polyhedral oligomeric silsesquioxane (POSS) cages: understanding the energy of insertion using quantum chemical calculations.

    PubMed

    Skelton, A A; Fried, J R

    2013-03-28

    Density functional theory (DFT) calculations using the B3LYP and ωB97XD functionals and Møller-Plesset (MP2) calculations have been used to determine the energy of insertion of seven molecules (CO2, N2, O2, CO, CH4, He and H2O) into two sizes of polyhedral oligomeric silsesquioxane (POSS) cages, T10 and T12. Geometry optimization results of each molecule inserted into the center of the POSS cage and transition-energy searches of the molecules in the largest face of both T10 and T12 (identified as the Si5 face) are discussed. The main factors that affect the energy of a molecule in a particular POSS cage are the size (number of atoms) and shape of the POSS cage and the strength of dispersion and electrostatic interactions. The largest of the molecules, CO2 and CH4, have the largest interaction energies within the center and the face of the T10 and T12 cages. Interaction energies for the diatomic molecules increase in the order H2 < O2 < N2 ∼ CO and differences between interaction energies can be attributed, in part, to differences in electron transfer between the cage and molecule. Electrostatic interactions also play a significant role in determining the interaction energy. For example, H2 and He are only slightly charged when inside the POSS cages, providing little repulsive or attractive interactions, while polar CO provides significant repulsive interaction. In the case of water, the interaction energies are low because of hydrogen bonding between the water hydrogen atoms and the POSS oxygen atoms. The interaction energies of the absorbates at the center of T12 are typically smaller than for T10 due to the larger cavity size of T12. The Si5 face has the same basic structure for both T10 and T12 cages and, consequently, the interaction energies of the absorbate molecules at the face are similar. Interaction energies obtained using MP2 calculations are lower than those obtained from DFT calculations depending on the choice of the functional. For example, use

  11. Wide-band exciplex halogen lamps operating on inert gas mixtures with chlorine and Freon-12 molecules

    NASA Astrophysics Data System (ADS)

    Shuaibov, A. K.; Shevera, I. V.

    2007-09-01

    The results of analysis of the spectral characteristics of short-wave radiation sources operating on transitions in argon, krypton, and xenon monohalogenides, as well as chlorine molecules, excited by a longitudinal low-pressure glow discharge are considered. Radiation emitted by ArCl*, KrCl*, XeCl*, Cl{2/**}, and Cl{2/*} molecules in a spectral range of 170-350 nm is optimized using complex working mixtures of Ar-Kr-(Xe)-Cl2 in the lamps. The average radiation power of the lamps ranges from 1 to 10 W for an efficiency of ≤25%. Optimization of wide-band lamps on transitions in chlorine molecules and the decay products of Freon-12 molecules (CF2Cl2) is carried out on mixtures of helium with chlorine and Freon-12 molecules. This makes it possible to develop lamps emitting in a spectral range of 140-270 nm and containing no costly inert gases (Xe or Kr) in their working mixtures. Exciplex halogen lamps with a wide-band emission spectrum in the VUV-UV range can be used in spectrometers as radiation sources in experiments with absorption and in high-energy chemistry, ecology, and medicine.

  12. Effect of hydration on the organo-noble gas molecule HKrCCH: role of krypton in the stabilization of hydrated HKrCCH complexes.

    PubMed

    Biswas, Biswajit; Singh, Prashant Chandra

    2015-11-11

    The effect of hydration on the fluorine free organo-noble gas compound HKrCCH and the role of krypton in the stabilization of the hydrated HKrCCH complexes have been investigated using the quantum chemical calculations on the HKrCCH-(H2O)n=1-6 clusters. Structure and energetics calculations show that water stabilizes HKrCCH through the π hydrogen bond in which the OH group of water interacts with the C[triple bond, length as m-dash]C group of HKrCCH. A maximum of four water molecules can directly interact with the C[triple bond, length as m-dash]C of HKrCCH and after that only inter-hydrogen bonding takes place between the water molecules indicating that the primary hydration shell contains four water molecules. Atom in molecule analysis depicts that π hydrogen bonded complexes of the hydrated HKrCCH are cyclic structures in which the OKr interaction cooperates in the formation of strong O-HC[triple bond, length as m-dash]C interaction. Structure, energetics and charge analysis clearly established that krypton plays an important role in the stabilization as well as the formation of the primary hydration shell of hydrated HKrCCH complexes.

  13. The electronic spectrum of CUONg4 (Ng = Ne, Ar, Kr, Xe): New insights in the interaction of the CUO molecule with noble gas matrices

    NASA Astrophysics Data System (ADS)

    Tecmer, Paweł; van Lingen, Henk; Gomes, André Severo Pereira; Visscher, Lucas

    2012-08-01

    The electronic spectrum of the CUO molecule was investigated with the IHFSCC-SD (intermediate Hamiltonian Fock-space coupled cluster with singles and doubles) method and with TD-DFT (time-dependent density functional theory) employing the PBE and PBE0 exchange-correlation functionals. The importance of both spin-orbit coupling and correlation effects on the low-lying excited-states of this molecule are analyzed and discussed. Noble gas matrix effects on the energy ordering and vibrational frequencies of the lowest electronic states of the CUO molecule were investigated with density functional theory (DFT) and TD-DFT in a supermolecular as well as a frozen density embedding (FDE) subsystem approach. This data is used to test the suitability of the FDE approach to model the influence of different matrices on the vertical electronic transitions of this molecule. The most suitable potential was chosen to perform relativistic wave function theory in density functional theory calculations to study the vertical electronic spectra of the CUO and CUONg4 with the IHFSCC-SD method.

  14. Formation and Fragmentation of Protonated Molecules after Ionization of Amino Acid and Lactic Acid Clusters by Collision with Ions in the Gas Phase.

    PubMed

    Poully, Jean-Christophe; Vizcaino, Violaine; Schwob, Lucas; Delaunay, Rudy; Kocisek, Jaroslav; Eden, Samuel; Chesnel, Jean-Yves; Méry, Alain; Rangama, Jimmy; Adoui, Lamri; Huber, Bernd

    2015-08-03

    Collisions between O(3+) ions and neutral clusters of amino acids (alanine, valine and glycine) as well as lactic acid are performed in the gas phase, in order to investigate the effect of ionizing radiation on these biologically relevant molecular systems. All monomers and dimers are found to be predominantly protonated, and ab initio quantum-chemical calculations on model systems indicate that for amino acids, this is due to proton transfer within the clusters after ionization. For lactic acid, which has a lower proton affinity than amino acids, a significant non-negligible amount of the radical cation monomer is observed. New fragment-ion channels observed from clusters, as opposed to isolated molecules, are assigned to the statistical dissociation of protonated molecules formed upon ionization of the clusters. These new dissociation channels exhibit strong delayed fragmentation on the microsecond time scale, especially after multiple ionization. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Effective method to compute vibrationally resolved optical spectra of large molecules at finite temperature in the gas phase and in solution.

    PubMed

    Santoro, Fabrizio; Lami, Alessandro; Improta, Roberto; Barone, Vincenzo

    2007-05-14

    The authors present a new method for the computation of vibrationally resolved optical spectra of large molecules, including the Duschinsky rotation of the normal modes and the effect of thermal excitation. The method automatically selects the relevant vibronic contributions to the spectrum, independently of their frequency, and it is able to provide fully converged spectra with moderate computational times, both in vacuo and in solution. By describing the electronic states in the frame of the density functional theory and its time-dependent extension, they computed the room temperature absorption spectra of coumarin C153 and trans-stilbene in cyclohexane and the phosphorescence spectrum of porphyrazine in gas phase, showing that the method is fast and efficient. The comparison with experiment for trans-stilbene and coumarin C153 is very satisfactory, confirming the progress made toward a reliable method for the computation and interpretation for the optical spectra of large molecules.

  16. Laboratory Studies on the Formation of Carbon-Bearing Molecules in Extraterrestrial Environments: From the Gas Phase to the Solid State

    NASA Technical Reports Server (NTRS)

    Jamieson, C. S.; Guo, Y.; Gu, X.; Zhang, F.; Bennett, C. J.; Kaiser, R. I.

    2006-01-01

    A detailed knowledge of the formation of carbon-bearing molecules in interstellar ices and in the gas phase of the interstellar medium is of paramount interest to understand the astrochemical evolution of extraterrestrial environments (1). This research also holds strong implications to comprehend the chemical processing of Solar System environments such as icy planets and their moons together with the atmospheres of planets and their satellites (2). Since the present composition of each interstellar and Solar System environment reflects the matter from which it was formed and the processes which have changed the chemical nature since the origin (solar wind, planetary magnetospheres, cosmic ray exposure, photolysis, chemical reactions), a detailed investigation of the physicochemical mechanisms altering the pristine environment is of paramount importance to grasp the contemporary composition. Once these underlying processes have been unraveled, we can identify those molecules, which belonged to the nascent setting, distinguish molecular species synthesized in a later stage, and predict the imminent chemical evolution of, for instance, molecular clouds. Laboratory experiments under controlled physicochemical conditions (temperature, pressure, chemical composition, high energy components) present ideal tools for simulating the chemical evolution of interstellar and Solar System environments. Here, laboratory experiments can predict where and how (reaction mechanisms; chemicals necessary) in extraterrestrial environments and in the interstellar medium complex, carbon bearing molecules can be formed on interstellar grains and in the gas phase. This paper overviews the experimental setups utilized in our laboratory to mimic the chemical processing of gas phase and solid state (ices) environments. These are a crossed molecular beams machine (3) and a surface scattering setup (4). We also present typical results of each setup (formation of amino acids, aldehydes, epoxides

  17. Intercomparison of stratospheric water vapor observed by satellite experiments - Stratospheric Aerosol and Gas Experiment II versus Limb Infrared Monitor of the Stratosphere and Atmospheric Trace Molecule Spectroscopy

    NASA Technical Reports Server (NTRS)

    Chiou, E. W.; Mccormick, M. P.; Mcmaster, L. R.; Chu, W. P.; Larsen, J. C.; Rind, D.; Oltmans, S.

    1993-01-01

    A comparison is made of the stratospheric water vapor measurements made by the satellite sensors of the Stratospheric Aerosol and Gas Experiment II (SAGE II), the Nimbus-7 LIMS, and the Spacelab 3 Atmospheric Trace Molecule Spectroscopy (ATMOS) experiment. It was found that, despite differences in the measurement techniques, sampling bias, and observational periods, the three experiments have disclosed a generally consistent pattern of stratospheric water vapor distribution. The only significant difference occurs at high southern altitudes in May below 18 km, where LIMS measurements were 2-3 ppmv greater than those of SAGE II and ATMOS.

  18. Towards reliable modelling of large clusters: on the overall accuracy of the diatomics-in-molecule method for rare gas cluster ions

    NASA Astrophysics Data System (ADS)

    Naumkin, Fedor Yu.; Knowles, Peter J.; Murrell, John N.

    1995-04-01

    The accuracy of the diatomics-in-molecules (DIM) method is examined for the case of rare gas ionic clusters through a series of careful calibration calculations. Ab initio potential energy functions for Rg 3+ and Rg 4+ (RgHe, Ne, Ar) are compared with the DIM model, taking diatomic potentials computed at exactly the same level of ab initio theory as input. For Ne n+, agreement is satisfactory (in most important regions within 0.05 eV), whereas for He n+, large deviations occur.

  19. Towards reliable modelling of large clusters: On the overall accuracy of the diatomics-in-molecule method for rare gas cluster ions

    NASA Astrophysics Data System (ADS)

    Naumkin, Fedor Yu.; Knowles, Peter J.; Murrell, John N.

    1995-04-01

    The accuracy of the diatomics-in-molecules (DIM) method is examined for the case of rare gas ionic clusters through a series of careful calibration calculations. Ab initio potential energy functions for Rg3(+) and Rg4(+) (Rg=He, Ne, Ar) are compared with the DIM model, taking diatomic potentials computed at exactly the same level of ab initio theory as input. For Ne(n)(+) and Ar(n)(+), agreement is satisfactory (in most important regions within 0.05 eV), whereas for He(n)(+), large deviations occur.

  20. Tuning the composition of guest molecules in clathrate hydrates: NMR identification and its significance to gas storage.

    PubMed

    Seo, Yutaek; Lee, Jong-Won; Kumar, Rajnish; Moudrakovski, Igor L; Lee, Huen; Ripmeester, John A

    2009-08-03

    Gas hydrates represent an attractive way of storing large quantities of gas such as methane and carbon dioxide, although to date there has been little effort to optimize the storage capacity and to understand the trade-offs between storage conditions and storage capacity. In this work, we present estimates for gas storage based on the ideal structures, and show how these must be modified given the little data available on hydrate composition. We then examine the hypothesis based on solid-solution theory for clathrate hydrates as to how storage capacity may be improved for structure II hydrates, and test the hypothesis for a structure II hydrate of THF and methane, paying special attention to the synthetic approach used. Phase equilibrium data are used to map the region of stability of the double hydrate in P-T space as a function of the concentration of THF. In situ high-pressure NMR experiments were used to measure the kinetics of reaction between frozen THF solutions and methane gas, and (13)C MAS NMR experiments were used to measure the distribution of the guests over the cage sites. As known from previous work, at high concentrations of THF, methane only occupies the small cages in structure II hydrate, and in accordance with the hypothesis posed, we confirm that methane can be introduced into the large cage of structure II hydrate by lowering the concentration of THF to below 1.0 mol %. We note that in some preparations the cage occupancies appear to fluctuate with time and are not necessarily homogeneous over the sample. Although the tuning mechanism is generally valid, the composition and homogeneity of the product vary with the details of the synthetic procedure. The best results, those obtained from the gas-liquid reaction, are in good agreement with thermodynamic predictions; those obtained for the gas-solid reaction do not agree nearly as well.

  1. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1996-01-01

    Part of the Annual Commodities Review 1995. Production of construction aggregates such as crushed stone and construction sand and gravel showed a marginal increase in 1995. Most of the 1995 increases were due to funding for highway construction work. The major areas of concern to the industry included issues relating to wetlands classification and the classification of crystalline silica as a probable human carcinogen. Despite this, an increase in demand is anticipated for 1996.

  2. Construction aggregates

    USGS Publications Warehouse

    Nelson, T.I.; Bolen, W.P.

    2007-01-01

    Construction aggregates, primarily stone, sand and gravel, are recovered from widespread naturally occurring mineral deposits and processed for use primarily in the construction industry. They are mined, crushed, sorted by size and sold loose or combined with portland cement or asphaltic cement to make concrete products to build roads, houses, buildings, and other structures. Much smaller quantities are used in agriculture, cement manufacture, chemical and metallurgical processes, glass production and many other products.

  3. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1993-01-01

    Part of a special section on the market performance of industrial minerals in 1992. Production of construction aggregates increased by 4.6 percent in 1992. This increase was due, in part, to the increased funding for transportation and infrastructure projects. The U.S. produced about 1.05 Gt of crushed stone and an estimated 734 Mt of construction sand and gravel in 1992. Demand is expected to increase by about 5 percent in 1993.

  4. 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

  5. Gas-phase dissociation of ionic liquid aggregates studied by electrospray ionisation mass spectrometry and energy-variable collision induced dissociation.

    PubMed

    Fernandes, Ana M; Coutinho, João A P; Marrucho, Isabel M

    2009-01-01

    Positive singly charged ionic liquid aggregates [(C(n)mim)(m+1)(BF(4))(m)](+) (mim = 3-methylimidazolium; n = 2, 4, 8 and 10) and [(C(4)mim)(m+1)(A)(m)](+) (A = Cl(-), BF(4) (-), PF(6) (-), CF(3)SO(3) (-) and (CF(3)SO(2))(2)N(-)) were investigated by electrospray ionisation mass spectrometry and energy-variable collision induced dissociation. The electrospray ionisation mass spectra (ESI-MS) showed the formation of an aggregate with extra stability for m = 4 for all the ionic liquids with the exception of [C(4)mim][CF(3)SO(3)]. ESI-MS-MS and breakdown curves of aggregate ions showed that their dissociation occurred by loss of neutral species ([C(n)mim][A])(a) with a >or= 1. Variable-energy collision induced dissociation of each aggregate from m = 1 to m = 8 for all the ionic liquids studied enabled the determination of E(cm, 1/2) values, whose variation with m showed that the monomers were always kinetically much more stable than the larger aggregates, independently of the nature of cation and anion. The centre-of-mass energy values correlate well with literature data on ionic volumes and interaction and hydrogen bond energies.

  6. Production of hyperpolarized H_{2} molecules from H[over →] atoms in gas-storage cells.

    PubMed

    Engels, R; Gaißer, M; Gorski, R; Grigoryev, K; Mikirtychyants, M; Nass, A; Rathmann, F; Seyfarth, H; Ströher, H; Weiss, P; Kochenda, L; Kravtsov, P; Trofimov, V; Tschernov, N; Vasilyev, A; Vznuzdaev, M; Schieck, H Paetz Gen

    2015-09-11

    The preservation of the nuclear polarization of hydrogen atoms during the recombination to molecules was observed on different surface materials in the temperature range from 45 to 100 K and for magnetic fields up to 1 T. On a gold and a fused quartz surface, the expected molecular polarization of about 50% or lower of the atomic polarization was measured, while a surface layer of perfluoropolyether (Fomblin) shows a nearly complete preservation (at least 97%) of the atomic polarization during the recombination process. Further experiments have the possibility of storing polarized deuterium molecules and to use them in nuclear-fusion installations. Another application might be the production of polarized substances for enhanced NMR techniques.

  7. In situ growth of metal-organic framework thin films with gas sensing and molecule storage properties.

    PubMed

    Li, Wei-Jin; Gao, Shui-Ying; Liu, Tian-Fu; Han, Li-Wei; Lin, Zu-Jin; Cao, Rong

    2013-07-09

    New porous metal-organic framework (MOF) films based on the flexible ligand 1,3,5-tris[4-(carboxyphenyl)oxamethyl]-2,4,6-trimethylbenzene (H3TBTC) were fabricated on α-Al2O3 substrates under solvent thermal conditions. The factors affecting the fabrication of films, such as the temperature of pre-activation and the dosage of the reagents, were investigated. Tuning the subtle factors on film fabrications, a series of MOF thin films with different morphologies and grain sizes were prepared. The morphology and grain size of the films are monitored by scanning electron microscopy (SEM). X-ray diffraction (XRD) and attenuated total reflection infrared (ATR-IR) were also used to characterize the MOF films. The results indicate that the temperature of pre-activation and the dosage of the reagents are the key parameters during the process of film formation. The properties of the films, especially the sensing and sorption behavior, have been studied by an optical digital cameral and ultraviolet-visible (UV-vis) spectra. The evidence shows that the films are sensitive to small organic molecules, such as methanol and pyridine. Meanwhile, the films can adsorb small dye molecules. Thus, the films may have potential applications in either organic vapor sensing or storage of small dye molecules.

  8. Benchmarking Time-Dependent Density Functional Theory for Excited State Geometries of Organic Molecules in Gas-Phase and in Solution.

    PubMed

    Guido, Ciro A; Knecht, Stefan; Kongsted, Jacob; Mennucci, Benedetta

    2013-05-14

    We analyze potentials and limits of the Time-Dependent Density Functional Theory (TD-DFT) approach for the determination of excited-state geometries of organic molecules in gas-phase and in solution. Three very popular DFT exchange-correlation functionals, two hybrids (B3LYP and PBE0) and one long-range corrected (CAM-B3LYP), are here investigated, and the results are compared to the correlated RI-CC2 wave function approach. Solvent effects are further analyzed by means of a polarizable continuum model. A total of 15 organic chromophores (including both small molecules and larger push-pull systems) are considered as prototypes of n → π* and π → π* singlet excitations. Our analysis allows to point out specific correlations between the accuracy of the various functionals and the type of excitation and/or the type of chemical bonds involved. We find that while the best ground-state geometries are obtained with PBE0 and B3LYP, CAM-B3LYP yields the most accurate description of electronic and geometrical characteristics of excited states, both in gas-phase and in solution.

  9. Gas-phase reactivity of the Ti8C12+ met-car with triatomic sulfur-containing molecules: CS2, SCO, and SO2.

    PubMed

    Lightstone, James M; Patterson, Melissa J; Liu, Ping; White, Michael G

    2006-03-16

    Gas-phase Ti(x)C(y)+ clusters (x/y = 3/5, 4/7, 5/9, 6/9, 7/12, 8/12, 9/12) including the magic Ti8C12+ (met-car) have been produced by reactive sputtering with a magnetron cluster source. The gas-phase reactivity of the met-car with SCO, CS2, and SO2 was investigated in a hexapole collision cell by way of tandem mass spectrometry. Results indicate an increase in activity as the oxygen-to-sulfur ratio increases (SO2 > SCO > CS2) with products ranging from association to break down of the met-car cluster. Trends in the mass spectra also indicate SCO and CS2 may bond to the met-car in a unique way not observed in previous reactivity studies on Ti8C12+. To investigate this, several possible single molecule-cluster bonding configurations were calculated with density functional theory. The results indicate that bridge bonding of the intact molecules is energetically preferred. In addition, the energy barriers and transition states leading to dissociation products were calculated and the trends are found to be in qualitative agreement with experiment. The effects of the different types of bonding and number of adsorbed species on the reactivity of the met-car along with proposed reaction mechanisms for product formation are also discussed.

  10. Combining density functional theory (DFT) and collision cross-section (CCS) calculations to analyze the gas-phase behaviour of small molecules and their protonation site isomers.

    PubMed

    Boschmans, Jasper; Jacobs, Sam; Williams, Jonathan P; Palmer, Martin; Richardson, Keith; Giles, Kevin; Lapthorn, Cris; Herrebout, Wouter A; Lemière, Filip; Sobott, Frank

    2016-06-20

    Electrospray ion mobility-mass spectrometry (IM-MS) data show that for some small molecules, two (or even more) ions with identical sum formula and mass, but distinct drift times are observed. In spite of showing their own unique and characteristic fragmentation spectra in MS/MS, no configurational or constitutional isomers are found to be present in solution. Instead the observation and separation of such ions appears to be inherent to their gas-phase behaviour during ion mobility experiments. The origin of multiple drift times is thought to be the result of protonation site isomers ('protomers'). Although some important properties of protomers have been highlighted by other studies, correlating the experimental collision cross-sections (CCSs) with calculated values has proven to be a major difficulty. As a model, this study uses the pharmaceutical compound melphalan and a number of related molecules with alternative (gas-phase) protonation sites. Our study combines density functional theory (DFT) calculations with modified MobCal methods (e.g. nitrogen-based Trajectory Method algorithm) for the calculation of theoretical CCS values. Calculated structures can be linked to experimentally observed signals, and a strong correlation is found between the difference of the calculated dipole moments of the protomer pairs and their experimental CCS separation.

  11. Different catalytic effects of a single water molecule: the gas-phase reaction of formic acid with hydroxyl radical in water vapor.

    PubMed

    Anglada, Josep M; Gonzalez, Javier

    2009-12-07

    The effect of a single water molecule on the reaction mechanism of the gas-phase reaction between formic acid and the hydroxyl radical was investigated with high-level quantum mechanical calculations using DFT-B3LYP, MP2 and CCSD(T) theoretical approaches in concert with the 6-311+G(2df,2p) and aug-cc-pVTZ basis sets. The reaction between HCOOH and HO has a very complex mechanism involving a proton-coupled electron transfer process (pcet), two hydrogen-atom transfer reactions (hat) and a double proton transfer process (dpt). The hydroxyl radical predominantly abstracts the acidic hydrogen of formic acid through a pcet mechanism. A single water molecule affects each one of these reaction mechanisms in different ways, depending on the way the water interacts. Very interesting is also the fact that our calculations predict that the participation of a single water molecule results in the abstraction of the formyl hydrogen of formic acid through a hydrogen atom transfer process (hat).

  12. Gas-phase electrophoretic molecular mobility analysis of size and stoichiometry of complexes of a common cold virus with antibody and soluble receptor molecules.

    PubMed

    Laschober, Christian; Wruss, Juergen; Blaas, Dieter; Szymanski, Wladyslaw W; Allmaier, Günter

    2008-03-15

    Attachment of a nonaggregating monoclonal antibody and of a soluble recombinant receptor molecule to the icosahedral nonenveloped human rhinovirus serotype 2 was studied with a nanoelectrospray ionization gas-phase electrophoretic molecular mobility analyzer (nESI-GEMMA). The virus mass, as determined via nESI-GEMMA, was within instrument accuracy (+/-6%) close to the theoretical value (8 x 10(6) Da) calculated from the sum of all constituents of one virus particle (60 copies of each of the four viral capsid proteins, the RNA genome, and one copy of the RNA-linked protein VpG). The formation of virus-antibody complexes of different stoichiometries (up to a mass 12.5 x 10(6) Da corresponding to 30 attached antibodies) and virus-receptor complexes (up to a mass 8.8 x 10(6) Da corresponding to 12 attached receptor molecules) was monitored. Via the volume derived from the electrophoretic mobility diameter (EMD), the stoichiometry of the HRV complexes was calculated. The accuracy of the EMD was within +/-0.5 nm, which corresponds to an accuracy of +/-4 antibodies and +/-5 receptor molecules in the respective complexes. For the first time, we here demonstrate the use of nESI-GEMMA for the analysis of the size and stoichiometry of biomolecules in high-order complexes in real time under normal pressure conditions.

  13. A Robust Highly Interpenetrated Metal−Organic Framework Constructed from Pentanuclear Clusters for Selective Sorption of Gas Molecules

    SciTech Connect

    Zhang, Zhangjing; Xiang, Shengchang; Chen, Yu-Sheng; Ma, Shengqian; Lee, Yongwoo; Phely-Bobin, Thomas; Chen, Banglin

    2010-10-22

    A three-dimensional microporous metal-organic framework, Zn{sub 5}(BTA){sub 6}(TDA){sub 2} {center_dot} 15DMF {center_dot} 8H{sub 2}O (1; HBTA = 1,2,3-benzenetriazole; H{sub 2}TDA = thiophene-2,5-dicarboxylic acid), comprising pentanuclear [Zn{sub 5}] cluster units, was obtained through an one-pot solvothermal reaction of Zn(NO{sub 3}){sub 2}, 1,2,3-benzenetriazole, and thiophene-2,5-dicarboxylate. The activated 1 displays type-I N{sub 2} gas sorption behavior with a Langmuir surface area of 607 m{sup 2} g{sup -1} and exhibits interesting selective gas adsorption for C{sub 2}H{sub 2}/CH{sub 4} and CO{sub 2}/CH{sub 4}.

  14. Aggregation and Interface Behaviour of Carotenoids

    NASA Astrophysics Data System (ADS)

    Köhn, Sonja; Kolbe, Henrike; Korger, Michael; Köpsel, Christian; Mayer, Bernhard; Auweter, Helmut; Lüddecke, Erik; Bettermann, Hans; Martin, Hans-Dieter

    Molecular aggregates attract considerable attention, as they bridge the gap between the physics of single molecules and structurally ordered crystals. Molecular self-assembly in biological systems is highly specific and fundamentally important for correct functioning in living organisms.

  15. Genetics Home Reference: tubular aggregate myopathy

    MedlinePlus

    ... in both type I and type II fibers, forming clumps of tube-like structures called tubular aggregates. ... Hyun C, Woo JS, Park CS, Kim do H, Lee EH. Stromal interaction molecule 1 (STIM1) regulates ...

  16. Adsorption of gas molecules on graphene-like InN monolayer: A first-principle study

    NASA Astrophysics Data System (ADS)

    Sun, Xiang; Yang, Qun; Meng, Ruishen; Tan, Chunjian; Liang, Qiuhua; Jiang, Junke; Ye, Huaiyu; Chen, Xianping

    2017-05-01

    Using first-principles calculation within density functional theory (DFT), we study the gas (CO, NH3, H2S, NO2, NO, SO2) adsorption properties on the surface of single-layer indium nitride (InN). Four different adsorption sites (Bridge, In, N, Hollow) are chosen to explore the most sensitive adsorption site. On the basis of the adsorption energy, band gap and charge transfer, we find that the most energetic favourable site is changeable between In site and N site for different gases. Moreover, our results reveal that InN is sensitive to NH3, SO2, H2S and NO2, by a physisorption or a chemisorption nature. We also perform a perpendicular electric field to the system and find that the applied electric field has a significant effect for the adsorption process. Besides, we also observed the desorption effects on NH3 adsorbed at the hollow site of InN when the electric field applied. In addition, the optical properties of InN monolayer affected by different gases are also discussed. Most of the gas adsorptions will cause the inhibition of light adsorption while the others can reduce the work function or enhance the adsorption ability in visible region. Our theoretical results indicate that monolayer InN is a promising candidate for gas sensing applications.

  17. Periodic DFT study of acidic trace atmospheric gas molecule adsorption on Ca- and Fe-doped MgO(001) surface basic sites.

    PubMed

    Baltrusaitis, Jonas; Hatch, Courtney; Orlando, Roberto

    2012-08-02

    The electronic properties of undoped and Ca- or Fe-doped MgO(001) surfaces, as well as their propensity toward atmospheric acidic gas (CO2, SO2, and NO2) uptake was investigated with an emphasis on gas adsorption on the basic MgO oxygen surface sites, O(surf), using periodic density functional theory (DFT) calculations. Adsorption energy calculations show that MgO doping will provide stronger interactions of the adsorbate with the O(surf) sites than the undoped MgO for a given adsorbate molecule. Charge transfer from the iron atom in Fe-doped MgO(001) to NO2 was shown to increase the binding interaction between adsorbate by an order of magnitude, when compared to that of undoped and Ca-doped MgO(001) surfaces. Secondary binding interactions of adsorbate oxygen atoms were observed with surface magnesium sites at distances close to those of the Mg-O bond within the crystal. These interactions may serve as a preliminary step for adsorption and facilitate further adsorbate transformations into other binding configurations. Impacts on global atmospheric chemistry are discussed as these adsorption phenomena can affect atmospheric gas budgets via altered partitioning and retention on mineral aerosol surfaces.

  18. Noble gas-actinide complexes of the CUO molecule with multiple Ar, Kr, and Xe atoms in noble-gas matrices.

    PubMed

    Andrews, Lester; Liang, Binyong; Li, Jun; Bursten, Bruce E

    2003-03-12

    Laser-ablated U atoms react with CO in excess argon to produce CUO, which is trapped in a triplet state in solid argon at 7 K, based on agreement between observed and relativistic density functional theory (DFT) calculated isotopic frequencies ((12)C(16)O, (13)C(16)O, (12)C(18)O). This observation contrasts a recent neon matrix investigation, which trapped CUO in a linear singlet state calculated to be about 1 kcal/mol lower in energy. Experiments with krypton and xenon give results analogous to those with argon. Similar work with dilute Kr and Xe in argon finds small frequency shifts in new four-band progressions for CUO in the same triplet states trapped in solid argon and provides evidence for four distinct CUO(Ar)(4-n)(Ng)(n) (Ng = Kr, Xe, n = 1, 2, 3, 4) complexes for each Ng. DFT calculations show that successively higher Ng complexes are responsible for the observed frequency progressions. This work provides the first evidence for noble gas-actinide complexes, and the first example of neutral complexes with four noble gas atoms bonded to one metal center.

  19. Protein aggregation: From background to inhibition strategies.

    PubMed

    Alam, Parvez; Siddiqi, Khursheed; Chturvedi, Sumit Kumar; Khan, Rizwan Hasan

    2017-10-01

    The aggregation of specific proteins is hypothesized to cause several pathological conditions, which are collectively known as amyloid disorders. The aggregation of peptides and proteins is mainly associated with the perturbation of cellular function, ageing and various human disorders. Mounting evidence suggests that protein aggregation is often caused by mutation, environmental stress or the cellular response to an imbalanced protein homeostasis. This review summarizes the background information on the protein folding, misfolding, cellular strategies against protein aggregation, factors affecting protein aggregation and mechanism of protein aggregation. We then focus on various inhibitors for protein aggregation both in vitro and in vivo. We conclude with a perspective that better therapeutics could be developed by using cocktail of small molecule inhibitors for the treatment of amyloid diseases. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Controlled growth of conical nickel oxide nanocrystals and their high performance gas sensing devices for ammonia molecule detection.

    PubMed

    Wang, Jian; Yang, Fan; Wei, Xiaowei; Zhang, Yafei; Wei, Liangming; Zhang, Jianjun; Tang, Qifeng; Guo, Biao; Xu, Lei

    2014-08-21

    NiO nanocones with good symmetry and highly ordered structure on NiO foil substrate have been successfully fabricated via a facile wet chemical approach combined with subsequent high temperature oxidation. These organized conical superstructures grow only along a certain direction and be controlled via the self-assembly and oriented attachment of a nucleus, which mainly rely on the similar surface energies and the extent of lattice matching of the oriented attached surfaces. During high temperature oxidation, the electric field created via the Ni(2+) and O(2-) facilitates Ni(2+) diffusion outward along the grain boundaries and O(2-) diffusion inward toward to meet the Ni(2+) ions, forming NiO. The as-grown NiO nanocones are 50-350 nm in diameter and 50-400 nm in height. The tip diameter of the nanocone is about 30 nm and the apex angle of the nanocone is about 40°. Meanwhile, we systematically investigated the gas sensing properties of the sensors based on the as-fabricated NiO foil covered with nanocone arrays for ammonia detection at room temperature. The results show that the gas sensing devices have outstanding sensitivity, reproducibility and selectivity, which are mainly because of the excellent connection between the NiO sensing materials and the Au electrodes, the strong electron donating ability of ammonia and the large active surface of selective physisorption for ammonia.

  1. Coherent Rayleigh-Brillouin scattering for in situ detection of nanoparticles and large molecules in gas and plasma

    NASA Astrophysics Data System (ADS)

    Gerakis, A.; Shneider, M. N.; Stratton, B. C.; Santra, B.; Car, R.; Raitses, Y.

    2016-09-01

    Laser-based diagnostics methods, such as Spontaneous and Coherent Rayleigh and Rayleigh-Brillouin scattering (SRBS and CRBS), can be used for in-situ detection and characterization of nanoparticle shape and size as well as their concentration in an inert gas atmosphere. We recently developed and tested this advanced diagnostic at PPPL. It was shown that the signal intensity of the CRBS signal depends on the gas-nanoparticle mixture composition, density and the polarizabilities of the mixture components. The measured results agree well with theoretical predictions of Refs. In this work, we report the application of this diagnostic to monitor nucleation and growth of nanoparticles in a carbon arc discharge. In support of these measurements, A time-dependent density functional theory was used to compute the frequency-dependent polarizabilities of various nanostructures in order to predict the corresponding Rayleigh scattering intensities as well as light depolarization. Preliminary results of measurements demonstrate that CRBS is capable to detect nanoparticles in volume. This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division.

  2. Interactions of neutral and singly charged keV atomic particles with gas-phase adenine molecules

    NASA Astrophysics Data System (ADS)

    Alvarado, Fresia; Bari, Sadia; Hoekstra, Ronnie; Schlathölter, Thomas

    2007-07-01

    KeV atomic particles traversing biological matter are subject to charge exchange and screening effects which dynamically change this particle's effective charge. The understanding of the collision cascade along the track thus requires a detailed knowledge of the interaction dynamics of radiobiologically relevant molecules, such as DNA building blocks or water, not only with ionic but also with neutral species. We have studied collisions of keV H+, He+, and C+ ions and H0, He0, and C0 atoms with the DNA base adenine by means of high resolution time-of-flight spectrometry. For H0 and H+ we find qualitatively very similar fragmentation patterns, while for carbon, strong differences are observed when comparing C0 and C+ impact. For collisions with He0 and He+ projectiles, a pronounced delayed fragmentation channel is observed, which has not been reported before.

  3. Effects of non-local exchange on core level shifts for gas-phase and adsorbed molecules

    NASA Astrophysics Data System (ADS)

    Van den Bossche, M.; Martin, N. M.; Gustafson, J.; Hakanoglu, C.; Weaver, J. F.; Lundgren, E.; Grönbeck, H.

    2014-07-01

    Density functional theory calculations are often used to interpret experimental shifts in core level binding energies. Calculations based on gradient-corrected (GC) exchange-correlation functionals are known to reproduce measured core level shifts (CLS) of isolated molecules and metal surfaces with reasonable accuracy. In the present study, we discuss a series of examples where the shifts calculated within a GC-functional significantly deviate from the experimental values, namely the CLS of C 1s in ethyl trifluoroacetate, Pd 3d in PdO and the O 1s shift for CO adsorbed on PdO(101). The deviations are traced to effects of the electronic self-interaction error with GC-functionals and substantially better agreements between calculated and measured CLS are obtained when a fraction of exact exchange is used in the exchange-correlation functional.

  4. The IRAM-30 m line survey of the Horsehead PDR. III. High abundance of complex (iso-)nitrile molecules in UV-illuminated gas

    NASA Astrophysics Data System (ADS)

    Gratier, P.; Pety, J.; Guzmán, V.; Gerin, M.; Goicoechea, J. R.; Roueff, E.; Faure, A.

    2013-09-01

    Context. Complex (iso-)nitrile molecules, such as CH3CN and HC3N, are relatively easily detected in our Galaxy and in other galaxies. Aims: We aim at constraining their chemistry through observations of two positions in the Horsehead edge: the photo-dissociation region (PDR) and the dense, cold, and UV-shielded core just behind it. Methods: We systematically searched for lines of CH3CN, HC3N, C3N, and some of their isomers in our sensitive unbiased line survey at 3, 2, and 1 mm. We stacked the lines of C3N to improve the detectability of this species. We derived column densities and abundances through Bayesian analysis using a large velocity gradient radiative transfer model. Results: We report the first clear detection of CH3NC at millimeter wavelength. We detected 17 lines of CH3CN at the PDR and 6 at the dense core position, and we resolved its hyperfine structure for 3 lines. We detected 4 lines of HC3N, and C3N is clearly detected at the PDR position. We computed new electron collisional rate coefficients for CH3CN, andwe found that including electron excitation reduces the derived column density by 40% at the PDR position, where the electron density is 1-5 cm-3. While CH3CN is 30 times more abundant in the PDR (2.5 × 10-10) than in the dense core (8 × 10-12), HC3N has similar abundance at both positions (8 × 10-12). The isomeric ratio CH3NC/CH3CN is 0.15 ± 0.02. Conclusions: The significant amount of complex (iso-)nitrile molecule in the UV illuminated gas is puzzling as the photodissociation is expected to be efficient. This is all the more surprising in the case of CH3CN, which is 30 times more abundant in the PDR than in the dense core. In this case, pure gas phase chemistry cannot reproduce the amount of CH3CN observed in the UV-illuminated gas. We propose that CH3CN gas phase abundance is enhanced when ice mantles of grains are destroyed through photo-desorption or thermal-evaporation in PDRs, and through sputtering in shocks. Based on observations

  5. Evaluation of various silicon-and boron-containing compounds for the detection of phosphorylation in peptides via gas-phase ion-molecule reactions.

    PubMed

    Piatkivskyi, Andrii; Pyatkivskyy, Yuriy; Ryzhov, Victor

    2014-01-01

    Gas-phase ion-molecule reactions [IMR] of various boron- and silicon-containing neutrals were investigated as a potential route for detecting phosphorylation within peptides in the negative ion mode. Trimethyl borate (TMB), triethyl borate (TEB) and N,O- Bis(trimethylsilyl)acetamide (TMSA), unlike diethylmethoxyborane (DEMB), diisopropoxymethylborane [DiPMB] and chlorotrimethylsi- Lane (TMSCIL], reacted differently if a phosphate moiety was present and thus are suitable to detect phosphorylation. During multistage collision-induced dissociation experiments of the reaction products of IMR with TMB and TEB, the [LSsF - 4H + B]- ion formed a modified y2 fragment allowing the phosphorylation site to be assigned, unlike reaction products of DEMB and DiPMB which lost both the phos- phoric acid and the boron-containing moiety.

  6. Interactions of neutral and singly charged keV atomic particles with gas-phase adenine molecules

    SciTech Connect

    Alvarado, Fresia; Bari, Sadia; Hoekstra, Ronnie; Schlathoelter, Thomas

    2007-07-21

    KeV atomic particles traversing biological matter are subject to charge exchange and screening effects which dynamically change this particle's effective charge. The understanding of the collision cascade along the track thus requires a detailed knowledge of the interaction dynamics of radiobiologically relevant molecules, such as DNA building blocks or water, not only with ionic but also with neutral species. We have studied collisions of keV H{sup +}, He{sup +}, and C{sup +} ions and H{sup 0}, He{sup 0}, and C{sup 0} atoms with the DNA base adenine by means of high resolution time-of-flight spectrometry. For H{sup 0} and H{sup +} we find qualitatively very similar fragmentation patterns, while for carbon, strong differences are observed when comparing C{sup 0} and C{sup +} impact. For collisions with He{sup 0} and He{sup +} projectiles, a pronounced delayed fragmentation channel is observed, which has not been reported before.

  7. Hydrogen gas acts as a novel bioactive molecule in enhancing plant tolerance to paraquat-induced oxidative stress via the modulation of heme oxygenase-1 signalling system.

    PubMed

    Jin, Qijiang; Zhu, Kaikai; Cui, Weiti; Xie, Yanjie; Han, Bin; Shen, Wenbiao

    2013-05-01

    Hydrogen gas (H2) was recently proposed as a novel antioxidant and signalling molecule in animals. However, the physiological roles of H2 in plants are less clear. Here, we showed that exposure of alfalfa seedlings to paraquat stress increased endogenous H2 production. When supplied with exogenous H2 or the heme oxygenase-1 (HO-1)-inducer hemin, alfalfa plants displayed enhanced tolerance to oxidative stress induced by paraquat. This was evidenced by alleviation of the inhibition of root growth, reduced lipid peroxidation and the decreased hydrogen peroxide and superoxide anion radical levels. The activities and transcripts of representative antioxidant enzymes were induced after exposure to either H2 or hemin. Further results showed that H2 pretreatment could dramatically increase levels of the MsHO-1 transcript, levels of the protein it encodes and HO-1 activity. The previously mentioned H2-mediated responses were specific for HO-1, given that the potent HO-1-inhibitor counteracted the effects of H2. The effects of H2 were reversed after the addition of an aqueous solution of 50% carbon monoxide (CO). We also discovered enhanced tolerance of multiple environmental stresses after plants were pretreated with H2 . Together, these results suggested that H2 might function as an important gaseous molecule that alleviates oxidative stress via HO-1 signalling. © 2012 Blackwell Publishing Ltd.

  8. Mechanism for the atomic layer deposition of copper using diethylzinc as the reducing agent: a density functional theory study using gas-phase molecules as a model.

    PubMed

    Dey, Gangotri; Elliott, Simon D

    2012-09-06

    We present theoretical studies based on first-principles density functional theory calculations for the possible gas-phase mechanism of the atomic layer deposition (ALD) of copper by transmetalation from common precursors such as Cu(acac)(2), Cu(hfac)(2), Cu(PyrIm(R))(2) with R = (i)Pr and Et, Cu(dmap)(2), and CuCl(2) where diethylzinc acts as the reducing agent. An effect on the geometry and reactivity of the precursors due to differences in electronegativity, steric hindrance, and conjugation present in the ligands was observed. Three reaction types, namely, disproportionation, ligand exchange, and reductive elimination, were considered that together comprise the mechanism for the formation of copper in its metallic state starting from the precursors. A parallel pathway for the formation of zinc in its metallic form was also considered. The model Cu(I) molecule Cu(2)L(2) was studied, as Cu(I) intermediates at the surface play an important role in copper deposition. Through our study, we found that accumulation of an LZnEt intermediate results in zinc contamination by the formation of either Zn(2)L(2) or metallic zinc. Ligand exchange between Cu(II) and Zn(II) should proceed through a Cu(I) intermediate, as otherwise, it would lead to a stable copper molecule rather than copper metal. Volatile ZnL(2) favors the ALD reaction, as it carries the reaction forward.

  9. A theoretical study of the XP and NEXAFS spectra of alanine: gas phase molecule, crystal, and adsorbate at the ZnO(10 ̅10) surface.

    PubMed

    Gao, You Kun; Traeger, Franziska; Kotsis, Konstantinos; Staemmler, Volker

    2011-06-14

    The adsorption of alanine on the mixed-terminated ZnO(10 ̅10) surface is studied by means of quantum-chemical ab initio calculations. Using a finite cluster model and the adsorption geometry as obtained both by periodic CPMD and embedded cluster calculations, the C1s, N1s and O1s X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectra are calculated for single alanine molecules on ZnO(10 ̅10). These spectra are compared with the spectra calculated for alanine in the gas phase and in its crystalline form and with experimental XPS and NEXAFS data for the isolated alanine molecule and for alanine adsorbed on ZnO(10 ̅10) at multilayer and monolayer coverage. The excellent agreement between the experimental and calculated XP and NEXAFS spectra confirms the calculated adsorption geometry: A single alanine molecule is bound to ZnO(10 ̅10) in a dissociated bidentate form with the two O atoms of the acid group bound to two Zn atoms of the surface and the proton transferred to one O atom of the surface. Other possible structures, such as adsorption of alanine in one of its neutral or zwitterionic forms in which the proton of the -COOH group remains at this group or is transferred to the amino group, can be excluded since they would give rise to quite different XP spectra. In the multilayer coverage regime, on the other hand, alanine is in its crystalline form as is also shown by the analysis of the XP spectra.

  10. The effect of H2O gas on volatilities of planet-forming major elements. I - Experimental determination of thermodynamic properties of Ca-, Al-, and Si-hydroxide gas molecules and its application to the solar nebula

    NASA Technical Reports Server (NTRS)

    Hashimoto, Akihiko

    1992-01-01

    The vapor pressures of Ca(OH)2(g), Al(OH)3(g), and Si(OH)4(g) molecules in equilibrium with solid calcium-, aluminum, and silicon-oxides, respectively, were determined, and were used to derive the heats of formation and entropies of these species, which are expected to be abundant under the currently postulated physical conditions in the primordial solar nebula. These data, in conjunction with thermodynamic data from literature, were used to calculate the relative abundances of M, MO(x), and M(OH)n gas species and relative volatilities of Fe, Mg, Si, Ca, and Al for ranges of temperature, total pressure, and H/O abundance ratio corresponding to the plausible ranges of physical conditions in the solar nebula. The results are used to explain how Ca and Al could have evaporated from Ca,Al-rich inclusions in carbonaceous chondrites, while Si, Mg, and Fe condensed onto them during the preaccretion alteration of CAIs.

  11. The effect of H2O gas on volatilities of planet-forming major elements. I - Experimental determination of thermodynamic properties of Ca-, Al-, and Si-hydroxide gas molecules and its application to the solar nebula

    NASA Technical Reports Server (NTRS)

    Hashimoto, Akihiko

    1992-01-01

    The vapor pressures of Ca(OH)2(g), Al(OH)3(g), and Si(OH)4(g) molecules in equilibrium with solid calcium-, aluminum, and silicon-oxides, respectively, were determined, and were used to derive the heats of formation and entropies of these species, which are expected to be abundant under the currently postulated physical conditions in the primordial solar nebula. These data, in conjunction with thermodynamic data from literature, were used to calculate the relative abundances of M, MO(x), and M(OH)n gas species and relative volatilities of Fe, Mg, Si, Ca, and Al for ranges of temperature, total pressure, and H/O abundance ratio corresponding to the plausible ranges of physical conditions in the solar nebula. The results are used to explain how Ca and Al could have evaporated from Ca,Al-rich inclusions in carbonaceous chondrites, while Si, Mg, and Fe condensed onto them during the preaccretion alteration of CAIs.

  12. Polar vortex dynamics during spring and fall diagnosed using trace gas observations from the Atmospheric Trace Molecule Spectroscopy instrument

    NASA Astrophysics Data System (ADS)

    Manney, G. L.; Michelsen, H. A.; Santee, M. L.; Gunson, M. R.; Irion, F. W.; Roche, A. E.; Livesey, N. J.

    1999-08-01

    Trace gases measured by the Atmospheric Trace Molecule Spectroscopy (ATMOS) instrument during three Atmospheric Laboratory for Applications and Science (ATLAS) space-shuttle missions, in March/April 1992 (AT-1), April 1993 (AT-2), and November 1994 (AT-3) have been mapped into equivalent latitude/potential temperature (EqL/θ) coordinates. The asymmetry of the spring vortices results in coverage of subtropical to polar EqLs. EqL/θ fields of long-lived tracers in spring in both hemispheres show the net effects of descent at high EqL throughout the winter, reflecting strong descent in the upper stratosphere, decreasing descent at lower altitudes, and evidence of greater descent at the edge of the lower stratospheric vortex than in the vortex center; these results are consistent with trajectory calculations examining the history of the air measured by ATMOS in the month prior to each mission. EqL/θ tracer fields, the derived fields CH4-CH4* (CH4* is the expected CH4 calculated from a prescribed relationship with N2O for fall) and NOy-NOy* (analogous to CH4*), and parcel histories all indicate regions of strong mixing in the 1994 Southern Hemisphere (SH) spring vortex above 500 K, with the strongest mixing confined to the vortex edge region between 500 and 700 K, and mixing throughout the Northern Hemisphere (NH) spring vortex in 1993 below about 850 K. Parcel histories indicate mixing of extravortex air with air near the vortex edge below 500 K in the SH but not with air in the vortex core; they show extravortex air mixing well into the vortex above ˜450 K in the NH and into the vortex edge region below. The effects of severe denitrification are apparent in EqL/θ HNO3 in the SH lower stratospheric spring vortex. The morphology of HNO3 in the Arctic spring lower stratospheric vortex is consistent with the effects of descent. EqL/θ fields of ATMOS NOy-NOy* show decreases consistent with the effects of mixing throughout the NH lower stratospheric vortex. The Eq

  13. Molecular Aggregation in Disodium Cromoglycate

    NASA Astrophysics Data System (ADS)

    Singh, Gautam; Agra-Kooijman, D.; Collings, P. J.; Kumar, Satyendra

    2012-02-01

    Details of molecular aggregation in the mesophases of the anti-asthmatic drug disodium cromoglycate (DSCG) have been studied using x-ray synchrotron scattering. The results show two reflections, one at wide angles corresponding to π-π stacking (3.32 å) of molecules, and the other at small angles which is perpendicular to the direction of molecular stacking and corresponds to the distance between the molecular aggregates. The latter varies from 35 - 41 å in the nematic (N) phase and 27 -- 32 å in the columnar (M) phase. The temperature evolution of the stack height, positional order correlations in the lateral direction, and orientation order parameter were determined in the N, M, and biphasic regions. The structure of the N and M phases and the nature of the molecular aggregation, together with their dependence on temperature and concentration, will be presented.

  14. 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)

  15. 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)

  16. Intraspecific Signals Inducing Aggregation in Periplaneta americana (Insecta: Dictyoptera).

    PubMed

    Imen, Saïd; Christian, Malosse; Virginie, Durier; Colette, Rivault

    2015-06-01

    Chemical communication is necessary to induce aggregation and to maintain the cohesion of aggregates in Periplaneta americana (L.) cockroaches. We aimed to identify the chemical message inducing aggregation in this species. Two types of bioassays were used-binary choice tests in Petri dishes and tests in Y-olfactometer. Papers conditioned by direct contact of conspecifics induce aggregation when proposed in binary choice tests and were attractive in a Y-olfactometer. The identification of the molecules present on these conditioned papers indicated that dichloromethane extracts contained mainly cuticular hydrocarbons whereas methanol extracts contained more volatile molecules. Only a mixture of extracts in both solvents induced aggregation. High concentrations of cuticular hydrocarbons are necessary to induce aggregation when presented alone. When presented with volatile molecules present in methanol extracts, low concentrations of cuticular hydrocarbons are sufficient to induce aggregation if they are presented in contact. Among volatile molecules collected on filter paper, a mixture of three compounds-hexadecanoic acid, pentadecanoic acid, and pentaethylene glycol-induced aggregation. Our results provide evidence that aggregation processes in P. americana relies on a dual mechanism: attraction over long distances by three volatile molecules and maintenance on site by contact with cuticular hydrocarbons.

  17. Selective IR multiphoton dissociation of molecules in a pulsed gas-dynamically cooled molecular flow interacting with a solid surface as an alternative to low-energy methods of molecular laser isotope separation

    NASA Astrophysics Data System (ADS)

    Makarov, G. N.; Petin, A. N.

    2016-03-01

    We report the results of studies on the isotope-selective infrared multiphoton dissociation (IR MFD) of SF6 and CF3I molecules in a pulsed, gas-dynamically cooled molecular flow interacting with a solid surface. The productivity of this method in the conditions of a specific experiment (by the example of SF6 molecules) is evaluated. A number of low-energy methods of molecular laser isotope separation based on the use of infrared lasers for selective excitation of molecules are analysed and their productivity is estimated. The methods are compared with those of selective dissociation of molecules in the flow interacting with a surface. The advantages of this method compared to the low-energy methods of molecular laser isotope separation and the IR MPD method in the unperturbed jets and flows are shown. It is concluded that this method could be a promising alternative to the low-energy methods of molecular laser isotope separation.

  18. GEOMETRIC CROSS SECTIONS OF DUST AGGREGATES AND A COMPRESSION MODEL FOR AGGREGATE COLLISIONS

    SciTech Connect

    Suyama, Toru; Wada, Koji; Tanaka, Hidekazu; Okuzumi, Satoshi

    2012-07-10

    Geometric cross sections of dust aggregates determine their coupling with disk gas, which governs their motions in protoplanetary disks. Collisional outcomes also depend on geometric cross sections of initial aggregates. In a previous paper, we performed three-dimensional N-body simulations of sequential collisions of aggregates composed of a number of sub-micron-sized icy particles and examined radii of gyration (and bulk densities) of the obtained aggregates. We showed that collisional compression of aggregates is not efficient and that aggregates remain fluffy. In the present study, we examine geometric cross sections of the aggregates. Their cross sections decrease due to compression as well as to their gyration radii. It is found that a relation between the cross section and the gyration radius proposed by Okuzumi et al. is valid for the compressed aggregates. We also refine the compression model proposed in our previous paper. The refined model enables us to calculate the evolution of both gyration radii and cross sections of growing aggregates and reproduces well our numerical results of sequential aggregate collisions. The refined model can describe non-equal-mass collisions as well as equal-mass cases. Although we do not take into account oblique collisions in the present study, oblique collisions would further hinder compression of aggregates.

  19. Classification and Characterization of Therapeutic Antibody Aggregates

    PubMed Central

    Joubert, Marisa K.; Luo, Quanzhou; Nashed-Samuel, Yasser; Wypych, Jette; Narhi, Linda O.

    2011-01-01

    A host of diverse stress techniques was applied to a monoclonal antibody (IgG2) to yield protein particles with varying attributes and morphologies. Aggregated solutions were evaluated for percent aggregation, particle counts, size distribution, morphology, changes in secondary and tertiary structure, surface hydrophobicity, metal content, and reversibility. Chemical modifications were also identified in a separate report (Luo, Q., Joubert, M. K., Stevenson, R., Narhi, L. O., and Wypych, J. (2011) J. Biol. Chem. 286, 25134–25144). Aggregates were categorized into seven discrete classes, based on the traits described. Several additional molecules (from the IgG1 and IgG2 subtypes as well as intravenous IgG) were stressed and found to be defined with the same classification system. The mechanism of protein aggregation and the type of aggregate formed depends on the nature of the stress applied. Different IgG molecules appear to aggregate by a similar mechanism under the same applied stress. Aggregates created by harsh mechanical stress showed the largest number of subvisible particles, and the class generated by thermal stress displayed the largest number of visible particles. Most classes showed a disruption of the higher order structure, with the degree of disorder depending on the stress process. Particles in all classes (except thermal stress) were at least partially reversible upon dilution in pH 5 buffer. High copper content was detected in isolated metal-catalyzed aggregates, a stress previously shown to produce immunogenic aggregates. In conclusion, protein aggregates can be a very heterogeneous population, whose qualities are the result of the type of stress that was experienced. PMID:21454532

  20. Intercomparison of stratospheric water vapor observed by satellite experiments: Stratospheric Aerosol and Gas Experiment II versus Limb Infrared Monitor of the Stratosphere and Atmospheric Trace Molecule Spectroscopy

    NASA Astrophysics Data System (ADS)

    Chiou, E. W.; McCormick, M. P.; McMaster, L. R.; Chu, W. P.; Larsen, J. C.; Rind, D.; Oltmans, S.

    1993-03-01

    This paper presents a comparison of the stratospheric water vapor measurements made by the satellite-borne sensors the Stratospheric Aerosol and Gas Experiment II (SAGE II), the Nimbus 7 Limb Infrared Monitor of the Stratosphere (LIMS), and the Spacelab 3 Atmospheric Trace Molecule Spectroscopy (ATMOS) experiment. LIMS obtained data for 7 months between November 1978 and May 1979; ATMOS was carried on Shuttle and observed eight profiles from April 30 to May 6, 1985 at approximately 30°N and 50°S; and, SAGE II continues to make measurements since its launch in October 1984. For both 30°N and 50°S in May, the comparisons between SAGE II and ATMOS show agreement within the estimated combined uncertainty of the two experiments. Several important features identified by LIMS observations have been confirmed by SAGE II: a well-developed hygropause in the lower stratosphere at low- to mid-latitudes, a poleward latitudinal gradient, increasing water vapor mixing ratios with altitude in the tropics, and the transport of dry lower stratospheric water vapor upward and southward in May, and upward and northward in November. A detailed comparative study also indicates that the two previously suggested corrections for LIMS, a correction in tropical lower stratosphere due to a positive temperature bias and the correction above 28 km based on improved emissivities will bring LIMS measurements much closer to those of SAGE II. The only significant difference occurs at high southern latitudes in May below 18 km, where LIMS measurements are 2-3 ppmv greater. It should be noted that LIMS observations are from 16 to 50 km, ATMOS from 14 to 86 km, and SAGE II from mid-troposphere to 40 km. With multiyear coverage, SAGE II observations should be useful for studying tropospheric-stratospheric exchange, for stratospheric transport, and for preparing water vapor climatologies for the stratosphere and the upper troposphere.

  1. Intercomparison of stratospheric water vapor observed by satellite experiments: Stratospheric Aerosol and Gas Experiment II versus Limb Infrared Monitor of the Stratosphere and Atmospheric Trace Molecule Spectroscopy

    SciTech Connect

    Chiou, E.W.; Larsen, J.C. ); McCormick, M.P.; McMaster, L.R.; Chu, W.P. ); Rind, D. ); Oltmans, S. )

    1993-03-20

    This paper presents a comparison of the stratospheric water vapor measurements made by the satellite-borne sensors the Stratospheric Aerosol and Gas Experiment II (SAGE II), the Nimbus 7 Limb Infrared Monitor of the Stratosphere (LIMS), and the Spacelab 3 Atmospheric Trace Molecule Spectroscopy (ATMOS) experiment. LIMS obtained data for 7 months between November 1978 and May 1979; ATMOS was carried on Shuttle and observed eight profiles from April 30 to May 6, 1985 at approximately 30[degrees]N and 50[degrees]S; and, SAGE II continues to make measurements since its launch in October 1984. For both 30[degrees]N and 50[degrees]S in May, the comparisons between SAGE II and ATMOS show agreement within the estimated combined uncertainty of the two experiments. Several important features identified by LIMS observations have been confirmed by SAGE II: a well-developed hygropause in the lower stratosphere at low- to mid-latitudes, a poleward latitudinal gradient, increasing water vapor mixing ratios with altitude in the tropics, and the transport of dry lower stratospheric water vapor upward and southward in May, and upward and northward in November. A detailed comparative study also indicates that the two previously suggested corrections for LIMS, a correction in tropical lower stratosphere due to a positive temperature bias and the correction above 28 km based on improved emissivities will bring LIMS measurements much closer to those of SAGE II. The only significant difference occurs at high southern latitudes in May below 18 km, where LIMS measurements are 2-3 ppmv greater. It should be noted that LIMS observations are from 16 to 50 km, ATMOS from 14 to 86 km, and SAGE II from mid-troposphere to 40 km. With multiyear coverage, SAGE II observations should be useful for studying tropospheric-stratospheric exchange, for stratospheric transport, and for preparing water vapor climatologies for the stratosphere and the upper troposphere. 32 refs., 14 figs., 2 tabs.

  2. Oxygen limitation within a bacterial aggregate.

    PubMed

    Wessel, Aimee K; Arshad, Talha A; Fitzpatrick, Mignon; Connell, Jodi L; Bonnecaze, Roger T; Shear, Jason B; Whiteley, Marvin

    2014-04-15

    ABSTRACT Cells within biofilms exhibit physiological heterogeneity, in part because of chemical gradients existing within these spatially structured communities. Previous work has examined how chemical gradients develop in large biofilms containing >10(8) cells. However, many bacterial communities in nature are composed of small, densely packed aggregates of cells (≤ 10(5) bacteria). Using a gelatin-based three-dimensional (3D) printing strategy, we confined the bacterium Pseudomonas aeruginosa within picoliter-sized 3D "microtraps" that are permeable to nutrients, waste products, and other bioactive small molecules. We show that as a single bacterium grows into a maximally dense (10(12) cells ml(-1)) clonal population, a localized depletion of oxygen develops when it reaches a critical aggregate size of ~55 pl. Collectively, these data demonstrate that chemical and phenotypic heterogeneity exists on the micrometer scale within small aggregate populations. IMPORTANCE Before developing into large, complex communities, microbes initially cluster into aggregates, and it is unclear if chemical heterogeneity exists in these ubiquitous micrometer-scale aggregates. We chose to examine oxygen availability within an aggregate since oxygen concentration impacts a number of important bacterial processes, including metabolism, social behaviors, virulence, and antibiotic resistance. By determining that oxygen availability can vary within aggregates containing ≤ 10(5) bacteria, we establish that physiological heterogeneity exists within P. aeruginosa aggregates, suggesting that such heterogeneity frequently exists in many naturally occurring small populations.

  3. A permeation method for detection of self-aggregation of doxorubicin in aqueous environment.

    PubMed

    Fülöp, Zoltán; Gref, Ruxandra; Loftsson, Thorsteinn

    2013-09-15

    For pharmaceutical scientists, it is important to know if dissolved drug molecules are present only as monomers or in the form of aggregates in a test solution or formulation. Amphiphilic or hydrophobic drugs frequently self-associate to form dimers, trimers or higher order aggregates. Doxorubicin aggregation was examined by a previously developed permeation technique to detect oligosaccharide aggregation in aqueous solutions. At very low doxorubicin concentrations dimers and trimers have been observed, but in aqueous 0.5mg/ml doxorubicin solutions aggregates containing about 40 molecules were observed. The permeation studies were supported by TEM studies. The results indicate that neutral doxorubicin molecules aggregate more readily than the protonated ones. Doxorubicin aggregation is a stepwise process resulting in formation of aggregates of variable sizes are enhanced aggregation with increasing doxorubicin concentration. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. Thermodynamics of Protein Aggregation

    NASA Astrophysics Data System (ADS)

    Osborne, Kenneth L.; Barz, Bogdan; Bachmann, Michael; Strodel, Birgit

    Amyloid protein aggregation characterizes many neurodegenerative disorders, including Alzheimer's, Parkinson's, and Creutz- feldt-Jakob disease. Evidence suggests that amyloid aggregates may share similar aggregation pathways, implying simulation of full-length amyloid proteins is not necessary for understanding amyloid formation. In this study we simulate GNNQQNY, the N-terminal prion-determining domain of the yeast protein Sup35 to investigate the thermodynamics of structural transitions during aggregation. We use a coarse-grained model with replica-exchange molecular dynamics to investigate the association of 3-, 6-, and 12-chain GNNQQNY systems and we determine the aggregation pathway by studying aggregation states of GN- NQQNY. We find that the aggregation of the hydrophilic GNNQQNY sequence is mainly driven by H-bond formation, leading to the formation of /3-sheets from the very beginning of the assembly process. Condensation (aggregation) and ordering take place simultaneously, which is underpinned by the occurrence of a single heat capacity peak only.

  5. Heme and iron induce protein aggregation.

    PubMed

    Travassos, Leonardo H; Vasconcellos, Luiz R C; Bozza, Marcelo T; Carneiro, Leticia A M

    2017-03-04

    Heme is an essential molecule expressed in many tissues where it plays key roles as the prosthetic group of several proteins involved in vital physiological and metabolic processes such as gas and electron transport. Structurally, heme is a tetrapyrrole ring containing an atom of iron (Fe) in its center. When released into the extracellular milieu, heme exerts several deleterious effects, which make it an important player in infectious and noninfectious hemolytic diseases where large amounts of free heme are observed such as malaria, dengue fever, β-thalassemia, sickle cell disease and ischemia-reperfusion. Our recent work has uncovered an unappreciated cellular response triggered by heme or Fe, one of its degradation products, on macrophages, which is the formation of protein aggregates known as aggresome-like induced structres (ALIS). This response was shown to be fully dependent on ROS production and the activation of the transcription factor NFE2L2/NRF2. In addition, we have demonstrated that heme degradation by HMOX1/HO-1 (heme oxygenase 1) is required and that Fe is essential for the formation of ALIS, as heme analogs lacking the central atom of Fe are not able to induce these structures. ALIS formation is also observed in vivo, in a model of phenylhydrazine (PHZ)-induced hemolysis, indicating that it is an integral part of the host response to excessive free heme and that it may play a role in cellular homeostasis.

  6. 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.

  7. 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.

  8. On mean type aggregation.

    PubMed

    Yager, R R

    1996-01-01

    We introduce and define the concept of mean aggregation of a collection of n numbers. We point out that the lack of associativity of this operation compounds the problem of the extending mean of n numbers to n+1 numbers. The closely related concepts of self identity and the centering property are introduced as one imperative for extending mean aggregation operators. The problem of weighted mean aggregation is studied. A new concept of prioritized mean aggregation is then introduced. We next show that the technique of selecting an element based upon the performance of a random experiment can be considered as a mean aggregation operation.

  9. Mass spectrometry study of multiply negatively charged, gas-phase NaAOT micelles: how does charge state affect micellar structure and encapsulation?

    PubMed

    Fang, Yigang; Liu, Fangwei; Liu, Jianbo

    2013-01-01

    We report the formation and characterization of multiply negatively charged sodium bis(2-ethylhexyl) sulfosuccinate (NaAOT) aggregates in the gas phase, by electrospray ionization of methanol/water solution of NaAOT followed by detection using a guided-ion-beam tandem mass spectrometer. Singly and doubly charged aggregates dominate the mass spectra with the compositions of [Na(n-z)AOT(n)](z-) (n = 1-18 and z = 1-2). Solvation by water was detected only for small aggregates [Na(n-1)AOT(n)H(2)O](-) of n = 3-9. Incorporation of glycine and tryptophan into [Na(n-z)AOT(n)](z-) aggregates was achieved, aimed at identifying effects of guest molecule hydrophobicity on micellar solubilization. Only one glycine molecule could be incorporated into each [Na(n-z)AOT(n)](z-) of n ≥ 7, and at most two glycine molecules could be hosted in that of n ≥ 13. In contrast to glycine, up to four tryptophan molecules could be accommodated within single aggregates of n ≥ 6. However, deprotonation of tryptophan significantly decrease its affinity towards aggregates. Collision-induced dissociation (CID) was carried out for mass-selected aggregate ions, including measurements of product ion mass spectra for both empty and amino acid-containing aggregates. CID results provide a probe for aggregate structures, surfactant-solute interactions, and incorporation sites of amino acids. The present data was compared with mass spectrometry results of positively charged [Na(n+z)AOT(n)](z+) aggregates. Contrary to their positive analogues, which form reverse micelles, negatively charged aggregates may adopt a direct micelle-like structure with AOT polar heads exposed and amino acids being adsorbed near the micellar outer surface.

  10. Molecule nanoweaver

    DOEpatents

    Gerald, II; Rex, E [Brookfield, IL; Klingler, Robert J [Glenview, IL; Rathke, Jerome W [Homer Glen, IL; Diaz, Rocio [Chicago, IL; Vukovic, Lela [Westchester, IL

    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.

  11. Protein aggregation in a membrane environment.

    PubMed

    Gorbenko, Galyna; Trusova, Valeriya

    2011-01-01

    Biological membranes are featured by a remarkable ability to modulate a wide range of physiological and pathological processes. Of these, protein aggregation is currently receiving the greatest attention, as one type of the ordered protein aggregates, amyloid fibrils, proved to be involved in molecular etiology of a number of fatal diseases. It has been hypothesized that nucleation of amyloid fibrils and toxic action of their precursors is mediated by lipid-protein interactions. Lipid bilayer provides a variety of environments in which aggregated state of polypeptide chain appears to be more thermodynamically favorable than its monomeric form. The major factors responsible for the enhanced self-association propensity of membrane-bound proteins include (i) structural transition of polypeptide chain into aggregation-prone conformation; (ii) protein crowding in a lipid phase; (iii) particular aggregation-favoring orientation and bilayer embedment of the protein molecules. All these factors are considered in the present review with an emphasis being put on the role of electrostatic, hydrophobic, and hydrogen-bonding phenomena in initiating and modulating the protein aggregation on a membrane template. Likewise, we survey the advanced experimental techniques employed for detection and structural characterization of the aggregated species in membrane systems.

  12. Detergent-mediated protein aggregation

    PubMed Central

    Neale, Chris; Ghanei, Hamed; Holyoake, John; Bishop, Russell E.; Privé, Gilbert G.; Pomès, Régis

    2016-01-01

    Because detergents are commonly used to solvate membrane proteins for structural evaluation, much attention has been devoted to assessing the conformational bias imparted by detergent micelles in comparison to the native environment of the lipid bilayer. Here, we conduct six 500-ns simulations of a system with >600,000 atoms to investigate the spontaneous self assembly of dodecylphosphocholine detergent around multiple molecules of the integral membrane protein PagP. This detergent formed equatorial micelles in which acyl chains surround the protein’s hydrophobic belt, confirming existing models of the detergent solvation of membrane proteins. In addition, unexpectedly, the extracellular and periplasmic apical surfaces of PagP interacted with the headgroups of detergents in other micelles 85 and 60% of the time, respectively, forming complexes that were stable for hundreds of nanoseconds. In some cases, an apical surface of one molecule of PagP interacted with an equatorial micelle surrounding another molecule of PagP. In other cases, the apical surfaces of two molecules of PagP simultaneously bound a neat detergent micelle. In these ways, detergents mediated the non-specific aggregation of folded PagP. These simulation results are consistent with dynamic light scattering experiments, which show that, at detergent concentrations ≥600 mM, PagP induces the formation of large scattering species that are likely to contain many copies of the PagP protein. Together, these simulation and experimental results point to a potentially generic mechanism of detergent-mediated protein aggregation. PMID:23466535

  13. Detergent-mediated protein aggregation.

    PubMed

    Neale, Chris; Ghanei, Hamed; Holyoake, John; Bishop, Russell E; Privé, Gilbert G; Pomès, Régis

    2013-04-01

    Because detergents are commonly used to solvate membrane proteins for structural evaluation, much attention has been devoted to assessing the conformational bias imparted by detergent micelles in comparison to the native environment of the lipid bilayer. Here, we conduct six 500-ns simulations of a system with >600,000 atoms to investigate the spontaneous self assembly of dodecylphosphocholine detergent around multiple molecules of the integral membrane protein PagP. This detergent formed equatorial micelles in which acyl chains surround the protein's hydrophobic belt, confirming existing models of the detergent solvation of membrane proteins. In addition, unexpectedly, the extracellular and periplasmic apical surfaces of PagP interacted with the headgroups of detergents in other micelles 85 and 60% of the time, respectively, forming complexes that were stable for hundreds of nanoseconds. In some cases, an apical surface of one molecule of PagP interacted with an equatorial micelle surrounding another molecule of PagP. In other cases, the apical surfaces of two molecules of PagP simultaneously bound a neat detergent micelle. In these ways, detergents mediated the non-specific aggregation of folded PagP. These simulation results are consistent with dynamic light scattering experiments, which show that, at detergent concentrations ≥600 mM, PagP induces the formation of large scattering species that are likely to contain many copies of the PagP protein. Together, these simulation and experimental results point to a potentially generic mechanism of detergent-mediated protein aggregation. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  14. STAND: Surface Tension for Aggregation Number Determination.

    PubMed

    Garrido, Pablo F; Brocos, Pilar; Amigo, Alfredo; García-Río, Luis; Gracia-Fadrique, Jesús; Piñeiro, Ángel

    2016-04-26

    Taking advantage of the extremely high dependence of surface tension on the concentration of amphiphilic molecules in aqueous solution, a new model based on the double equilibrium between free and aggregated molecules in the liquid phase and between free molecules in the liquid phase and those adsorbed at the air/liquid interface is presented and validated using literature data and fluorescence measurements. A key point of the model is the use of both the Langmuir isotherm and the Gibbs adsorption equation in terms of free molecules instead of the nominal concentration of the solute. The application of the model should be limited to non ionic compounds since it does not consider the presence of counterions. It requires several coupled nonlinear fittings for which we developed a software that is publicly available in our server as a web application. Using this tool, it is straightforward to get the average aggregation number of an amphiphile, the micellization free energy, the adsorption constant, the maximum surface excess (and so the minimum area per molecule), the distribution of solute in the liquid phase between free and aggregate species, and the surface coverage in only a couple of seconds, just by uploading a text file with surface tension vs concentration data and the corresponding uncertainties.

  15. A Kinetic Study of the Gas Phase Neutral-Neutral Reactions Between Sulfur- and Chlorine-Containing Molecules Present in the Atmosphere of Venus

    NASA Astrophysics Data System (ADS)

    Maffucci, D. M.; Woon, D. E.; Herbst, E.

    2017-05-01

    Using updated electronic structures, we employ a variety of kinetic theories to calculate the reaction rate constants for neutral-neutral chemical reactions between sulfur- and chlorine-containing molecules observed in the atmosphere of Venus.

  16. Pyridine Aggregation in Helium Nanodroplets

    NASA Astrophysics Data System (ADS)

    Nieto, Pablo; Poerschke, Torsten; Habig, Daniel; Schwaab, Gerhard; Havenith, Martina

    2012-06-01

    Pyridine crystals show the unusual property of isotopic polymorphism. Experimentally it has been observed that deuterated pyridine crystals exist in two phases while non-deuterated pyridine does not show a phase transition. Therefore, although isotopic substitution is the smallest possible modification of a molecule it greatly affects the stability of pyridine crystals. A possible experimental approach in order to understand this striking effect might be the study of pyridine aggregation for small clusters. By embedding the clusters in helium nanodroplets the aggregates can be stabilized and studied by means of Infrared Depletion Spectroscopy. Pyridine oligomers were investigated in the C-H asymmetric vibration region (2980-3100 cm-1) using this experimental technique. The number of molecules for the clusters responsibles for each band were determined by means of pick-up curves as well as mass sensitive depletion spectra. Furthermore, the intensity dependence of the different bands on applying a dc electric field was studied. The assignment of the different structures for pyridine clusters on the basis of these measurements were also carried out. S. Crawford et al., Angew. Chem. Int. Ed., 48, 755 (2009).

  17. Source of polarized hydrogen molecules

    NASA Astrophysics Data System (ADS)

    Toporkov, D. K.; Gramolin, A. V.; Nikolenko, D. M.; Rachek, I. A.; Sadykov, R. Sh.; Shestakov, Yu. V.; Yurchenko, A. V.; Zevakov, S. A.

    2017-10-01

    A novel source of polarized hydrogen and deuterium molecules has been tested. The use of sextupole superconducting magnets allows us to select molecules with the nuclear spin projection -1 for hydrogen and -2 for deuterium. The measured beam intensity of polarized hydrogen molecules for the nozzle temperature range of 6.5-30 K and a gas flow rate up to 5 ṡ 10-2 Torr ṡ l / s is presented. The measured flux of polarized hydrogen molecules of ≈ 3 ṡ 1012 mol / s is in reasonable agreement with estimations. The obtained results can be used as a basis for the development of a high-intensity source of polarized molecules.

  18. Interstellar molecules

    NASA Technical Reports Server (NTRS)

    Townes, C. H.

    1976-01-01

    Progress in the discovery and study of interstellar molecules is summarized. The 36 molecular species thus far identified in interstellar space are listed in several groups which include simple hydrides, oxides, and sulfides, various derivatives of ammonia, molecules involving linear carbon chains, cyanides, and molecules related in structure to formaldehyde, alcohols, or ethers. Several free radicals are described, the discovery of molecules in external galaxies is discussed, and possible mechanisms for molecular formation are noted. Methods for examining relative isotopic abundances by measuring molecules in interstellar clouds are outlined, mechanisms for the excitation of interstellar molecules are reviewed, and values are presented for the C-12/C-13 abundance ratio in a number of interstellar clouds. The detection of interstellar masers is discussed along with pumping mechanisms and masing transitions in H2CO, CH, OH, and SiO. The nature of dense interstellar clouds is examined in terms of several simple and complex cloud models, with emphasis on multiple condensation models.

  19. Selective IR multiphoton dissociation of molecules in a pulsed gas-dynamically cooled molecular flow interacting with a solid surface as an alternative to low-energy methods of molecular laser isotope separation

    SciTech Connect

    Makarov, G N; Petin, A N

    2016-03-31

    We report the results of studies on the isotope-selective infrared multiphoton dissociation (IR MFD) of SF{sub 6} and CF{sub 3}I molecules in a pulsed, gas-dynamically cooled molecular flow interacting with a solid surface. The productivity of this method in the conditions of a specific experiment (by the example of SF{sub 6} molecules) is evaluated. A number of low-energy methods of molecular laser isotope separation based on the use of infrared lasers for selective excitation of molecules are analysed and their productivity is estimated. The methods are compared with those of selective dissociation of molecules in the flow interacting with a surface. The advantages of this method compared to the low-energy methods of molecular laser isotope separation and the IR MPD method in the unperturbed jets and flows are shown. It is concluded that this method could be a promising alternative to the low-energy methods of molecular laser isotope separation. (laser separation of isotopes)

  20. Aggregations in Flatworms.

    ERIC Educational Resources Information Center

    Liffen, C. L.; Hunter, M.

    1980-01-01

    Described is a school project to investigate aggregations in flatworms which may be influenced by light intensity, temperature, and some form of chemical stimulus released by already aggregating flatworms. Such investigations could be adopted to suit many educational levels of science laboratory activities. (DS)

  1. Aggregations in Flatworms.

    ERIC Educational Resources Information Center

    Liffen, C. L.; Hunter, M.

    1980-01-01

    Described is a school project to investigate aggregations in flatworms which may be influenced by light intensity, temperature, and some form of chemical stimulus released by already aggregating flatworms. Such investigations could be adopted to suit many educational levels of science laboratory activities. (DS)

  2. Cell and Particle Interactions and Aggregation During Electrophoretic Motion

    NASA Technical Reports Server (NTRS)

    Davis, Robert H.

    2000-01-01

    The objectives of this research were (i) to perform experiments for observing and quantifying electrophoretic aggregation, (ii) to develop a theoretical description to appropriately analyze and compare with the experimental results, (iii) to study the combined effects of electrophoretic and gravitational aggregation of large particles, and the combined effects of electrophoretic and Brownian aggregation of small particles, and (iv) to perform a preliminary design of a potential future flight experiment involving electrophoretic aggregation. Electrophoresis refers to the motion of charged particles, droplets or molecules in response to an applied electric field. Electrophoresis is commonly used for analysis and separation of biological particles or molecules. When particles have different surface charge densities or potentials, they will migrate at different velocities in an electric field. This differential migration leads to the possibility that they will collide and aggregate, thereby preventing separation.

  3. 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)

  4. 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)

  5. Influence of Phenylalanine on Carotenoid Aggregation

    NASA Astrophysics Data System (ADS)

    Lu, L.; Ni, X.; Luo, X.

    2015-01-01

    The carotenoids lutein and β-carotene form, in 1:1 ethanol-water mixtures H-aggregates, of different strengths. The effects of phenylalanine on these aggregates were recorded by UV-Vis absorption, steady-state fluorescence, and Raman spectra. The H-aggregate of lutein was characterized by a large 78 nm blue shift in the absorption spectra, confirming the strong coupling between hydroxyl groups of adjacent molecules. The 15 nm blue shift in the β-carotene mixture also indicates that it was assembled by weak coupling between polyenes. After adding phenylalanine, the reducing absorption strength of the aggregates of lutein and reappearance of vibrational substructure indicate that the hydroxyl and amino groups of phenylalanine may coordinate to lutein and disaggregate the H-aggregates. However, phenylalanine had no effect on aggregates of β-carotene. The Raman spectra show three bands of carotenoids whose intensities decreased with increasing phenylalanine concentration. The frequency of ν1 corresponding to the length of the conjugated region was more sensitive to the solution of lutein. This coordination of phenylalanine to lutein could increase the length of the conjugated region. In addition, phenylalanine significantly affected the excited electronic states of carotenoids, which were crucial in the energy transfer from carotenoids to chlorophyll a in vivo.

  6. H- and J-aggregation of fluorene-based chromophores.

    PubMed

    Deng, Yonghong; Yuan, Wen; Jia, Zhe; Liu, Gao

    2014-12-11

    Understanding of H- and J-aggregation behaviors in fluorene-based polymers is significant both for determining the origin of various red-shifted emissions occurring in blue-emitting polyfluorenes and for developing polyfluorene-based device performance. In this contribution, we demonstrate a new theory of the H- and J-aggregation of polyfluorenes and oligofluorenes, and understand the influence of chromosphere aggregation on their photoluminescent properties. H- and J-aggregates are induced by a continuous increasing concentration of the oligofluorene or polyfluorene solution. A relaxed molecular configuration is simulated to illustrate the spatial arrangement of the bonding of fluorenes. It is indicated that the relaxed state adopts a 21 helical backbone conformation with a torsion angle of 18° between two connected repeat units. This configuration makes the formation of H- and J-aggregates through the strong π-π interaction between the backbone rings. A critical aggregation concentration is observed to form H- and J-aggregates for both polyfluorenes and oligofluorenes. These aggregates show large spectral shifts and distinct shape changes in photoluminescent excitation (PLE) and emission (PL) spectroscopy. Compared with "isolated" chromophores, H-aggregates induce absorption spectral blue-shift and fluorescence spectral red-shift but largely reduce fluorescence efficiency. "Isolated" chromophores not only refer to "isolated molecules" but also include those associated molecules if their conjugated backbones are not compact enough to exhibit perturbed absorption and emission. J-aggregates induce absorption spectral red-shift and fluorescence spectral red-shift but largely enhance fluorescence efficiency. The PLE and PL spectra also show that J-aggregates dominate in concentrated solutions. Different from the excimers, the H- and J-aggregate formation changes the ground-state absorption of fluorene-based chromophores. H- and J-aggregates show changeable

  7. Dynamics of Activated Molecules

    SciTech Connect

    Mullin, Amy S.

    2016-11-16

    Experimental studies have been performed to investigate the collisional energy transfer processes of gas-phase molecules that contain large amounts of internal energy. Such molecules are prototypes for molecules under high temperature conditions relevant in combustion and information about their energy transfer mechanisms is needed for a detailed understanding and modeling of the chemistry. We use high resolution transient IR absorption spectroscopy to measure the full, nascent product distributions for collisions of small bath molecules that relax highly vibrationally excited pyrazine molecules with E=38000 cm-1 of vibrational energy. To perform these studies, we developed new instrumentation based on modern IR light sources to expand our experimental capabilities to investigate new molecules as collision partners. This final report describes our research in four areas: the characterization of a new transient absorption spectrometer and the results of state-resolved collision studies of pyrazine(E) with HCl, methane and ammonia. Through this research we have gained fundamental new insights into the microscopic details of relatively large complex molecules at high energy as they undergo quenching collisions and redistribute their energy.

  8. Marine Synechococcus Aggregation

    NASA Astrophysics Data System (ADS)

    Neuer, S.; Deng, W.; Cruz, B. N.; Monks, L.

    2016-02-01

    Cyanobacteria are considered to play an important role in the oceanic biological carbon pump, especially in oligotrophic regions. But as single cells are too small to sink, their carbon export has to be mediated by aggregate formation and possible consumption by zooplankton producing sinking fecal pellets. Here we report results on the aggregation of the ubiquitous marine pico-cyanobacterium Synechococcus as a model organism. We first investigated the mechanism behind such aggregation by studying the potential role of transparent exopolymeric particles (TEP) and the effects of nutrient (nitrogen or phosphorus) limitation on the TEP production and aggregate formation of these pico-cyanobacteria. We further studied the aggregation and subsequent settling in roller tanks and investigated the effects of the clays kaolinite and bentonite in a series of concentrations. Our results show that despite of the lowered growth rates, Synechococcus in nutrient limited cultures had larger cell-normalized TEP production, formed a greater volume of aggregates, and resulted in higher settling velocities compared to results from replete cultures. In addition, we found that despite their small size and lack of natural ballasting minerals, Synechococcus cells could still form aggregates and sink at measureable velocities in seawater. Clay minerals increased the number and reduced the size of aggregates, and their ballasting effects increased the sinking velocity and carbon export potential of aggregates. In comparison with the Synechococcus, we will also present results of the aggregation of the pico-cyanobacterium Prochlorococcus in roller tanks. These results contribute to our understanding in the physiology of marine Synechococcus as well as their role in the ecology and biogeochemistry in oligotrophic oceans.

  9. Sans study of asphaltene aggregation

    SciTech Connect

    Overfield, R.E.; Sheu, E.Y.; Sinha, S.K.; Liang, K.S. )

    1988-06-01

    The colloidal properties of asphaltenes have long been recognized from peculiarities in their solubility and colligative properties. A layered micellar model or asphaltenes was proposed by others in which a highly condensed alkyl aromatic formed the central part, and molecules of decreasingly aromatic character (resins) clustered around them. Numerous studies, based on a variety of techniques such as ultracentrifugation and electron microscopy indicated a particulate nature for asphaltenes with size 20-40 A diameter. Others have proposed a refined model based on x-ray diffraction and small angle scattering. In this model, interactions between flat sheets of condensed aromatic rings form the central ''crystallite'' part of a spherical particle with the outer part being comprised of the aliphatic positions of the same molecules. These particles are bunched together with some degree of entanglement into ''micelles''. Concentration and solvent dependent radii of gyration, ranging from 30-50 A were reported. The aggregation creates a good deal of uncertainty as to the true molecular size or weight of asphaltenes. Neutron scattering offers novel contrast relative to light scattering (refractive index) and x-ray scattering (electron density). This is because the scattering length of proton is negative, whereas that from deuterium and other nuclei such as C, S, O, and N are positive. Thus by replacing hydrogen with deuterium in either the solvent or the scatterer the contrast can be varied, and different parts of the molecule can be highlighted.

  10. Aggregate and the environment

    USGS Publications Warehouse

    Langer, William H.; Drew, Lawrence J.; Sachs, J.S.

    2004-01-01

    This book is designed to help you understand our aggregate resources-their importance, where they come from, how they are processed for our use, the environmental concerns related to their mining and processing, how those concerns are addressed, and the policies and regulations designed to safeguard workers, neighbors, and the environment from the negative impacts of aggregate mining. We hope this understanding will help prepare you to be involved in decisions that need to be made-individually and as a society-to be good stewards of our aggregate resources and our living planet.

  11. Global optimization of cholic acid aggregates

    NASA Astrophysics Data System (ADS)

    Jójárt, Balázs; Viskolcz, Béla; Poša, Mihalj; Fejer, Szilard N.

    2014-04-01

    In spite of recent investigations into the potential pharmaceutical importance of bile acids as drug carriers, the structure of bile acid aggregates is largely unknown. Here, we used global optimization techniques to find the lowest energy configurations for clusters composed between 2 and 10 cholate molecules, and evaluated the relative stabilities of the global minima. We found that the energetically most preferred geometries for small aggregates are in fact reverse micellar arrangements, and the classical micellar behaviour (efficient burial of hydrophobic parts) is achieved only in systems containing more than five cholate units. Hydrogen bonding plays a very important part in keeping together the monomers, and among the size range considered, the most stable structure was found to be the decamer, having 17 hydrogen bonds. Molecular dynamics simulations showed that the decamer has the lowest dissociation propensity among the studied aggregation numbers.

  12. High resolution UV resonance enhanced two-photon ionization spectroscopy with mass selection of biologically relevant molecules in the gas phase

    NASA Astrophysics Data System (ADS)

    Chervenkov, S.; Wang, P. Q.; Karaminkov, R.; Chakraborty, T.; Braun, Juergen E.; Neusser, Hans J.

    2005-04-01

    The high resolution Doppler-free resonance-enhanced two-photon ionization (R2PI) spectroscopy with mass selection of jet-cooled (2-12 K) molecular species is a powerful experimental method providing comprehensive information on both isolated molecules and molecular clusters. We have demonstrated for the first time that this technique can be applied to large molecules and provides detailed information on their conformational structure. It allows rotationally resolved (FWHM = 70 MHz) spectra of the vibronic bands of the S1<--S0 electronic transition of the studied molecular systems to be measured. A specially designed computer-assisted fitting routine based on genetic algorithms is used to determine their rotational constants in the ground and excited electronic states, respectively, and the transition moment ratio. To interpret the experimental information and to discriminate and unambiguously assign the observed approach to the study of the neurotransmitter molecule, ephedrine. The results elucidate the role of the intramolecular hydrogen bonds stabilizing the respective conformations and affecting their intrinsic properties.

  13. Mobius Molecules

    ERIC Educational Resources Information Center

    Eckert, J. M.

    1973-01-01

    Discusses formation of chemical molecules via Mobius strip intermediates, and concludes that many special physics-chemical properties of the fully closed circular form (1) of polyoma DNA are explainable by this topological feature. (CC)

  14. 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)

  15. 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.

  16. 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)

  17. Mobius Molecules

    ERIC Educational Resources Information Center

    Eckert, J. M.

    1973-01-01

    Discusses formation of chemical molecules via Mobius strip intermediates, and concludes that many special physics-chemical properties of the fully closed circular form (1) of polyoma DNA are explainable by this topological feature. (CC)

  18. 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.

  19. Protein Colloidal Aggregation Project

    NASA Technical Reports Server (NTRS)

    Oliva-Buisson, Yvette J. (Compiler)

    2014-01-01

    To investigate the pathways and kinetics of protein aggregation to allow accurate predictive modeling of the process and evaluation of potential inhibitors to prevalent diseases including cataract formation, chronic traumatic encephalopathy, Alzheimer's Disease, Parkinson's Disease and others.

  20. Propagation of Tau aggregates.

    PubMed

    Goedert, Michel; Spillantini, Maria Grazia

    2017-05-30

    Since 2009, evidence has accumulated to suggest that Tau aggregates form first in a small number of brain cells, from where they propagate to other regions, resulting in neurodegeneration and disease. Propagation of Tau aggregates is often called prion-like, which refers to the capacity of an assembled protein to induce the same abnormal conformation in a protein of the same kind, initiating a self-amplifying cascade. In addition, prion-like encompasses the release of protein aggregates from brain cells and their uptake by neighbouring cells. In mice, the intracerebral injection of Tau inclusions induced the ordered assembly of monomeric Tau, followed by its spreading to distant brain regions. Short fibrils constituted the major species of seed-competent Tau. The existence of several human Tauopathies with distinct fibril morphologies has led to the suggestion that different molecular conformers (or strains) of aggregated Tau exist.

  1. Marine aggregate dynamics

    NASA Astrophysics Data System (ADS)

    The direction and scope of the Office of Naval Research's Marine Aggregate Dynamics Accelerated Research Initiative will be the topic of an open-house style meeting February 14, 7:30-10:00 P.M. in Ballroom D of the Hyatt Regency New Orleans at the Louisiana Superdome. This meeting is scheduled during the AGU/American Society of Limnology and Oceanography Ocean Sciences Meeting February 12-16 in New Orleans.The critical focus of the ARI is the measurement and modeling of the dynamics of the biological, physical, chemical and molecular processes that drive aggregation and produce aggregates. This new ARI will provide funding in Fiscal Years 1991-1995 to identify and quantify mechanisms that determine the distribution, abundance and size spectrum of aggregated particulate matter in the ocean.

  2. Aggregation and Averaging.

    ERIC Educational Resources Information Center

    Siegel, Irving H.

    The arithmetic processes of aggregation and averaging are basic to quantitative investigations of employment, unemployment, and related concepts. In explaining these concepts, this report stresses need for accuracy and consistency in measurements, and describes tools for analyzing alternative measures. (BH)

  3. Aggregation of retail stores

    NASA Astrophysics Data System (ADS)

    Jensen, Pablo; Boisson, Jean; Larralde, Hernán

    2005-06-01

    We propose a simple model to understand the economic factors that induce aggregation of some businesses over small geographical regions. The model incorporates price competition with neighboring stores, transportation costs and the satisfaction probability of finding the desired product. We show that aggregation is more likely for stores selling expensive products and/or stores carrying only a fraction of the business variety. We illustrate our model with empirical data collected in the city of Lyon.

  4. Critical lines for an unequal size of molecules in a binary gas-liquid mixture around the van Laar point using the combination of the Tompa model and the van der Waals equation.

    PubMed

    Gençaslan, Mustafa; Keskin, Mustafa

    2012-02-14

    We combine the modified Tompa model with the van der Waals equation to study critical lines for an unequal size of molecules in a binary gas-liquid mixture around the van Laar point. The van Laar point is coined by Meijer and it is the only point at which the mathematical double point curve is stable. It is the intersection of the tricritical point and the double critical end point. We calculate the critical lines as a function of χ(1) and χ(2), the density of type I molecules and the density of type II molecules for various values of the system parameters; hence the global phase diagrams are presented and discussed in the density-density plane. We also investigate the connectivity of critical lines at the van Laar point and its vicinity and discuss these connections according to the Scott and van Konynenburg classifications. It is also found that the critical lines and phase behavior are extremely sensitive to small modifications in the system parameters.

  5. Gas sensing at the nanoscale: engineering SWCNT-ITO nano-heterojunctions for the selective detection of NH3 and NO2 target molecules.

    PubMed

    Rigoni, F; Drera, G; Pagliara, S; Perghem, E; Pintossi, C; Goldoni, A; Sangaletti, L

    2017-01-20

    The gas response of single-wall carbon nanotubes (SWCNT) functionalized with indium tin oxide (ITO) nanoparticles (NP) has been studied at room temperature and an enhanced sensitivity to ammonia and nitrogen dioxide is demonstrated. The higher sensitivity in the functionalized sample is related to the creation of nano-heterojunctions at the interface between SWCNT bundles and ITO NP. Furthermore, the different response of the two devices upon NO2 exposure provides a way to enhance also the selectivity. This behavior is rationalized by considering a gas sensing mechanism based on the build-up of space-charge layers at the junctions. Finally, full recovery of the signal after exposure to NO2 is achieved by UV irradiation for the functionalized sample, where the ITO NP can play a role to hinder the poisoning effects on SWCNT due to NO2 chemisorption.

  6. Gas sensing at the nanoscale: engineering SWCNT-ITO nano-heterojunctions for the selective detection of NH3 and NO2 target molecules

    NASA Astrophysics Data System (ADS)

    Rigoni, F.; Drera, G.; Pagliara, S.; Perghem, E.; Pintossi, C.; Goldoni, A.; Sangaletti, L.

    2017-01-01

    The gas response of single-wall carbon nanotubes (SWCNT) functionalized with indium tin oxide (ITO) nanoparticles (NP) has been studied at room temperature and an enhanced sensitivity to ammonia and nitrogen dioxide is demonstrated. The higher sensitivity in the functionalized sample is related to the creation of nano-heterojunctions at the interface between SWCNT bundles and ITO NP. Furthermore, the different response of the two devices upon NO2 exposure provides a way to enhance also the selectivity. This behavior is rationalized by considering a gas sensing mechanism based on the build-up of space-charge layers at the junctions. Finally, full recovery of the signal after exposure to NO2 is achieved by UV irradiation for the functionalized sample, where the ITO NP can play a role to hinder the poisoning effects on SWCNT due to NO2 chemisorption.

  7. Protein aggregation and prionopathies.

    PubMed

    Renner, M; Melki, R

    2014-06-01

    Prion protein and prion-like proteins share a number of characteristics. From the molecular point of view, they are constitutive proteins that aggregate following conformational changes into insoluble particles. These particles escape the cellular clearance machinery and amplify by recruiting the soluble for of their constituting proteins. The resulting protein aggregates are responsible for a number of neurodegenerative diseases such as Creutzfeldt-Jacob, Alzheimer, Parkinson and Huntington diseases. In addition, there are increasing evidences supporting the inter-cellular trafficking of these aggregates, meaning that they are "transmissible" between cells. There are also evidences that brain homogenates from individuals developing Alzheimer and Parkinson diseases propagate the disease in recipient model animals in a manner similar to brain extracts of patients developing Creutzfeldt-Jacob's disease. Thus, the propagation of protein aggregates from cell to cell may be a generic phenomenon that contributes to the evolution of neurodegenerative diseases, which has important consequences on human health issues. Moreover, although the distribution of protein aggregates is characteristic for each disease, new evidences indicate the possibility of overlaps and crosstalk between the different disorders. Despite the increasing evidences that support prion or prion-like propagation of protein aggregates, there are many unanswered questions regarding the mechanisms of toxicity and this is a field of intensive research nowadays. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  8. Search for evidence of life in space: analysis of enantiomeric organic molecules by N,N-dimethylformamide dimethylacetal derivative dependant Gas Chromatography-Mass Spectrometry.

    PubMed

    Freissinet, C; Buch, A; Sternberg, R; Szopa, C; Geffroy-Rodier, C; Jelinek, C; Stambouli, M

    2010-01-29

    Within the context of the future space missions to Mars (MSL 2011 and Exomars 2016), which aim at searching for traces of life at the surface, the detection and quantitation of enantiomeric organic molecules is of major importance. In this work, we have developed and optimized a method to derivatize and analyze chiral organic molecules suitable for space experiments, using N,N-dimethylformamide dimethylacetal (DMF-DMA) as the derivatization agent. The temperature, duration of the derivatization reaction, and chromatographic separation parameters have been optimized to meet instrument design constraints imposed upon space experiment devices. This work demonstrates that, in addition to its intrinsic qualities, such as production of light-weight derivatives and a great resistance to drastic operating conditions, DMF-DMA facilitates simple and fast derivatization of organic compounds (three minutes at 140 degrees C in a single-step) that is suitable for an in situ analysis in space. By using DMF-DMA as the derivatization agent, we have successfully identified 19 of the 20 proteinic amino acids and been able to enantiomerically separate ten of the potential 19 (glycine being non-chiral). Additionally, we have minimized the percentage of racemized amino acid compounds produced by optimizing the conditions of the derivatization reaction itself. Quantitative linearity studies and the determination of the limit of detection show that the proposed method is also suitable for the quantitative determination of both enantiomeric forms of most of the tested amino acids, as limits of detection obtained are lower than the ppb level of organic molecules already detected in Martian meteorites.

  9. The mechanism of oxidation-induced low-density lipoprotein aggregation: an analogy to colloidal aggregation and beyond?

    PubMed Central

    Xu, S; Lin, B

    2001-01-01

    Atherosclerosis is a disease initiated by lipoprotein aggregation and deposition in artery walls. In this study, the de novo low-density lipoprotein aggregation process was examined. Nine major intermediates were identified in two stages of the aggregation process. In the aggregation stage, low-density lipoprotein molecules aggregate and form nucleation units. The nucleation units chain together and form linear aggregates. The linear aggregates branch and interact with one another, forming fractals. In the fusion stage, spatially adjacent nucleation units in the fractal fuse into curved membrane surfaces, which, in turn, fuse into multilamellar or unilamellar vesicles. Alternatively, some adjacent nucleation units in the fractals assemble in a straight line and form rods. Subsequently, the rods flatten out into rough and then into smooth ribbons. Occasionally, tubular membrane vesicles are formed from the fractals. The aggregation stage seems to be analogous to colloidal aggregation and amyloid fiber formation. The fusion stage seems to be characteristic of the lipid-rich lipoproteins and is beyond colloidal aggregation and amyloid fiber formation. PMID:11566810

  10. Gas hydrates

    SciTech Connect

    Berecz, E.; Balla-Achs, M.

    1983-01-01

    In the presence of water, particularly at low temperatures, many industrial gas systems under pressure tend to form solid crystalline compounds. These compounds are referred to as gas hydrates, and result from the association of the gas molecules with water. This book draws attention to the theoretical, practical and technological aspects of this interesting and important class of compounds. The topics covered include the structures, properties and thermodynamic characteristics of the gas hydrates, the changes induced in the equilibrium conditions by additives, and the methods and studies relating to the prevention and elimination of hydrate plugs in technological operations with industrial gases. In the discussion of the technological aspects, special emphasis is given to the production and transportation of natural gas and to the application of freon coolants. Such questions as the possibility of the desalination of seawater and the formation of gas hydrates in interplanetary space are also dealt with.

  11. Aggregates in monoclonal antibody manufacturing processes.

    PubMed

    Vázquez-Rey, María; Lang, Dietmar A

    2011-07-01

    Monoclonal antibodies have proved to be a highly successful class of therapeutic products. Large-scale manufacturing of pharmaceutical antibodies is a complex activity that requires considerable effort in both process and analytical development. If a therapeutic protein cannot be stabilized adequately, it will lose partially or totally its therapeutic properties or even cause immunogenic reactions thus potentially further endangering the patients' health. The phenomenon of protein aggregation is a common issue that compromises the quality, safety, and efficacy of antibodies and can happen at different steps of the manufacturing process, including fermentation, purification, final formulation, and storage. Aggregate levels in drug substance and final drug product are a key factor when assessing quality attributes of the molecule, since aggregation might impact biological activity of the biopharmaceutical. In this review it is analyzed how aggregates are formed during monoclonal antibody industrial production, why they have to be removed and the manufacturing process steps that are designed to either minimize or remove aggregates in the final product. Copyright © 2011 Wiley Periodicals, Inc.

  12. Protonation favors aggregation of lysozyme with SDS.

    PubMed

    Khan, Javed M; Chaturvedi, Sumit K; Rahman, Shah K; Ishtikhar, Mohd; Qadeer, Atiyatul; Ahmad, Ejaz; Khan, Rizwan H

    2014-04-21

    Different proteins have different amino acid sequences as well as conformations, and therefore different propensities to aggregate. Electrostatic interactions have an important role in the aggregation of proteins as revealed by our previous report (J. M. Khan et al., PLoS One, 2012, 7, e29694). In this study, we designed and executed experiments to gain knowledge of the role of charge variations on proteins during the events of protein aggregation with lysozyme as a model protein. To impart positive and negative charges to proteins, we incubated lysozyme at different pH values of below and above the pI (∼11). Negatively charged SDS was used to 'antagonize' positive charges on lysozyme. We examined the effects of pH variations on SDS-induced amyloid fibril formation by lysozyme using methods such as far-UV circular dichroism, Rayleigh scattering, turbidity measurements, dye binding assays and dynamic light scattering. We found that sub-micellar concentrations of SDS (0.1 to 0.6 mM) induced amyloid fibril formation by lysozyme in the pH range of 10.0-1.0 and maximum aggregation was observed at pH 1.0. The morphology of aggregates was fibrillar in structure, as visualized by transmission electron microscopy. Isothermal titration calorimetry studies demonstrated that fibril formation is exothermic. To the best of our current understanding of the mechanism of aggregation, this study demonstrates the crucial role of electrostatic interactions during amyloid fibril formation. The model proposed here will help in designing molecules that can prevent or reverse the amyloid fibril formation or the aggregation.

  13. Characterization of Ovine Dermal Papilla Cell Aggregation

    PubMed Central

    Sari, Agnes Rosarina Prita; Rufaut, Nicholas Wolfgang; Jones, Leslie Norman; Sinclair, Rodney Daniel

    2016-01-01

    Context: The dermal papilla (DP) is a condensation of mesenchymal cells at the proximal end of the hair follicle, which determines hair shaft size and regulates matrix cell proliferation and differentiation. DP cells have the ability to regenerate new hair follicles. These cells tend to aggregate both in vitro and in vivo. This tendency is associated with the ability of papilla cells to induce hair growth. However, human papilla cells lose their hair-inducing activity in later passage number. Ovine DP cells are different from human DP cells since they do not lose their aggregative behavior or hair-inducing activity in culture. Nonetheless, our understanding of ovine DP cells is still limited. Aim: The aim of this study was to observe the expression of established DP markers in ovine cells and their association with aggregation. Subjects and Methods: Ovine DP cells from three different sheep were compared. Histochemistry, immunoflourescence, and polymerase chain reaction experiments were done to analyze the DP markers. Results: We found that ovine DP aggregates expressed all the 16 markers evaluated, including alkaline phosphatase and versican. Expression of the versican V0 and V3 isoforms, neural cell adhesion molecule, and corin was increased significantly with aggregation, while hey-1 expression was significantly decreased. Conclusions: Overall, the stable expression of numerous markers suggests that aggregating ovine DP cells have a similar phenotype to papillae in vivo. The stability of their molecular phenotype is consistent with their robust aggregative behavior and retained follicle-inducing activity after prolonged culture. Their phenotypic stability in culture contrasts with DP cells from other species, and suggests that a better understanding of ovine DP cells might provide opportunities to improve the hair-inducing activity and therapeutic potential of human cells. PMID:27625564

  14. Collisional Aggregation Due to Turbulence

    NASA Astrophysics Data System (ADS)

    Pumir, Alain; Wilkinson, Michael

    2016-03-01

    Collisions between particles suspended in a fluid play an important role in many physical processes. As an example, collisions of microscopic water droplets in clouds are a necessary step in the production of macroscopic raindrops. Collisions of dust grains are also conjectured to be important for planet formation in the gas surrounding young stars and to play a role in the dynamics of sand storms. In these processes, collisions are favored by fast turbulent motions. Here we review recent advances in the understanding of collisional aggregation due to turbulence. We discuss the role of fractal clustering of particles and caustic singularities of their velocities. We also discuss limitations of the Smoluchowski equation for modeling such processes. These advances lead to a semiquantitative understanding on the influence of turbulence on collision rates and point to deficiencies in the current understanding of rainfall and planet formation.

  15. Fibronectin Aggregation and Assembly

    PubMed Central

    Ohashi, Tomoo; Erickson, Harold P.

    2011-01-01

    The mechanism of fibronectin (FN) assembly and the self-association sites are still unclear and contradictory, although the N-terminal 70-kDa region (I1–9) is commonly accepted as one of the assembly sites. We previously found that I1–9 binds to superfibronectin, which is an artificial FN aggregate induced by anastellin. In the present study, we found that I1–9 bound to the aggregate formed by anastellin and a small FN fragment, III1–2. An engineered disulfide bond in III2, which stabilizes folding, inhibited aggregation, but a disulfide bond in III1 did not. A gelatin precipitation assay showed that I1–9 did not interact with anastellin, III1, III2, III1–2, or several III1–2 mutants including III1–2KADA. (In contrast to previous studies, we found that the III1–2KADA mutant was identical in conformation to wild-type III1–2.) Because I1–9 only bound to the aggregate and the unfolding of III2 played a role in aggregation, we generated a III2 domain that was destabilized by deletion of the G strand. This mutant bound I1–9 as shown by the gelatin precipitation assay and fluorescence resonance energy transfer analysis, and it inhibited FN matrix assembly when added to cell culture. Next, we introduced disulfide mutations into full-length FN. Three disulfide locks in III2, III3, and III11 were required to dramatically reduce anastellin-induced aggregation. When we tested the disulfide mutants in cell culture, only the disulfide bond in III2 reduced the FN matrix. These results suggest that the unfolding of III2 is one of the key factors for FN aggregation and assembly. PMID:21949131

  16. Low symmetry in molecules with heavy peripheral atoms. The gas-phase structure of perfluoro(methylcyclohexane), C6F11CF3.

    PubMed

    Kafka, Graeme R; Masters, Sarah L; Wann, Derek A; Robertson, Heather E; Rankin, David W H

    2010-10-21

    When refining structures using gas electron diffraction (GED) data, assumptions are often made in order to reduce the number of required geometrical parameters. Where these relate to light, peripheral atoms there is little effect on the refined heavy-atom structure, which is well defined by the GED data. However, this is not the case when heavier atoms are involved. We have determined the gas-phase structure of perfluoro(methylcyclohexane), C(6)F(11)CF(3), using three different refinement methods and have shown that our new method, which makes use of both MP2 and molecular mechanics (MM) calculations to restrain the peripheral-atom geometry, gives a realistic structure without the need for damaging constraints. Only the conformer with the CF(3) group in an equatorial position was considered, as ab initio calculations showed this to be 25 kJ mol(-1) lower in energy than the axial conformer. Refinements combining both high-level and low-level calculations to give constraints were superior both to those based only on molecular mechanics and to those in which assumptions about the geometry were imposed.

  17. Observing Convective Aggregation

    NASA Astrophysics Data System (ADS)

    Holloway, Christopher E.; Wing, Allison A.; Bony, Sandrine; Muller, Caroline; Masunaga, Hirohiko; L'Ecuyer, Tristan S.; Turner, David D.; Zuidema, Paquita

    2017-06-01

    Convective self-aggregation, the spontaneous organization of initially scattered convection into isolated convective clusters despite spatially homogeneous boundary conditions and forcing, was first recognized and studied in idealized numerical simulations. While there is a rich history of observational work on convective clustering and organization, there have been only a few studies that have analyzed observations to look specifically for processes related to self-aggregation in models. Here we review observational work in both of these categories and motivate the need for more of this work. We acknowledge that self-aggregation may appear to be far-removed from observed convective organization in terms of time scales, initial conditions, initiation processes, and mean state extremes, but we argue that these differences vary greatly across the diverse range of model simulations in the literature and that these comparisons are already offering important insights into real tropical phenomena. Some preliminary new findings are presented, including results showing that a self-aggregation simulation with square geometry has too broad distribution of humidity and is too dry in the driest regions when compared with radiosonde records from Nauru, while an elongated channel simulation has realistic representations of atmospheric humidity and its variability. We discuss recent work increasing our understanding of how organized convection and climate change may interact, and how model discrepancies related to this question are prompting interest in observational comparisons. We also propose possible future directions for observational work related to convective aggregation, including novel satellite approaches and a ground-based observational network.

  18. Observing convective aggregation

    NASA Astrophysics Data System (ADS)

    Holloway, Christopher; Wing, Allison; Bony, Sandrine; Muller, Caroline; Masunaga, Hirohiko; L'Ecuyer, Tristan; Turner, David; Zuidema, Paquita

    2017-04-01

    Convective self-aggregation was first recognized and studied in idealized numerical simulations. While there is a rich history of observational work on convective clustering and organization, there have been only a few studies that have analyzed observations to look specifically for processes related to self-aggregation in models. Here we review observational work in both of these categories and motivate the need for more of this work. We acknowledge that self-aggregation may appear to be far-removed from observed convective organization in terms of time scales, initial conditions, initiation processes, and mean state extremes, but we argue that these differences vary greatly across the diverse range of model simulations in the literature and that these comparisons are already offering important insights into real tropical phenomena. Some preliminary new findings are presented, including results showing that a self-aggregation simulation with square geometry has too broad a distribution of humidity and is too dry in the driest regions when compared with radiosonde records from Nauru, while an elongated channel simulation has realistic representations of atmospheric humidity and its variability. We discuss recent work increasing our understanding of how organized convection and climate change may interact, and how model discrepancies related to this question are prompting interest in observational comparisons. We also propose possible future directions for observational work related to convective aggregation, including novel satellite approaches and a ground-based observational network.

  19. Structure and mechanism of action of tau aggregation inhibitors

    PubMed Central

    Cisek, Katryna; Cooper, Grace L.; Huseby, Carol J.; Kuret, Jeff

    2015-01-01

    Since the discovery of phenothiazines as tau protein aggregation inhibitors, many additional small molecule inhibitors of diverse chemotype have been discovered and characterized in biological model systems. Although direct inhibition of tau aggregation has shown promise as a potential treatment strategy for depressing neurofibrillary lesion formation in Alzheimer’s disease, the mechanism of action of these compounds has been unclear. However, recent studies have found that tau aggregation antagonists exert their effects through both covalent and non-covalent means, and have identified associated potency and selectivity driving features. Here we review small-molecule tau aggregation inhibitors with a focus on compound structure and inhibitory mechanism. The elucidation of inhibitory mechanism has implications for maximizing on-target efficacy while minimizing off-target side effects. PMID:25387336

  20. Broadband Microwave Spectroscopy as a Tool to Study the Structures of Odorant Molecules and Weakly Bound Complexes in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Zinn, Sabrina; Betz, Thomas; Medcraft, Chris; Schnell, Melanie

    2015-06-01

    The rotational spectrum of trans-cinnamaldehyde ((2E)-3-phenylprop-2-enal) has been obtained with chirped-pulse microwave spectroscopy in the frequency range of 2 - 8.5 GHz. The odorant molecule is the essential component in cinnamon oil and causes the characteristic smell. In the measured high-resolution spectrum, we were able to assign the rotational spectra of two conformers of trans-cinnamaldehyde as well as all singly 13C-substituted species of the lowest-energy conformer in natural abundance. Two different methods were used to determine the structure from the rotational constants, which will be compared within this contribution. In addition, the current progress of studying ether-alcohol complexes, aiming at an improved understanding of the interplay between hydrogen bonding and dispersion interaction, will be reported. Here, a special focus is placed on the complexes of diphenylether with small aliphatic alcohols.

  1. Electron-induced damage of biotin studied in the gas phase and in the condensed phase at a single-molecule level

    NASA Astrophysics Data System (ADS)

    Keller, Adrian; Kopyra, Janina; Gothelf, Kurt V.; Bald, Ilko

    2013-08-01

    Biotin is an essential vitamin that is, on the one hand, relevant for the metabolism, gene expression and in the cellular response to DNA damage and, on the other hand, finds numerous applications in biotechnology. The functionality of biotin is due to two particular sub-structures, the ring structure and the side chain with carboxyl group. The heterocyclic ring structure results in the capability of biotin to form strong intermolecular hydrogen and van der Waals bonds with proteins such as streptavidin, whereas the carboxyl group can be employed to covalently bind biotin to other complex molecules. Dissociative electron attachment (DEA) to biotin results in a decomposition of the ring structure and the carboxyl group, respectively, within resonant features in the energy range 0-12 eV, thereby preventing the capability of biotin for intermolecular binding and covalent coupling to other molecules. Specifically, the fragment anions (M-H)-, (M-O)-, C3N2O-, CH2O2-, OCN-, CN-, OH- and O- are observed, and exemplarily the DEA cross section of OCN- formation is determined to be 3 × 10-19 cm2. To study the response of biotin to electrons within a complex condensed environment, we use the DNA origami technique and determine a dissociation yield of (1.1 ± 0.2) × 10-14 cm2 at 18 eV electron energy, which represents the most relevant energy for biomolecular damage induced by secondary electrons. The present results thus have important implications for the use of biotin as a label in radiation experiments.

  2. Controlled Assembly of Biocompatible Metallic Nanoaggregates Using a Small Molecule Crosslinker

    PubMed Central

    Van Haute, Desiree; Longmate, Julia M.; Berlin, Jacob M.

    2015-01-01

    By introducing a capping step and controlling reaction parameters, the assembly of metallic nanoparticle aggregates can be achieved using a small molecule crosslinker. Aggregates can be assembled from particles of varied size and composition and the size of the aggregates can be systematically adjusted. Following cell uptake of 60 nm aggregates, the aggregates are stable and non-toxic to macrophage cells up to 55mM Au. PMID:26208123

  3. Binodal Colloidal Aggregation Test - 4: Polydispersion

    NASA Technical Reports Server (NTRS)

    Chaikin, Paul M.

    2008-01-01

    Binodal Colloidal Aggregation Test - 4: Polydispersion (BCAT-4-Poly) will use model hard-spheres to explore seeded colloidal crystal nucleation and the effects of polydispersity, providing insight into how nature brings order out of disorder. Crewmembers photograph samples of polymer and colloidal particles (tiny nanoscale spheres suspended in liquid) that model liquid/gas phase changes. Results will help scientists develop fundamental physics concepts previously cloaked by the effects of gravity.

  4. Conformational stability as a design target to control protein aggregation.

    PubMed

    Costanzo, Joseph A; O'Brien, Christopher J; Tiller, Kathryn; Tamargo, Erin; Robinson, Anne Skaja; Roberts, Christopher J; Fernandez, Erik J

    2014-05-01

    Non-native protein aggregation is a prevalent problem occurring in many biotechnological manufacturing processes and can compromise the biological activity of the target molecule or induce an undesired immune response. Additionally, some non-native aggregation mechanisms lead to amyloid fibril formation, which can be associated with debilitating diseases. For natively folded proteins, partial or complete unfolding is often required to populate aggregation-prone conformational states, and therefore one proposed strategy to mitigate aggregation is to increase the free energy for unfolding (ΔGunf) prior to aggregation. A computational design approach was tested using human γD crystallin (γD-crys) as a model multi-domain protein. Two mutational strategies were tested for their ability to reduce/increase aggregation rates by increasing/decreasing ΔGunf: stabilizing the less stable domain and stabilizing the domain-domain interface. The computational protein design algorithm, RosettaDesign, was implemented to identify point variants. The results showed that although the predicted free energies were only weakly correlated with the experimental ΔGunf values, increased/decreased aggregation rates for γD-crys correlated reasonably well with decreases/increases in experimental ΔGunf, illustrating improved conformational stability as a possible design target to mitigate aggregation. However, the results also illustrate that conformational stability is not the sole design factor controlling aggregation rates of natively folded proteins.

  5. Aggregation kinetics of human mesenchymal stem cells under wave motion.

    PubMed

    Tsai, Ang-Chen; Liu, Yijun; Yuan, Xuegang; Chella, Ravindran; Ma, Teng

    2016-12-20

    Human mesenchymal stem cells (hMSCs) are primary candidates in cell therapy and regenerative medicine but preserving their therapeutic potency following culture expansion is a significant challenge. hMSCs can spontaneously assemble into three-dimensional (3D) aggregates that enhance their regenerative properties. The present study investigated the impact of hydrodynamics conditions on hMSC aggregation kinetics under controlled rocking motion. While various laboratory methods have been developed for hMSC aggregate production, the rocking platform provides gentle mixing and can be scaled up using large bags as in wave motion bioreactors. The results show that the hMSC aggregation is mediated by cell adhesion molecules and that aggregate size distribution is influenced by seeding density, culture time, and hydrodynamic conditions. The analysis of fluid shear stress by COMSOL indicated that aggregate size distribution is inversely correlated with shear stress and that the rocking angle had a more pronounced effect on aggregate size distribution than the rocking speed due to its impact on shear stress. hMSC aggregates obtained from the bioreactor exhibit increased stemness, migratory properties, and expression of angiogenic factors. The results demonstrate the potential of the rocking platform to produce hMSC aggregates with controlled size distribution for therapeutic application.

  6. A study of the aggregation of cyclodextrins: Determination of the critical aggregation concentration, size of aggregates and thermodynamics using isodesmic and K2-K models.

    PubMed

    Do, Thao Thi; Van Hooghten, Rob; Van den Mooter, Guy

    2017-04-15

    The aggregation of three different cyclodextrins (CDs): 2-hydroxypropyl-β-cyclodextrin (HP-β-CD), 2-hydroxypropyl-γ-cyclodextrin (HP-γ-CD) and sulfobutylether-β-cyclodextrin (SBE-β-CD) was studied. The critical aggregation concentration (cac) of these three CDs is quite similar and is situated at ca. 2% (m/v). There was only a small difference in the cac values determined by DLS and (1)H NMR. DLS measurements revealed that CDs in solution have three size populations wherein one of them is that of a single CD molecule. The size of aggregates determined by TEM appears to be similar to the size of the aggregates in the second size distribution determined by DLS. Isodesmic and K2-K self-assembly models were used for studying the aggregation process of HP-β-CD, HP-γ-CD and SBE-β-CD. The results showed that the aggregation process of these CDs is a cooperative one, where the first step of aggregation is less favorable than the next steps. The determined thermodynamic parameters showed that the aggregation process of all three CDs is spontaneous and exothermic and it is driven by an increase of the entropy of the environment. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Technology meets aggregate

    SciTech Connect

    Wilson, C.; Swan, C.

    2007-07-01

    New technology carried out at Tufts University and the University of Massachusetts on synthetic lightweight aggregate has created material from various qualities of fly ash from coal-fired power plants for use in different engineered applications. In pilot scale manufacturing tests an 'SLA' containing 80% fly ash and 20% mixed plastic waste from packaging was produced by 'dry blending' mixed plastic with high carbon fly ash. A trial run was completed to produce concrete masonry unit (CMU) blocks at a full-scale facility. It has been shown that SLA can be used as a partial substitution of a traditional stone aggregate in hot asphalt mix. 1 fig., 2 photos.

  8. Rapid Coagulation of Porous Dust Aggregates outside the Snow Line: A Pathway to Successful Icy Planetesimal Formation

    NASA Astrophysics Data System (ADS)

    Okuzumi, Satoshi; Tanaka, Hidekazu; Kobayashi, Hiroshi; Wada, Koji

    2012-06-01

    Rapid orbital drift of macroscopic dust particles is one of the major obstacles to planetesimal formation in protoplanetary disks. We re-examine this problem by considering the porosity evolution of dust aggregates. We apply a porosity model based on recent N-body simulations of aggregate collisions, which allows us to study the porosity change upon collision for a wide range of impact energies. As a first step, we neglect collisional fragmentation and instead focus on dust evolution outside the snow line, where the fragmentation has been suggested to be less significant than inside the snow line because of the high sticking efficiency of icy particles. We show that dust particles can evolve into highly porous aggregates (with internal densities of much less than 0.1 g cm-3) even if collisional compression is taken into account. We also show that the high porosity triggers significant acceleration in collisional growth. This acceleration is a natural consequence of the particles' aerodynamical properties at low Knudsen numbers, i.e., at particle radii larger than the mean free path of the gas molecules. Thanks to this rapid growth, the highly porous aggregates are found to overcome the radial drift barrier at orbital radii less than 10 AU (assuming the minimum-mass solar nebula model). This suggests that, if collisional fragmentation is truly insignificant, formation of icy planetesimals is possible via direct collisional growth of submicron-sized icy particles.

  9. RAPID COAGULATION OF POROUS DUST AGGREGATES OUTSIDE THE SNOW LINE: A PATHWAY TO SUCCESSFUL ICY PLANETESIMAL FORMATION

    SciTech Connect

    Okuzumi, Satoshi; Kobayashi, Hiroshi; Tanaka, Hidekazu; Wada, Koji

    2012-06-20

    Rapid orbital drift of macroscopic dust particles is one of the major obstacles to planetesimal formation in protoplanetary disks. We re-examine this problem by considering the porosity evolution of dust aggregates. We apply a porosity model based on recent N-body simulations of aggregate collisions, which allows us to study the porosity change upon collision for a wide range of impact energies. As a first step, we neglect collisional fragmentation and instead focus on dust evolution outside the snow line, where the fragmentation has been suggested to be less significant than inside the snow line because of the high sticking efficiency of icy particles. We show that dust particles can evolve into highly porous aggregates (with internal densities of much less than 0.1 g cm{sup -3}) even if collisional compression is taken into account. We also show that the high porosity triggers significant acceleration in collisional growth. This acceleration is a natural consequence of the particles' aerodynamical properties at low Knudsen numbers, i.e., at particle radii larger than the mean free path of the gas molecules. Thanks to this rapid growth, the highly porous aggregates are found to overcome the radial drift barrier at orbital radii less than 10 AU (assuming the minimum-mass solar nebula model). This suggests that, if collisional fragmentation is truly insignificant, formation of icy planetesimals is possible via direct collisional growth of submicron-sized icy particles.

  10. Aggregation risk prediction for antibodies and its application to biotherapeutic development

    PubMed Central

    Obrezanova, Olga; Arnell, Andreas; de la Cuesta, Ramón Gómez; Berthelot, Maud E; Gallagher, Thomas RA; Zurdo, Jesús; Stallwood, Yvette

    2015-01-01

    Aggregation is a common problem affecting biopharmaceutical development that can have a significant effect on the quality of the product, as well as the safety to patients, particularly because of the increased risk of immune reactions. Here, we describe a new high-throughput screening algorithm developed to classify antibody molecules based on their propensity to aggregate. The tool, constructed and validated on experimental aggregation data for over 500 antibodies, is able to discern molecules with a high aggregation propensity as defined by experimental criteria relevant to bioprocessing and manufacturing of these molecules. Furthermore, we show how this tool can be combined with other computational approaches during early drug development to select molecules with reduced risk of aggregation and optimal developability properties. PMID:25760769

  11. Aggregation risk prediction for antibodies and its application to biotherapeutic development.

    PubMed

    Obrezanova, Olga; Arnell, Andreas; de la Cuesta, Ramón Gómez; Berthelot, Maud E; Gallagher, Thomas R A; Zurdo, Jesús; Stallwood, Yvette

    2015-01-01

    Aggregation is a common problem affecting biopharmaceutical development that can have a significant effect on the quality of the product, as well as the safety to patients, particularly because of the increased risk of immune reactions. Here, we describe a new high-throughput screening algorithm developed to classify antibody molecules based on their propensity to aggregate. The tool, constructed and validated on experimental aggregation data for over 500 antibodies, is able to discern molecules with a high aggregation propensity as defined by experimental criteria relevant to bioprocessing and manufacturing of these molecules. Furthermore, we show how this tool can be combined with other computational approaches during early drug development to select molecules with reduced risk of aggregation and optimal developability properties.

  12. J-aggregates of thiacyanine dye organized in LB films: Effect of irradiation of light

    NASA Astrophysics Data System (ADS)

    Hussain, Syed Arshad; Dey, Dibyendu; Chakraborty, S.; Bhattacharjee, D.

    2011-08-01

    In the present communication we report the preparation and characterizations of Langmuir and Langmuir-Blodgett films of a thiacyanine dye-dioctadecyl thiacyanine perchlorate (NK) mixed with Octadecyl trimethyl ammonium bromide (OTAB). The relationship between the molar ratio of OTAB and NK and the orientation of molecules at the air-water interface was investigated using surface pressure - area per molecule ({\\pi}-A) isotherm. UV-Vis absorption and fluorescence spectroscopic investigations reveal that prominent J-aggregation of NK molecule was observed in the LB films lifted at higher surface pressure. This J-aggregation can be controlled by diluting the NK molecules with OTAB. It was observed that the J-aggregates of NK decayed to monomer and H-aggregates when the NK-LB film was exposed to a monochromatic light of wavelength 460 nm (Lambda max of J - aggregates).

  13. Development of tau aggregation inhibitors for Alzheimer's disease.

    PubMed

    Bulic, Bruno; Pickhardt, Marcus; Schmidt, Boris; Mandelkow, Eva-Maria; Waldmann, Herbert; Mandelkow, Eckhard

    2009-01-01

    A variety of human diseases are suspected to be directly linked to protein misfolding. Highly organized protein aggregates, called amyloid fibrils, and aggregation intermediates are observed; these are considered to be mediators of cellular toxicity and thus attract a great deal of attention from investigators. Neurodegenerative pathologies such as Alzheimer's disease account for a major part of these protein misfolding diseases. The last decade has witnessed a renaissance of interest in inhibitors of tau aggregation as potential disease-modifying drugs for Alzheimer's disease and other "tauopathies". The recent report of a phase II clinical trial with the tau aggregation inhibitor MTC could hold promise for the validation of the concept. This Review summarizes the available data concerning small-molecule inhibitors of tau aggregation from a medicinal chemistry point of view.

  14. Different Strategies for Aggregation in Social Amoeba Colonies

    NASA Astrophysics Data System (ADS)

    Franck, Carl; Monaghan, Ryan; Bae, Albert; Loh, Duane; Bodenschatz, Eberhard

    2007-03-01

    When confronted by starvation, collections of the amoeba Dictyostelium discoideum seek to aggregate in order to form genome-preserving stalk and spore structures. We have been interested in the means by which individual cells unite for this purpose. It has long been recognized that communication by means of diffusion of small molecules affords one such strategy: periodic chemical wave signaling can direct individual cells to an aggregation site. By employing thin layer substrates that presumably alter the propagation characteristics of such waves, we have shifted the colonial aggregation strategies to modes that rely on adhesive interactions for initial stages of multicellular assembly. Besides relentless aggregation of individual cells into large scale streams, these substrates reveal remarkable structures composed of only a few cells which we call ``squads'' that search for each other in order to achieve sufficient aggregation mass in sparse populations.

  15. H- and J-aggregate behavior in polymeric semiconductors.

    PubMed

    Spano, Frank C; Silva, Carlos

    2014-01-01

    Aggregates of conjugated polymers exhibit two classes of fundamental electronic interactions: those occurring within a given chain and those occurring between chains. The impact of such excitonic interactions on the photophysics of polymer films can be understood using concepts of J- and H-aggregation originally developed by Kasha and coworkers to treat aggregates of small molecules. In polymer assemblies, intrachain through-bond interactions lead to J-aggregate behavior, whereas interchain Coulombic interactions lead to H-aggregate behavior. The photophysics of common emissive conjugated polymer films are determined by a competition between intrachain, J-favoring interactions and interchain, H-favoring interactions. We review formalisms describing absorption and photoluminescence lineshapes, based on intra- and intermolecular excitonic coupling, electron-vibrational coupling, and correlated energetic disorder. Examples include regioregular polythiophenes, pheneylene-vinylenes, and polydiacetylene.

  16. Circularly Polarized Luminescence from Simple Organic Molecules.

    PubMed

    Sánchez-Carnerero, Esther M; Agarrabeitia, Antonia R; Moreno, Florencio; Maroto, Beatriz L; Muller, Gilles; Ortiz, María J; de la Moya, Santiago

    2015-09-21

    This article aims to show the identity of "circularly polarized luminescent active simple organic molecules" as a new concept in organic chemistry due to the potential interest of these molecules, as availed by the exponentially growing number of research articles related to them. In particular, it describes and highlights the interest and difficulty in developing chiral simple (small and non-aggregated) organic molecules able to emit left- or right-circularly polarized light efficiently, the efforts realized up to now to reach this challenging objective, and the most significant milestones achieved to date. General guidelines for the preparation of these interesting molecules are also presented.

  17. In situ analysis of martian regolith with the SAM experiment during the first mars year of the MSL mission: Identification of organic molecules by gas chromatography from laboratory measurements

    NASA Astrophysics Data System (ADS)

    Millan, M.; Szopa, C.; Buch, A.; Coll, P.; Glavin, D. P.; Freissinet, C.; Navarro-Gonzalez, R.; François, P.; Coscia, D.; Bonnet, J. Y.; Teinturier, S.; Cabane, M.; Mahaffy, P. R.

    2016-09-01

    The Sample Analysis at Mars (SAM) instrument onboard the Curiosity rover, is specifically designed for in situ molecular and isotopic analyses of martian surface materials and atmosphere. It contributes to the Mars Science Laboratory (MSL) missions primary scientific goal to characterize the potential past, present or future habitability of Mars. In all of the analyses of solid samples delivered to SAM so far, chlorinated organic compounds have been detected above instrument background levels and identified by gas chromatography coupled to mass spectrometry (GC-MS) (Freissinet et al., 2015; Glavin et al., 2013). While some of these may originate from reactions between oxychlorines and terrestrial organic carbon present in the instrument background (Glavin et al., 2013), others have been demonstrated to originate from indigenous organic carbon present in samples (Freissinet et al., 2015). We present here laboratory calibrations that focused on the analyses performed with the MXT-CLP GC column (SAM GC-5 channel) used for nearly all of the GC-MS analyses of the martian soil samples carried out with SAM to date. Complementary to the mass spectrometric data, gas chromatography allows us to separate and identify the species analyzable in a nominal SAM-GC run time of about 21 min. To characterize the analytical capabilities of this channel within the SAM Flight Model (FM) operating conditions on Mars, and their implications on the detection of organic matter, it is required to perform laboratory experimental tests and calibrations on spare model components. This work assesses the SAM flight GC-5 column efficiency, confirms the identification of the molecules based on their retention time, and enables a better understanding of the behavior of the SAM injection trap (IT) and its release of organic molecules. This work will enable further optimization of the SAM-GC runs for additional samples to be analyzed during the MSL mission.

  18. In Situ Analysis of Martian Regolith with the SAM Experiment During the First Mars Year of the MSL Mission: Identification of Organic Molecules by Gas Chromatography from Laboratory Measurements

    NASA Technical Reports Server (NTRS)

    Millan, M.; Szopa, C.; Buch, A.; Coll, P.; Glavin, D. P.; Freissinet, C.; Navarro-Gonzalez, R.; Francois, P.; Coscia, D.; Bonnet, J. Y.; hide

    2016-01-01

    The Sample Analysis at Mars (SAM) instrument onboard the Curiosity rover, is specifically designed for in situ molecular and isotopic analyses of martian surface materials and atmosphere. It contributes to the Mars Science Laboratory (MSL) missions primary scientific goal to characterize the potential past, present or future habitability of Mars. In all of the analyses of solid samples delivered to SAM so far, chlorinated organic compounds have been detected above instrument background levels and identified by gas chromatography coupled to mass spectrometry (GC-MS) (Freissinet et al., 2015; Glavin et al., 2013). While some of these may originate from reactions between oxychlorines and terrestrial organic carbon present in the instrument background (Glavin et al., 2013), others have been demonstrated to originate from indigenous organic carbon present in samples (Freissinet et al., 2015). We present here laboratory calibrations that focused on the analyses performed with the MXT-CLP GC column (SAM GC-5 channel) used for nearly all of the GC-MS analyses of the martian soil samples carried out with SAM to date. Complementary to the mass spectrometric data, gas chromatography allows us to separate and identify the species analyzable in a nominal SAM-GC run time of about 21 min. To characterize the analytical capabilities of this channel within the SAM Flight Model (FM) operating conditions on Mars, and their implications on the detection of organic matter, it is required to perform laboratory experimental tests and calibrations on spare model components. This work assesses the SAM flight GC-5 column efficiency, confirms the identification of the molecules based on their retention time, and enables a better understanding of the behavior of the SAM injection trap (IT) and its release of organic molecules. This work will enable further optimization of the SAM-GC runs for additional samples to be analyzed during the MSL mission.

  19. Stable Colloidal Drug Aggregates Catch and Release Active Enzymes

    PubMed Central

    McLaughlin, Christopher K.; Duan, Da; Ganesh, Ahil N.; Torosyan, Hayarpi

    2016-01-01

    Small molecule aggregates are considered nuisance compounds in drug discovery, but their unusual properties as colloids could be exploited to form stable vehicles to preserve protein activity. We investigated the co-aggregation of seven molecules chosen because they had been previously intensely studied as colloidal aggregators, co-formulating them with bis-azo dyes. The co-formulation reduced colloid sizes to <100 nm, and improved uniformity of the particle size distribution. The new colloid formulations are more stable than previous aggregator particles. Specifically, co-aggregation of Congo Red with sorafenib, tetraiodophenolphthalein (TIPT) or vemurafenib produced particles that are stable in solutions of high ionic strength and high protein concentrations. Like traditional, single compound colloidal aggregates, the stabilized colloids adsorbed and inhibited enzymes like β-lactamase, malate dehydrogenase and trypsin. Unlike traditional aggregates, the co-formulated colloid-protein particles could be centrifuged and re-suspended multiple times, and from re-suspended particles, active trypsin could be released up to 72 hours after adsorption. Unexpectedly, the stable colloidal formulations can sequester, stabilize, and isolate enzymes by spin-down, resuspension and release. PMID:26741163

  20. Coupling of aggregation and immunogenicity in biotherapeutics: T- and B-cell immune epitopes may contain aggregation-prone regions.

    PubMed

    Kumar, Sandeep; Singh, Satish K; Wang, Xiaoling; Rup, Bonita; Gill, Davinder

    2011-05-01

    Biotherapeutics, including recombinant or plasma-derived human proteins and antibody-based molecules, have emerged as an important class of pharmaceuticals. Aggregation and immunogenicity are among the major bottlenecks during discovery and development of biotherapeutics. Computational tools that can predict aggregation prone regions as well as T- and B-cell immune epitopes from protein sequence and structure have become available recently. Here, we describe a potential coupling between aggregation and immunogenicity: T-cell and B-cell immune epitopes in therapeutic proteins may contain aggregation-prone regions. The details of biological mechanisms behind this observation remain to be understood. However, our observation opens up an exciting potential for rational design of de-immunized novel, as well as follow on biotherapeutics with reduced aggregation propensity.

  1. Aggregates, broccoli and cauliflower

    NASA Astrophysics Data System (ADS)

    Grey, Francois; Kjems, Jørgen K.

    1989-09-01

    Naturally grown structures with fractal characters like broccoli and cauliflower are discussed and compared with DLA-type aggregates. It is suggested that the branching density can be used to characterize the growth process and an experimental method to determine this parameter is proposed.

  2. Gas-Sensing Devices Based on Zn-Doped NiO Two-Dimensional Grainy Films with Fast Response and Recovery for Ammonia Molecule Detection.

    PubMed

    Wang, Jian; Wei, Xiaowei; Wangyang, Peihua

    2015-12-01

    Zn-doped NiO two-dimensional grainy films on glass substrates are shown to be an ammonia-sensing material with excellent comprehensive performance, which could real-time detect and monitor ammonia (NH3) in the surrounding environment. The morphology and structure analysis indicated that the as-fabricated semiconductor films were composed of particles with diameters ranging from 80 to 160 nm, and each particle was composed of small crystalline grain with a narrow size about 20 nm, which was the face-centered cubic single crystal structure. X-ray diffraction peaks shifted toward lower angle, and the size of the lattice increased compared with undoped NiO, which demonstrated that zinc ions have been successfully doped into the NiO host structure. Simultaneously, we systematically investigated the gas-sensing properties of the Zn-doped NiO sensors for NH3 detection at room temperature. The sensor based on doped NiO sensing films gave four to nine times faster response and four to six times faster recovery speeds than those of sensor with undoped NiO films, which is important for the NiO sensor practical applications. Moreover, we found that the doped NiO sensors owned outstanding selectivity toward ammonia.

  3. First application of mass spectrometry and gas chromatography in investigation of α-cellulose hydrolysates: the influence of climate changes on glucose molecules in pine tree-rings.

    PubMed

    Sensuła, Barbara M; Pazdur, Anna; Marais, Marie-France

    2011-02-28

    We present the first results of the quantitative and qualitative gas chromatographic and isotope ratio mass spectrometric analysis of monosaccharides derived from acid hydrolysis of α-cellulose extracted from annual pine tree-rings. The conifers investigated in this study grew in the Niepolomice Forest in Poland, and the annual rings covered the time span from 1940 to 2000 AD. The main components of the α-cellulose samples were two saccharides: glucose and mannose. The amount of glucose in the annual rings varied between 17 and 44%. The δ(13)C of glucose was found to be less negative than that of α-cellulose and the δ(18)O values in glucose were less positive than those in α-cellulose. The content of monosaccharides in the α-cellulose samples has an influence on the isotope fractionation factors. The values of the carbon isotope fractionation factor increase with an increase in the monosaccharides concentration in α-cellulose, while the values of the oxygen isotope fractionation factor decrease with an increase in monosaccharides concentration in α-cellulose. The challenge is to establish, with respect to climate changes and environmental conditions, the significance of the interannual variations in the observed monosaccharide concentration.

  4. A selected ion flow tube study of the reactions of NO + and O + 2 ions with some organic molecules: The potential for trace gas analysis of air

    NASA Astrophysics Data System (ADS)

    Španěl, Patrik; Smith, David

    1996-02-01

    A study has been carried out using our selected ion flow tube apparatus of the reactions of NO+ and O+2 ions in their vibronic ground states with ten organic species: the hydrocarbons, benzene, toluene, isoprene, cyclopropane, and n-pentane; the oxygen-containing organics, methanol, ethanol, acetaldehyde, acetone, and diethyl ether. The major objectives of this work are, on the one hand, to fully understand the processes involved in these reactions and, on the other hand, to explore the potential of NO+ and O+2 as chemical ionization agents for the analysis of trace gases in air and on human breath. Amongst the NO+ reactions, charge transfer, hydride-ion transfer, and termolecular association occur, and the measured rate coefficients, k, for the reactions vary from immeasurably small to the maximum value, collisional rate coefficient, kc. The O+2 reactions are all fast, in each case the k being equal to or an appreciable fraction of kc, and charge transfer producing the parent organic ion or dissociative charge transfer resulting in two or three fragments of the parent ion are the reaction processes that occur. We conclude from these studies, and from previous studies, that NO+ ions and O+2 ions can be used to great effect as chemical ionization agents for trace gas analysis, especially in combination with H3O+ ions which we now routinely use for this purpose.

  5. SDS-assisted hydrothermal synthesis of NiO flake-flower architectures with enhanced gas-sensing properties

    NASA Astrophysics Data System (ADS)

    Miao, Ruiyang; Zeng, Wen; Gao, Qi

    2016-10-01

    A facile hydrothermal route was developed for the preparation of well-aligned hierarchical flower-like NiO nanostructure with the assistance of SDS that served as a structure-directing agent as well as a capping agent in the process of aggregation and assembly. Notably, the NiO sensors exhibit enhanced gas-sensing performance towards ethanol, which could be explained in association with the ultrathin nanosheets that are close to Debye length (LD) scale and thus get the majority carriers fully depleted due to the ionization of adsorbed oxygen, abundant effective gas diffusion paths as well as high surface-to-volume ratio to promote sufficient contact and reaction between the NiO sample and ethanol molecules, and numerous miniature reaction rooms assembled with nanosheets to make the test gas molecules stay long enough for completed gas-sensing reactions. Besides, a novel growth mechanism with the passage of reaction time was also proposed in detail.

  6. Unequilibrated, equilibrated, and reduced aggregates in anhydrous interplanetary dust particles

    NASA Astrophysics Data System (ADS)

    Bradley, J. P.

    1993-03-01

    Track-rich anhydrous IDP's are probably the most primitive IDP's because they have escaped significant post-accretional alteration; they exhibit evidence of (nebular) gas phase reactions; their mineralogy is similar to comet Halley's dust; and some of them exhibit comet-like IR spectral characteristics. However, basic questions about the mineralogy and petrography of anhydrous IDP's remain unanswered, because they contain aggregated components that can be heterogeneous on a scale of nanometers. In some IDP's, aggregates account for greater than 75 percent of the volume of the particle. The aggregates have been systematically examined using an analytical electron microscope (AEM), which provides probe-forming optics and (x-ray and electron) spectrometers necessary to analyze individual nanometer-sized grains. The AEM results reveal at least three mineralogically distinct classes of aggregates in an hydrous IDP's, with mineralogies reflecting significantly different formation/aggregation environments.

  7. The in situ gas-phase formation of a C-glycoside ion obtained during electrospray ionization tandem mass spectrometry. A unique intramolecular mechanism involving an ion-molecule reaction.

    PubMed

    Banoub, Joseph H; Demian, Wael L L; Piazzetta, Paolo; Sarkis, George; Kanawati, Basem; Lafont, Dominique; Laurent, Nicolas; Vaillant, Celine; Randell, Edward; Giorgi, Gianluca; Fridgen, Travis D

    2015-10-15

    This study examines the electrospray ionization mass spectrometry (ESI-MS), in-source collision-induced dissociation (CID) fragmentation and low-energy collision-induced dissociation tandem mass spectrometry (CID-MS/MS) of a synthetic pair of β- and α-anomers of the amphiphilic cholesteryl polyethoxy neoglycolipids containing the 2-azido-2-deoxy-D-galactosyl-D-GalN3 moiety. We describe the novel and unique in situ gas-phase formation of a C-glycoside ion formed during all these gas-phase processes and propose a reasonable mechanism for its formation. The synthetic amphiphilic glycolipids were composed of the 2-deoxy-2-azido-D-galactosyl moiety (GalN3, the hydrophilic part) covalently attached to a polyethoxy spacer which is covalently linked to the cholesteryl moiety (hydrophobic part). The 2-azido-2-deoxy-α- and β-D-galactosyl-containing glycolipids were studied by in-time and in-space ESI-MS and CID-MS/MS in positive ion mode, with quadrupole ion trap (QIT), quadrupole-quadrupole-time-of-flight (QqTOF), and Fourier transform ion cyclotron resonance (FTICR) instruments. Conventional single-stage ESI-MS analysis showed the formation of the protonated molecule. During the single-stage ESI-MS analysis and the CID-MS/MS of the [M+H](+) and [M+NH4](+) adducts obtained from both glycolipid anomers, the presence of a series of specific product ions with different intensities was observed, consistent with the [C-glycoside+H-N2](+), [cholestadiene+H](+), 2-deoxy-2-D-azido-galactosyl [GalN3](+), [GalNH](+) and [sugar-Spacer+H](+) ions. The gas-phase formation of the [C-glycoside+H-N2](+) ion isolated from the glycolipid anomers was observed during both the ESI-MS of the glycolipids and the CID-MS/MS analyses of the [M+H](+) ions and it was found to occur by an intramolecular rearrangement involving an ion-molecule complex. CID-QqTOF-MS/MS and CID-FTICR-MS(2) analysis allowed the differentiation of the two glycolipid anomers and showed noticeable variation in the

  8. Aggregation of MBP in chronic demyelination

    PubMed Central

    Frid, Kati; Einstein, Ofira; Friedman-Levi, Yael; Binyamin, Orli; Ben-Hur, Tamir; Gabizon, Ruth

    2015-01-01

    Objectives Misfolding of key disease proteins to an insoluble state is associated with most neurodegenerative conditions, such as prion, Parkinson, and Alzheimer’s diseases. In this work, and by studying animal models of multiple sclerosis, we asked whether this is also the case for myelin basic protein (MBP) in the late and neurodegenerative phases of demyelinating diseases. Methods To this effect, we tested whether MBP, an essential myelin component, present prion-like properties in animal models of MS, as is the case for Cuprizone-induced chronic demyelination or chronic phases of Experimental Autoimmune Encephalomyelitis (EAE). Results We show here that while total levels of MBP were not reduced following extensive demyelination, part of these molecules accumulated thereafter as aggregates inside oligodendrocytes or around neuronal cells. In chronic EAE, MBP precipitated concomitantly with Tau, a marker of diverse neurodegenerative conditions, including MS. Most important, analysis of fractions from Triton X-100 floatation gradients suggest that the lipid composition of brain membranes in chronic EAE differs significantly from that of naïve mice, an effect which may relate to oxidative insults and subsequently prevent the appropriate insertion and compaction of new MBP in the myelin sheath, thereby causing its misfolding and aggregation. Interpretation Prion-like aggregation of MBP following chronic demyelination may result from an aberrant lipid composition accompanying this pathological status. Such aggregation of MBP may contribute to neuronal damage that occurs in the progressive phase of MS. PMID:26273684

  9. Stay connected: Electrical conductivity of microbial aggregates.

    PubMed

    Li, Cheng; Lesnik, Keaton Larson; Liu, Hong

    2017-11-01

    The discovery of direct extracellular electron transfer offers an alternative to the traditional understanding of diffusional electron exchange via small molecules. The establishment of electronic connections between electron donors and acceptors in microbial communities is critical to electron transfer via electrical currents. These connections are facilitated through conductivity associated with various microbial aggregates. However, examination of conductivity in microbial samples is still in its relative infancy and conceptual models in terms of conductive mechanisms are still being developed and debated. The present review summarizes the fundamental understanding of electrical conductivity in microbial aggregates (e.g. biofilms, granules, consortia, and multicellular filaments) highlighting recent findings and key discoveries. A greater understanding of electrical conductivity in microbial aggregates could facilitate the survey for additional microbial communities that rely on direct extracellular electron transfer for survival, inform rational design towards the aggregates-based production of bioenergy/bioproducts, and inspire the construction of new synthetic conductive polymers. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Asphaltene aggregation and impact of alkylphenols.

    PubMed

    Goual, Lamia; Sedghi, Mohammad; Wang, Xiaoxiao; Zhu, Ziming

    2014-05-20

    The main objective of this study was to provide novel insights into the mechanism of asphaltene aggregation in toluene/heptane (Heptol) solutions and the effect of alkylphenols on asphaltene dispersion through the integration of advanced experimental and modeling methods. High-resolution transmission electron microscope (HRTEM) images revealed that the onset of asphaltene flocculation occurs near a toluene/heptane volume ratio of 70:30 and that flocculates are well below 1 μm in size. To assess the impact of alkylphenols on asphaltene aggregation, octylphenol (OP) and dodecylphenol (DP) were evaluated by impedance analysis based on their ability to delay the precipitation onset and to reduce the size of nonflocculated asphaltene aggregates in 80:20 toluene/heptane solutions. Although a longer dispersant chain length did not affect the precipitation onset, it reduced the size of the aggregates. Molecular dynamics simulations were then performed to understand the mechanism of interaction between a model asphaltene and OP in heptane. OP molecules saturated the H-bonding sites of asphaltenes and prevented them from interacting laterally between themselves. This explained why OP favored the formation of flocculates with filamentary rather than globular structures, which were clearly observed by HRTEM. Although OP proved to be an effective dispersant, its effectiveness was hindered by its self-association and the fact that it interacted at the periphery of asphaltenes, leaving their aromatic cores uncovered.

  11. Explicit solvent simulations of the aqueous oxidation potential and reorganization energy for neutral molecules: gas phase, linear solvent response, and non-linear response contributions.

    PubMed

    Guerard, Jennifer J; Tentscher, Peter R; Seijo, Marianne; Samuel Arey, J

    2015-06-14

    First principles simulations were used to predict aqueous one-electron oxidation potentials (Eox) and associated half-cell reorganization energies (λaq) for aniline, phenol, methoxybenzene, imidazole, and dimethylsulfide. We employed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations of the oxidized and reduced species in an explicit aqueous solvent, followed by EOM-IP-CCSD computations with effective fragment potentials for diabatic energy gaps of solvated clusters, and finally thermodynamic integration of the non-linear solvent response contribution using classical MD. A priori predicted Eox and λaq values exhibit mean absolute errors of 0.17 V and 0.06 eV, respectively, compared to experiment. We also disaggregate Eox into several well-defined free energy properties, including the gas phase adiabatic free energy of ionization (7.73 to 8.82 eV), the solvent-induced shift in the free energy of ionization due to linear solvent response (-2.01 to -2.73 eV), and the contribution from non-linear solvent response (-0.07 to -0.14 eV). The linear solvent response component is further apportioned into contributions from the solvent-induced shift in vertical ionization energy of the reduced species (ΔVIEaq) and the solvent-induced shift in negative vertical electron affinity of the ionized species (ΔNVEAaq). The simulated ΔVIEaq and ΔNVEAaq are found to contribute the principal sources of uncertainty in computational estimates of Eox and λaq. Trends in the magnitudes of disaggregated solvation properties are found to correlate with trends in structural and electronic features of the solute. Finally, conflicting approaches for evaluating the aqueous reorganization energy are contrasted and discussed, and concluding recommendations are given.

  12. Vibrational wave packets: Molecular state reconstruction in the gas phase and mixed quantum/semiclassical descriptions of small-molecule dynamics in low-temperature solid media

    NASA Astrophysics Data System (ADS)

    Chapman, Craig Thomas

    We explore the reconstruction of B-state vibrational wave packets in I2 from simulated two-color nonlinear wave packet interferometry data. As a simplification of earlier proposals, we make use of different vibrational energy ranges in the B-state---rather than different electronic potential surfaces---for the short-pulse preparation and propagation of both target and reference wave packets. Numerical results from noisy interferograms indicate that experimental reconstruction should be possible with high fidelity (>0.99). Time-resolved coherent nonlinear optical experiments on small molecules in low-temperature host crystals are exposing valuable information on quantum mechanical dynamics in condensed media. We make use of generic features of these systems to frame two simple, comprehensive theories that will enable the efficient calculation of their ultrafast spectroscopic signals and support their interpretation in terms of the underlying chemical dynamics. Both treatments rely on the identification of normal coordinates to unambiguously partition the well-structured guest-host complex into a system and a bath and expand the overall wave function as a sum of product states between fully anharmonic vibrational basis states for the system and approximate Gaussian wave packets for the bath degrees of freedom. The theories exploit the fact that ultrafast experiments typically drive large-amplitude motion in a few intramolecular degrees of freedom of higher frequency than the crystal phonons, while these intramolecular vibrations indirectly induce smaller-amplitude---but still perhaps coherent---motion among the lattice modes. The equations of motion for the time-dependent parameters of the bath wave packets are fairly compact in a fixed vibrational basis/Gaussian bath (FVB/GB) approach. An alternative adiabatic vibrational basis/Gaussian bath (AVB/GB) treatment leads to more complicated equations of motion involving adiabatic and nonadiabatic vector potentials

  13. 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.

  14. 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.

  15. Aggregation methodology for the circum-arctic resource appraisal

    USGS Publications Warehouse

    Schuenemeyer, John H.; Gautier, Donald L.

    2009-01-01

    This paper presents a methodology that intends to aggregate the results of a recent assessment of undiscovered conventional oil and gas resources of the Arctic by the U.S. Geological Survey. The assessment occurred in 48 geologically defined regions called assessment units. The methodology includes using assessor specified pair-wise correlations as the basis to construct a correlation matrix. Sampling from this matrix generates more realistic uncertainty estimates of aggregated resources than if assumptions of total independence or total dependence are made. The latter two assumptions result in overly narrow or overly broad estimates. Aggregation results for resources in regions north of the Arctic Circle are presented.

  16. Variation and decomposition of the partial molar volume of small gas molecules in different organic solvents derived from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Klähn, Marco; Martin, Alistair; Cheong, Daniel W.; Garland, Marc V.

    2013-12-01

    The partial molar volumes, bar V_i, of the gas solutes H2, CO, and CO2, solvated in acetone, methanol, heptane, and diethylether are determined computationally in the limit of infinite dilution and standard conditions. Solutions are described with molecular dynamics simulations in combination with the OPLS-aa force field for solvents and customized force field for solutes. bar V_i is determined with the direct method, while the composition of bar V_i is studied with Kirkwood-Buff integrals (KBIs). Subsequently, the amount of unoccupied space and size of pre-formed cavities in pure solvents is determined. Additionally, the shape of individual solvent cages is analyzed. Calculated bar V_i deviate only 3.4 cm3 mol-1 (7.1%) from experimental literature values. Experimental bar V_i variations across solutions are reproduced qualitatively and also quantitatively in most cases. The KBI analysis identifies differences in solute induced solvent reorganization in the immediate vicinity of H2 (<0.7 nm) and solvent reorganization up to the third solvation shell of CO and CO2 (<1.6 nm) as the origin of bar V_i variations. In all solutions, larger bar V_i are found in solvents that exhibit weak internal interactions, low cohesive energy density and large compressibility. Weak internal interactions facilitate solvent displacement by thermal solute movement, which enhances the size of solvent cages and thus bar V_i. Additionally, attractive electrostatic interactions of CO2 and the solvents, which do not depend on internal solvent interactions only, partially reversed the bar V_i trends observed in H2 and CO solutions where electrostatic interactions with the solvents are absent. More empty space and larger pre-formed cavities are found in solvents with weak internal interactions, however, no evidence is found that solutes in any considered solvent are accommodated in pre-formed cavities. Individual solvent cages are found to be elongated in the negative direction of solute

  17. Strain-dependent profile of misfolded prion protein aggregates

    PubMed Central

    Morales, Rodrigo; Hu, Ping Ping; Duran-Aniotz, Claudia; Moda, Fabio; Diaz-Espinoza, Rodrigo; Chen, Baian; Bravo-Alegria, Javiera; Makarava, Natallia; Baskakov, Ilia V.; Soto, Claudio

    2016-01-01

    Prions are composed of the misfolded prion protein (PrPSc) organized in a variety of aggregates. An important question in the prion field has been to determine the identity of functional PrPSc aggregates. In this study, we used equilibrium sedimentation in sucrose density gradients to separate PrPSc aggregates from three hamster prion strains (Hyper, Drowsy, SSLOW) subjected to minimal manipulations. We show that PrPSc aggregates distribute in a wide range of arrangements and the relative proportion of each species depends on the prion strain. We observed a direct correlation between the density of the predominant PrPSc aggregates and the incubation periods for the strains studied. The relative presence of PrPSc in fractions of different sucrose densities was indicative of the protein deposits present in the brain as analyzed by histology. Interestingly, no association was found between sensitivity to proteolytic degradation and aggregation profiles. Therefore, the organization of PrP molecules in terms of the density of aggregates generated may determine some of the particular strain properties, whereas others are independent from it. Our findings may contribute to understand the mechanisms of strain variation and the role of PrPSc aggregates in prion-induced neurodegeneration. PMID:26877167

  18. Strain-dependent profile of misfolded prion protein aggregates.

    PubMed

    Morales, Rodrigo; Hu, Ping Ping; Duran-Aniotz, Claudia; Moda, Fabio; Diaz-Espinoza, Rodrigo; Chen, Baian; Bravo-Alegria, Javiera; Makarava, Natallia; Baskakov, Ilia V; Soto, Claudio

    2016-02-15

    Prions are composed of the misfolded prion protein (PrP(Sc)) organized in a variety of aggregates. An important question in the prion field has been to determine the identity of functional PrP(Sc) aggregates. In this study, we used equilibrium sedimentation in sucrose density gradients to separate PrP(Sc) aggregates from three hamster prion strains (Hyper, Drowsy, SSLOW) subjected to minimal manipulations. We show that PrP(Sc) aggregates distribute in a wide range of arrangements and the relative proportion of each species depends on the prion strain. We observed a direct correlation between the density of the predominant PrP(Sc) aggregates and the incubation periods for the strains studied. The relative presence of PrP(Sc) in fractions of different sucrose densities was indicative of the protein deposits present in the brain as analyzed by histology. Interestingly, no association was found between sensitivity to proteolytic degradation and aggregation profiles. Therefore, the organization of PrP molecules in terms of the density of aggregates generated may determine some of the particular strain properties, whereas others are independent from it. Our findings may contribute to understand the mechanisms of strain variation and the role of PrP(Sc) aggregates in prion-induced neurodegeneration.

  19. Association equation of state (AEOS) based on aggregate formation for pure substance

    NASA Astrophysics Data System (ADS)

    Mohsen-Nia, M.; Modarress, H.

    2007-07-01

    Based on the statistical mechanical theories and by using the concept of grand canonical ensemble a new equation of state for aggregate formations in the association fluids has been proposed. The compressibility factor for aggregate formation in an association fluid is represented by the following equation: Z=Z+Z-1 where Zagg is the aggregate compressibility factor due to aggregate formation by hydrogen bonding of molecules and Zdis is the dispersed compressibility factor due to dispersion interactions. Each aggregate is considered as an open system in the grand canonical ensemble in which a molecule can enter to form a larger aggregate or leave to form a smaller aggregate. The average number of molecules in an aggregate is used to obtain the compressibility factor Zagg and M4 equation of state previously proposed by Mohsen-Nia et al. [M. Mohsen-Nia, H. Modarress, G.A. Mansoori, Fluid Phase Equilibr. 206 (2003) 27.] for non-association compounds is used to obtain Zdis. The obtained new association equation of state (AEOS) based on the proposed compressibility factor is used for saturated properties calculations of pure well-known association fluids: water, ammonia and methanol. The results indicate that the saturated properties are well correlated by the new AEOS with a reasonable average number of molecules in each aggregate which is in agreement with spectroscopic experimental data and ab initio calculations.

  20. Tau protein and tau aggregation inhibitors.

    PubMed

    Bulic, Bruno; Pickhardt, Marcus; Mandelkow, Eva-Maria; Mandelkow, Eckhard

    2010-01-01

    Alzheimer disease is characterized by pathological aggregation of two proteins, tau and Abeta-amyloid, both of which are considered to be toxic to neurons. In this review we summarize recent advances on small molecule inhibitors of protein aggregation with emphasis on tau, with activities mediated by the direct interference of self-assembly. The inhibitors can be clustered in several compound classes according to their chemical structure, with subsequent description of the structure-activity relationships, showing that hydrophobic interactions are prevailing. The description is extended to the pharmacological profile of the compounds in order to evaluate their drug-likeness, with special attention to toxicity and bioavailability. The collected data indicate that following the improvements of the in vitro inhibitory potencies, the consideration of the in vivo pharmacokinetics is an absolute prerequisite for the development of compounds suitable for a transfer from bench to bedside.