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.

Influence of reactive gas admixture on transition metal cluster nucleation in a gas aggregation cluster source

NASA Astrophysics Data System (ADS)

Peter, Tilo; Polonskyi, Oleksandr; Gojdka, Björn; Mohammad Ahadi, Amir; Strunskus, Thomas; Zaporojtchenko, Vladimir; Biederman, Hynek; Faupel, Franz

2012-12-01

We quantitatively assessed the influence of reactive gases on the formation processes of transition metal clusters in a gas aggregation cluster source. A cluster source based on a 2 in. magnetron is used to study the production rate of titanium and cobalt clusters. Argon served as working gas for the DC magnetron discharge, and a small amount of reactive gas (oxygen and nitrogen) is added to promote reactive cluster formation. We found that the cluster production rate depends strongly on the reactive gas concentration for very small amounts of reactive gas (less than 0.1% of total working gas), and no cluster formation takes place in the absence of reactive species. The influence of discharge power, reactive gas concentration, and working gas pressure are investigated using a quartz micro balance in a time resolved manner. The strong influence of reactive gas is explained by a more efficient formation of nucleation seeds for metal-oxide or nitride than for pure metal.

A permanent magnet trap for buffer gas cooled atoms and molecules

NASA Astrophysics Data System (ADS)

Nohlmans, D.; Skoff, S. M.; Hendricks, R. J.; Segal, D. M.; Sauer, B. E.; Hinds, E. A.; Tarbutt, M. R.

2013-05-01

Cold molecules are set to provide a wealth of new science compared to their atomic counterparts. Here we want to present preliminary results for cooling and trapping atoms/molecules in a permanent magnetic trap. By replacing the conventional buffer gas cell with an arrangement of permanent magnets, we will be able to trap a fraction of the molecules right where they are cooled. For this purpose we have designed a quadrupole trap using NdFeB magnets, which has a trap depth of 0.4 K for molecules with a magnetic moment of 1 μB. Cold helium gas is pulsed into the trap region by a solenoid valve and the atoms/molecules are subsequently ablated into this and cooled via elastic collisions, leaving a fraction of them trapped. This new set-up is currently being tested with lithium atoms as they are easier to make. After having optimised the trapping and detection processes, we will use the same trap for YbF molecules.

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

PubMed

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

2017-03-08

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 IC 50s 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.

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.

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.

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.

Detection of gas molecules on single Mn adatom adsorbed graphyne: a DFT-D study

NASA Astrophysics Data System (ADS)

Lu, Zhansheng; Lv, Peng; Ma, Dongwei; Yang, Xinwei; Li, Shuo; Yang, Zongxian

2018-02-01

As one of the prominent applications in intelligent systems, gas sensing technology has attracted great interest in both industry and academia. In the current study, the pristine graphyne (GY) without and with a single Mn atom is investigated to detect the gas molecules (CO, CH4, CO2, NH3, NO and O2). The pristine GY is promising to detect O2 molecules because of its chemical adsorption on GY with large electron transfer. The great stability of the Mn/GY is found, and the Mn atom prefers to anchor at the alkyne ring as a single atom. Upon single Mn atom anchoring, the sensitivity and selectivity of GY based gas sensors is significantly improved for various molecules, except CH4. The recovery time of the Mn/GY after detecting the gas molecules may help to appraise the detection efficiency for the Mn/GY. The current study will help to understand the mechanism of detecting the gas molecules, and extend the potentially fascinating applications of GY-based materials.

Erythrocyte interactions - Comparison of the aggregation power of polymer molecules used in medicine - Not only size does matter.

PubMed

Jovtchev, S; Alexandrov, S; Hristova-Avakumova, N; Miteva, S; Traikov, L; Gerasimova, D; Stoeff, S

2016-01-01

Different colloids are used as a part of solutions for fluid resuscitation and organ preservation: hydroxyethyl starches (HES), dextran (Dx), polyethylene glycols (PEG), polyvinyl pyrrolidone (PVP). Some of the problems associated with their application are addressed to alteration in erythrocyte (ERY) rheology. We intended to estimate in vitro and compare the aggregation power (AP) of these molecules related to ERY interactions. Washed human ERY are used during the study. The zeta sedimentation technique is used to quantify the cell aggregation. Zeta sedimentation ratio (ZSR) based indices (AI) are calculated. The hydrodynamic radius (Rh) of the polymer molecules is determined using viscometry. For all polymers tested a linear range in the relationship AI - concentration was found. The slope of the calculated line was interpreted as measure of the molecule's AP. The following ranking was obtained: PEG >PVP >DX >HES. Within the same chemical type of polymer, increasing Rh of the molecules leads to elevated AI. Comparison of the AP of molecules with similar Rh reveals a significant dependence on their chemical nature. Our results show that molecule's AP is significantly dependent on their chemical nature - i.e. not only molecular size does matter.

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.

Adsorption of gas molecules on Cu impurities embedded monolayer MoS2: A first- principles study

NASA Astrophysics Data System (ADS)

Zhao, B.; Li, C. Y.; Liu, L. L.; Zhou, B.; Zhang, Q. K.; Chen, Z. Q.; Tang, Z.

2016-09-01

Adsorption of small gas molecules (O2, NO, NO2 and NH3) on transition-metal Cu atom embedded monolayer MoS2 was investigated by first-principles calculations based on the density-functional theory (DFT). The embedded Cu atom is strongly constrained on the sulfur vacancy of monolayer MoS2 with a high diffusion barrier. The stable adsorption geometry, charge transfer and electronic structures of these gas molecules on monolayer MoS2 embedded with transition-metal Cu atom are discussed in detail. It is found that the monolayer MoS2 with embedded Cu atom can effectively capture these gas molecules with high adsorption energy. The NH3 molecule acts as electron donor after adsorption, which is different from the other gas molecules (O2, NO, and NO2). The results suggest that MoS2-Cu system may be promising for future applications in gas molecules sensing and catalysis, which is similar to those of the transition-metal embedded graphene.

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.

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.

Influence of source parameters on the growth of metal nanoparticles by sputter-gas-aggregation

NASA Astrophysics Data System (ADS)

Khojasteh, Malak; Kresin, Vitaly V.

2017-11-01

We describe the production of size-selected manganese nanoclusters using a magnetron sputtering/aggregation source. Since nanoparticle production is sensitive to a range of overlapping operating parameters (in particular, the sputtering discharge power, the inert gas flow rates, and the aggregation length), we focus on a detailed map of the influence of each parameter on the average nanocluster size. In this way, it is possible to identify the main contribution of each parameter to the physical processes taking place within the source. The discharge power and argon flow supply the metal vapor, and argon also plays a crucial role in the formation of condensation nuclei via three-body collisions. However, the argon flow and the discharge power have a relatively weak effect on the average nanocluster size in the exiting beam. Here the defining role is played by the source residence time, governed by the helium supply (which raises the pressure and density of the gas column inside the source, resulting in more efficient transport of nanoparticles to the exit) and by the aggregation path length.

Complex organic molecules in strongly UV-irradiated gas.

PubMed

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 H 2 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 H 2 CO J K a , K c = 5 1,5 → 4 1,4 and C 18 O J = 3 → 2 emission at 0.9 mm. Despite being a harsh environment, we detect more than 250 lines from COMs and related precursors: H 2 CO, CH 3 OH, HCO, H 2 CCO, CH 3 CHO, H 2 CS, HCOOH, CH 3 CN, CH 2 NH, HNCO, [Formula: see text] and HC 3 N (in decreasing order of abundance). For each species, the large number of detected lines allowed us to accurately constrain their rotational temperatures ( T rot ) and column densities ( N ). Owing to subthermal excitation and intricate spectroscopy of some COMs (symmetric- and asymmetric-top molecules such as CH 3 CN and H 2 CO, respectively), a correct determination of N and T rot requires building rotational population diagrams of their rotational ladders separately. The inferred column densities are in the 10 11 - 10 13 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, CH 3 O, CH 3 NC, CH 3 CCH, CH 3 OCH 3 , HCOOCH 3 , CH 3 CH 2 OH, CH 3 CH 2 CN, and CH 2 CHCN). 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, H 2 CO and CH 3 CN survive in the extended gas directly exposed to the strong FUV flux ( T k = 150 - 250 K and T d ≳ 60 K), whereas CH 3 OH only arises from denser and cooler gas clumps in the more shielded PDR interior

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Mark D.; Lee, Won Suk

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 rapidmore » 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

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

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

Fabrication of Ni@Ti core-shell nanoparticles by modified gas aggregation source

NASA Astrophysics Data System (ADS)

Hanuš, J.; Vaidulych, M.; Kylián, O.; Choukourov, A.; Kousal, J.; Khalakhan, I.; Cieslar, M.; Solař, P.; Biederman, H.

2017-11-01

Ni@Ti core-shell nanoparticles were prepared by a vacuum based method using the gas aggregation source (GAS) of nanoparticles. Ni nanoparticles fabricated in the GAS were afterwards coated by a Ti shell. The Ti shell was deposited by means of magnetron sputtering. The Ni nanoparticles were decelerated in the vicinity of the magnetron to the Ar drift velocity in the second deposition chamber. X-ray photoelectron spectroscopy and energy dispersive x-ray spectroscopy analysis of the nanoparticles showed the core-shell structure. It was shown that the thickness of the shell can be easily tuned by the process parameters with a maximum achieved thickness of the Ti shell ~2.5 nm. The core-shell structure was confirmed by the STEM analysis of the particles.

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.

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. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Early-stage aggregation in three-dimensional charged granular gas.

PubMed

Singh, Chamkor; Mazza, Marco G

2018-02-01

Neutral grains made of the same dielectric material can attain considerable charges due to collisions and generate long-range interactions. We perform molecular dynamic simulations in three dimensions for a dilute, freely cooling granular gas of viscoelastic particles that exchange charges during collisions. As compared to the case of clustering of viscoelastic particles solely due to dissipation, we find that the electrostatic interactions due to collisional charging alter the characteristic size, morphology, and growth rate of the clusters. The average cluster size grows with time as a power law, whose exponent is relatively larger in the charged gas than the neutral case. The growth of the average cluster size is found to be independent of the ratio of characteristic Coulomb to kinetic energy, or equivalently, of the typical Bjerrum length. However, this ratio alters the crossover time of the growth. Both simulations and mean-field calculations based on Smoluchowski's equation suggest that a suppression of particle diffusion due to the electrostatic interactions helps in the aggregation process.

Early-stage aggregation in three-dimensional charged granular gas

NASA Astrophysics Data System (ADS)

Singh, Chamkor; Mazza, Marco G.

2018-02-01

Neutral grains made of the same dielectric material can attain considerable charges due to collisions and generate long-range interactions. We perform molecular dynamic simulations in three dimensions for a dilute, freely cooling granular gas of viscoelastic particles that exchange charges during collisions. As compared to the case of clustering of viscoelastic particles solely due to dissipation, we find that the electrostatic interactions due to collisional charging alter the characteristic size, morphology, and growth rate of the clusters. The average cluster size grows with time as a power law, whose exponent is relatively larger in the charged gas than the neutral case. The growth of the average cluster size is found to be independent of the ratio of characteristic Coulomb to kinetic energy, or equivalently, of the typical Bjerrum length. However, this ratio alters the crossover time of the growth. Both simulations and mean-field calculations based on Smoluchowski's equation suggest that a suppression of particle diffusion due to the electrostatic interactions helps in the aggregation process.

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.

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

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 [Zn 3(btca) 2(OH) 2]·(guest) n (H 2btca = 1,2,3-benzotriazole-5-carboxylic acid) that exhibits guest molecule-controlled dynamic gas adsorption is reported in which carbon dioxide molecules rather than N 2, 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 highlymore » selective adsorption of CO 2/N 2, CO 2/Ar, and CO 2/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

Nanoarchitectonics of molecular aggregates: science and technology.

PubMed

Ramanathan, Muruganathan; Hong, Kunlun; Ji, Qingmin; Yonamine, Yusuke; Hill, Jonathan P; Ariga, Katsuhiko

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.

Nanoarchitectonics of Molecular Aggregates: Science and Technology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramanathan, Nathan Muruganathan; Hong, Kunlun; Ji, Dr. Qingmin

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.

Matrix-assisted laser-induced gas-phase aggregation of C 60 oxides

NASA Astrophysics Data System (ADS)

Barrow, Mark P.; Tower, Nicole J.; Taylor ^*, , Roger; Drewello, Thomas

1998-08-01

Matrix-assisted laser desorption/ionisation of C 60 oxides, in conjunction with reflectron time-of-flight mass spectrometry, leads to an unprecedented gas-phase aggregation resulting in the formation of C 120O n- ·. products. The analysis of the product distribution obtained for oxides of varying oxygen content strongly suggests that the structures of these species are closely related to oxo-bridged isolated fullerene cages rather than to species featuring a fused giant fullerene core.

Adsorption of CO and O2 molecules on Li metal adsorbed graphene: Search for graphene based gas sensors

NASA Astrophysics Data System (ADS)

Kaur, Gagandeep; Gupta, Shuchi; Sachdeva, Ritika; Dharamvir, Keya

2018-05-01

Adsorption of small gas molecules (such as CO and O2) on pristine graphene (PG) and Li-adsorbed graphene (PG-Li) have been investigated using first principles methods within density functional theory (DFT). We also notice that PG-Li has a higher chemical reactivity towards the gas molecules as compared to PG and these molecules have higher adsorption energy on this surface. Moreover, the strong interactions between PG-Li and the adsorbed molecules (as compared to PG and gas molecules) induce dramatic changes to the electronic properties of PG adsorbed with Li and make PG-Li a promising candidate as sensing material for CO and O2 gases.

Communication: Potentials of mean force study of ionic liquid ion pair aggregation in polar covalent molecule solvents

NASA Astrophysics Data System (ADS)

Bandlamudi, Santosh Rathan Paul; Benjamin, Kenneth M.

2018-05-01

Molecular dynamics (MD) simulations were conducted for 1-ethyl-3-methylimidazolium methylsulfate [EMIM][MeSO4] dissolved in six polar covalent molecules [acetic acid, acetone, chloroform, dimethyl sulfoxide (DMSO), isopropyl alcohol, and methanol] to understand the free energies of ionic liquid (IL) ion pairing/aggregation in the limit of infinite dilution. Free energy landscapes or potentials of mean force (PMF) were computed using umbrella sampling and the weighted histogram analysis method. The PMF studies showed the strongest IL ion pairing in chloroform, and the strength of IL ion pairing decreases in the order of chloroform, acetone, propanol, acetic acid, DMSO, and methanol. In the limit of infinite dilution, the free energy curves for IL ion aggregation in co-solvents were characterized by two distinct minima [global (˜3.6 Å) and local (˜5.7 Å)], while free energy values at these minima differed significantly for IL in each co-solvent. The PMF studies were extended for determining the free energy of IL ion aggregation as a function of concentration of methanol. Studies showed that as the concentration of methanol increased, the free energy of ion aggregation decreased, suggesting greater ion pair stability, in agreement with previously reported MD clustering and radial distribution function data.

The gas phase origin of complex organic molecules precursors in prestellar cores

NASA Astrophysics Data System (ADS)

Bacmann, A.; Faure, A.

2015-05-01

Complex organic molecules (COMs) have long been observed in the warm regions surrounding nascent protostars. The recent discovery of oxygen-bearing COMs like methyl formate or dimethyl ether in prestellar cores (Bacmann et al. [2]), where gas and dust temperatures rarely exceed 10-15 K, has challenged the previously accepted models according to which COM formation relied on the diffusion of heavy radicals on warm (˜30 K) grains. Following these detections, new questions have arisen: do non-thermal processes play a role in increasing radical mobility or should new gas-phase routes be explored? The radicals involved in the formation of the aforementioned COMs, HCO and CH3O represent intermediate species in the grain-surface synthesis of methanol which proceeds via successive hydrogenations of CO molecules in the ice. We present here observations of methanol and its grain-surface precursors HCO, H2CO, CH3O in a sample of prestellar cores and derive their relative abundances. We find that the relative abundances HCO:H2CO:CH3O:CH3OH are constant across the core sample, close to 10:100:1:100. Our results also show that the amounts of HCO and CH3O are consistent with a gas-phase synthesis of these species from H2CO and CH3OH via radical-neutral or ion-molecule reactions followed by dissociative recombinations. Thus, while grain chemistry is necessary to explain the abundances of the parent volatile CH3OH, and possibly H2CO, the reactive species HCO and CH3O might be daughter molecules directly produced in the gas-phase.

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.

Tunable electronic and optical properties of gas molecules adsorbed monolayer graphitic ZnO: Implications for gas sensor and environment monitoring

NASA Astrophysics Data System (ADS)

Zhang, Wei; Du, Qikui; Zhang, Lifa

2017-12-01

Due to the large surface area and the peculiar electronic characters, great attention has been paid to 2D materials for the gas sensing applications. Here, using the hybrid density functional calculations, we systematically study the adsorptions of gas molecules on the monolayer graphitic ZnO (g-ZnO), including CO, H2, H2O, H2S, NH3, NO, NO2, O2, and SO2. For most of the molecules, g-ZnO shows superior sensing performance to the well-known MoS2, black phosphorus, blue phosphorus, antimonene, and germanene. H2S, NO, NO2, and SO2 act as charge acceptors, and CO, H2, H2O, and NH3 serve as charge donors. These molecules also induce distinct modifications to the electronic structures, work functions, and optical adsorptions. NO, NO2, and O2 form flat bands in the bandgaps of the spin-up or spin-down states, whereas other molecules mainly tune the bandgaps and the orbital couplings. In particular, g-ZnO is most likely to adsorb the atmospheric pollutant SO2, which has the strongest interaction through hybridizing its widely broadened 2p orbitals with the 3d orbitals of g-ZnO. Moreover, the improved visible light absorption is demonstrated in the NO2 adsorbed g-ZnO. Our results not only confirm that the electronic and optical properties of g-ZnO can be effectively tuned by the selective adsorption of gas molecules but also provide insightful guidance for the potential application of g-ZnO in the field of gas sensors.

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.

Rotational relaxation of fluoromethane molecules in low-temperature collisions with buffer-gas helium

NASA Astrophysics Data System (ADS)

Li, Xingjia; Xu, Liang; Yin, Yanning; Xu, Supeng; Xia, Yong; Yin, Jianping

2016-06-01

We propose a method to study the rotational relaxation of polar molecules [here taking fluoromethane (CH3F ) as an example] in collisions with 3.5 K buffer-gas helium (He) atoms by using an electrostatic guiding technique. The dependence of the guiding signal of CH3F on the injected He flux and the dependence of the guiding efficiency of CH3F on its rotational temperature are investigated both theoretically and experimentally. By comparing the experimental and simulated results, we find that the translational and rotational temperatures of the buffer-gas cooled CH3F molecules can reach to about 5.48 and 0.60 K, respectively, and the ratio between the translational and average rotational collisional cross sections of CH3F -He is γ =σt/σr=36.49 ±6.15 . In addition, the slowing, cooling, and boosting effects of the molecular beam with different injected He fluxes are also observed and their forming conditions are investigated in some detail. Our study shows that our proposed method can not only be used to measure the translational and rotational temperatures of the buffer-gas cooled molecules, but also to measure the ratio of the translational collisional cross section to the average rotational collisional cross section, and even to measure the average rotational collisional cross section when the translational collisional cross section is measured by fitting the lifetime of molecule signal to get a numerical solution from the diffusion equation of buffer-gas He atoms in the cell.

Assessing the Role of Capping Molecules in Controlling Aggregative Growth of Gold Nanoparticles in Heated Solution.

PubMed

Cheng, Han-Wen; Schadt, Mark J; Zhong, Chuan-Jian

2016-01-01

This report describes findings of an investigation of the role of capping molecules in the size growth in the aggregative growth of pre-formed small-sized gold nanoparticles capped with alkanethiolate monolayers toward monodispersed larger sizes. The size controllability depends on the thiolate chain length and concentration in the thermal solution. The size evolution in solution at different concentrations of alkanethiols is analyzed in relation to adsorption isotherms and cohesive energy. The size dependence on thiolate chain length is also analyzed by considering the cohesive energy of the capping molecules, revealing the importance of cohesive energy in the capping structure. Theoretical and experimental comparisons of the surface plasmonic resonance optical properties have also provided new insights into the mechanism, thus enabling the exploitation of size-dependent nanoscale properties. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

First-principles study on the structure and electronic property of gas molecules adsorption on Ge2Li2 monolayer

NASA Astrophysics Data System (ADS)

Hu, Yiwei; Long, Linbo; Mao, Yuliang; Zhong, Jianxin

2018-06-01

Using first-principles methods, we have studied the adsorption of gas molecules (CO2, CH4, H2S, H2 and NH3) on two dimensional Ge2Li2 monolayer. The adsorption geometries, adsorption energies, charge transfer, and band structures of above mentioned gas molecules adsorption on Ge2Li2 monolayer are analyzed. It is found that the adsorption of CO2 on Ge2Li2 monolayer is a kind of strong chemisorption, while other gas molecules such as CH4, H2S, H2 and NH3 are physisorption. The strong covalent binding is formed between the CO2 molecule and the nearest Ge atom in Ge2Li2 monolayer. This adsorption of CO2 molecule on Ge2Li2 monolayer leads to a direct energy gap of 0.304 eV. Other gas molecules exhibit mainly ionic binding to the nearest Li atoms in Ge2Li2 monolayer, which leads to indirect energy gap after adsorptions. Furthermore, it is found that the work function of Ge2Li2 monolayer is sensitive with the variation of adsorbents. Our results reveal that the Ge2Li2 monolayer can be used as a kind of nano device for gas molecules sensor.

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

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

PubMed

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

2017-02-01

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.

Thermophoretic aggregation of particles in a protoplanetary disc

NASA Astrophysics Data System (ADS)

Smith, Francis J.

2018-04-01

Thermophoresis causes particles to move down a temperature gradient to a cooler region of a neutral gas. An example is the temperature gradient in the gas around a large cold object, such as an aggregate of particles, cooled by radiation in a protoplanetary disc. Particles near this aggregate move down the temperature gradient to the aggregate, equivalent to the particles being attracted to it by an inter-particle thermophoretic force. This force is proportional to the temperature difference between gas and aggregate, to the gas density and to the cross-section of the aggregate. The force can be large. For example, calculations based on the equations of motion of the interacting particles show that it can be large enough in an optically thin environment to increase the rate of aggregation by up to six orders of magnitude when an aggregate radius lies between 0.1 μm and 1 mm. From 1 mm to about 10 cm aggregates drift inwards through the gas too quickly for the thermophoretic attraction to increase aggregation significantly; so they grow slowly, causing an observed accumulation of particles at these sizes. Particles above 10 cm move more quickly, causing aggregation due to collisions, but also causing fragmentation. However, calculations show that fragmenting particles and bouncing particles in inelastic collisions often have low enough relative velocities that thermophoresis brings them together again. This allows particles to grow above 1 m, which is otherwise difficult to explain.

Charging of nanoparticles in stationary plasma in a gas aggregation cluster source

NASA Astrophysics Data System (ADS)

Blažek, J.; Kousal, J.; Biederman, H.; Kylián, O.; Hanuš, J.; Slavínská, D.

2015-10-01

Clusters that grow into nanoparticles near the magnetron target of the gas aggregation cluster source (GAS) may acquire electric charge by collecting electrons and ions or through other mechanisms like secondary- or photo-electron emissions. The region of the GAS close to magnetron may be considered as stationary plasma. The steady state charge distribution on nanoparticles can be determined by means of three possible models—fluid model, kinetic model and model employing Monte Carlo simulations—of cluster charging. In the paper the mathematical and numerical aspects of these models are analyzed in detail and close links between them are clarified. Among others it is shown that Monte Carlo simulation may be considered as a particular numerical technique of solving kinetic equations. Similarly the equations of the fluid model result, after some approximation, from averaged kinetic equations. A new algorithm solving an in principle unlimited set of kinetic equations is suggested. Its efficiency is verified on physical models based on experimental input data.

Cryogenic buffer-gas loading and magnetic trapping of CrH and MnH molecules

NASA Astrophysics Data System (ADS)

Stoll, Michael; Bakker, Joost M.; Steimle, Timothy C.; Meijer, Gerard; Peters, Achim

2008-09-01

We report on the buffer-gas cooling and trapping of CrH and MnH molecules in a magnetic quadrupole trap with densities on the order of 106cm-3 at a temperature of 650mK . Storage times of up to 180ms have been observed, corresponding to a 20-fold lifetime enhancement with respect to the field-free diffusion through the He3 buffer-gas. Using Monte Carlo trajectory simulations, inelastic molecule- He3 collision cross sections of 1.6×10-18 and 3.1×10-17cm2 are extracted for CrH and MnH, respectively. Furthermore, elastic molecule- He3 collision cross sections of 1.4(±0.5)×10-14cm2 are determined for both species. We conclude that the confinement time of these molecules in a magnetic trapping field is limited by inelastic collisions with the helium atoms leading to Zeeman relaxation.

Can H-aggregates serve as light-harvesting antennae? Triplet-triplet energy transfer between excited aggregates and monomer thionine in aerosol-OT solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Das, S.; Kamat, P.V.

1999-01-07

The cationic dye thionine undergoes slow dissolution in aerosol-OT (AOT) containing solutions of heptane and toluene. By controlling the ratio of [dye]/[AOT], it is possible to obtain varying amounts of monomer, dimer, and higher order aggregates (trimer) in dilute dye solutions. The thionine aggregates exhibit characteristic absorption maxima at 565 and 530 nm for the dimer and trimer forms, respectively. The singlet excited states of these dye aggregates are short-lived ({tau} = 40--63 ps) as they undergo efficient intersystem crossing to generate the triplet excited states. Triplet energy transfer from the excited dye aggregates to monomeric thionine molecules was observedmore » upon excitation with a 532 nm laser pulse. Pulse radiolysis experiments, in which the excited triplet states were generated indirectly, also confirm the finding that the triplet energy cascades down from excited trimer to dimer to monomeric dye. These studies demonstrate the possibility of using H-type dye aggregates as antenna molecules to harvest light energy whereby the aggregate molecules absorb light in different spectral regions and subsequently transfer energy to the monomeric dye.« less

Effect of lattice-gas atoms on the adsorption behaviour of thioether molecules.

PubMed

Pan, Yi; Yang, Bing; Hulot, Catherine; Blechert, Siegfried; Nilius, Niklas; Freund, Hans-Joachim

2012-08-21

Using STM topographic imaging and spectroscopy, we have investigated the adsorption of two thioether molecules, 1,2-bis(phenylthio)benzene and (bis(3-phenylthio)-phenyl)sulfane, on noble and transition metal surfaces. The two substrates show nearly antipodal behaviour. Whereas complexes with one or two protruding centres are observed on Au(111), only flat and uniform ad-structures are found on NiAl(110). The difference is ascribed to the possibility of the thioethers to form metal-organic complexes by coordinating lattice-gas atoms on the Au(111), while only the pristine molecules adsorb on the alloy surface. The metal coordination in the first case is driven by the formation of strong Au-S bonds and enables the formation of characteristic monomer, dimer and chain-like structures of the thioethers, using the Au atoms as linkers. A similar mechanism is not available on the NiAl, because no lattice gas develops at this surface at room temperature. Our work demonstrates how surface properties, i.e. the availability of mobile ad-species, determine the interaction of organic molecules with metallic substrates.

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.

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

Neisseria gonorrhoeae Aggregation Reduces Its Ceftriaxone Susceptibility.

PubMed

Wang, Liang-Chun; Litwin, Madeline; Sahiholnasab, Zahraossadat; Song, Wenxia; Stein, Daniel C

2018-06-15

Antibiotic resistance in Neisseria gonorrhoeae (GC) has become an emerging threat worldwide and heightens the need for monitoring treatment failures. N. gonorrhoeae , a gram-negative bacterium responsible for gonorrhea, infects humans exclusively and can form aggregates during infection. While minimal inhibitory concentration (MIC) tests are often used for determining antibiotic resistance development and treatment, the knowledge of the true MIC in individual patients and how it relates to this laboratory measure is not known. We examined the effect of aggregation on GC antibiotic susceptibility and the relationship between bacterial aggregate size and their antibiotic susceptibility. Aggregated GC have a higher survival rate when treated with ceftriaxone than non-aggregated GC, with bacteria in the core of the aggregates surviving the treatment. GC lacking opacity-associated protein or pili, or expressing a truncated lipooligosaccharide, three surface molecules that mediate GC-GC interactions, reduce both aggregation and ceftriaxone survival. This study demonstrates that the aggregation of N. gonorrhoeae can reduce the susceptibility to antibiotics, and suggests that antibiotic utilization can select for GC surface molecules that promote aggregation which in turn drive pathogen evolution. Inhibiting aggregation may be a potential way of increasing the efficacy of ceftriaxone treatment, consequently reducing treatment failure.

Interactions between nitrogen and oxygen molecules studied by gas-phase NMR spectroscopy

NASA Astrophysics Data System (ADS)

Garbacz, Piotr; Misiak, Maria; Jackowski, Karol

2018-05-01

Gas-phase 14N and 15N NMR studies of nitrogen and synthetic air pressurized up to 300 bar were performed. It was found that the magnetic shielding of an isolated N2 molecule, σ0(N) = -63.4(2) ppm, is in good agreement with the results of ab initio calculations. The binary N2-O2 interactions contribute to shielding an order of the magnitude larger than the N2-N2 pairs. For nitrogen the three body collisions become observable by NMR for pressure higher than 200 bar and the appropriate coefficient can be practically assigned to the interaction between one molecule of N2 and a pair of O2 molecules.

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.

High Selective Gas Detection for small molecules based on Germanium selenide monolayer

NASA Astrophysics Data System (ADS)

Liu, Lian; Yang, Qun; Wang, Zeping; Ye, Huaiyu; Chen, Xianping; Fan, Xuejun; Zhang, Guoqi

2018-03-01

Predictive calculations based on density functional theory (DFT) are used here to study the electronic and optical properties of GeSe monolayer after adsorbing gas molecules (O2, NH3, SO2, H2, CO2, H2S, NO2, CH4, H2O, NO, CO). Our results reveal that for all the gas molecules considered, only NH3 is adsorbed on GeSe monolayer by physisorption. Whereas SO2 and NO2 are chemisorbed on GeSe monolayer with strong adsorption energies. In addition, the adsorption of O2, NO and NO2 distinctly enhances the optical absorbance and broaden the absorbance range of GeSe monolayer in visible light region. Also, it is found that the adsorption of H2S, NO and NH3 can reduce the work function of the GeSe monolayer. The results indicate that GeSe monolayer is not only a promising candidate for the sensing, capture, and storage of NH3, but also an anticipated disposable gas sensor or metal-free catalyst for detecting and catalyzing SO2 and NO2. Furthermore, it has excellent potential to be applied to optical sensors, solar cells, nanoelectronics or optoelectronics devices.

Rydberg aggregates

NASA Astrophysics Data System (ADS)

Wüster, S.; Rost, J.-M.

2018-02-01

We review Rydberg aggregates, assemblies of a few Rydberg atoms exhibiting energy transport through collective eigenstates, considering isolated atoms or assemblies embedded within clouds of cold ground-state atoms. We classify Rydberg aggregates, and provide an overview of their possible applications as quantum simulators for phenomena from chemical or biological physics. Our main focus is on flexible Rydberg aggregates, in which atomic motion is an essential feature. In these, simultaneous control over Rydberg-Rydberg interactions, external trapping and electronic energies, allows Born-Oppenheimer surfaces for the motion of the entire aggregate to be tailored as desired. This is illustrated with theory proposals towards the demonstration of joint motion and excitation transport, conical intersections and non-adiabatic effects. Additional flexibility for quantum simulations is enabled by the use of dressed dipole-dipole interactions or the embedding of the aggregate in a cold gas or Bose-Einstein condensate environment. Finally we provide some guidance regarding the parameter regimes that are most suitable for the realization of either static or flexible Rydberg aggregates based on Li or Rb atoms. The current status of experimental progress towards enabling Rydberg aggregates is also reviewed.

Synthesis and studies of axial chiral bisbenzocoumarins: Aggregation-induced emission enhancement properties and aggregation-annihilation circular dichroism effects

NASA Astrophysics Data System (ADS)

Chen, Shaojin; Liu, Wei; Ge, Zhaohai; Zhang, Wenxuan; Wang, Kunpeng; Hu, Zhiqiang

2018-03-01

Axial chiral bisbenzocoumarins were synthesized for the first time by converting naphthanol units in 1,1‧-binaphthol (BINOL) molecule to the benzocoumarin rings. The substitute groups on 3,3‧-positions of bisbenzocoumarins showed significant influence on their aggregation-induced emission enhancement (AEE) properties. It was also found that BBzC1 with ester groups on 3,3‧-positions exhibit an abnormal aggregation-annihilation circular dichroism (AACD) phenomenon, which could be caused by the decrease of the dihedral angle between adjacent benzocoumarin rings in the aggregation state. The single crystal structure of BBzC1 showed that the large dihedral angle in molecule prohibited the strong π-π stacking interactions, which could be main factors for its AEE properties.

Discrete unified gas kinetic scheme for all Knudsen number flows. III. Binary gas mixtures of Maxwell molecules

NASA Astrophysics Data System (ADS)

Zhang, Yue; Zhu, Lianhua; Wang, Ruijie; Guo, Zhaoli

2018-05-01

Recently a discrete unified gas kinetic scheme (DUGKS) in a finite-volume formulation based on the Boltzmann model equation has been developed for gas flows in all flow regimes. The original DUGKS is designed for flows of single-species gases. In this work, we extend the DUGKS to flows of binary gas mixtures of Maxwell molecules based on the Andries-Aoki-Perthame kinetic model [P. Andries et al., J. Stat. Phys. 106, 993 (2002), 10.1023/A:1014033703134. A particular feature of the method is that the flux at each cell interface is evaluated based on the characteristic solution of the kinetic equation itself; thus the numerical dissipation is low in comparison with that using direct reconstruction. Furthermore, the implicit treatment of the collision term enables the time step to be free from the restriction of the relaxation time. Unlike the DUGKS for single-species flows, a nonlinear system must be solved to determine the interaction parameters appearing in the equilibrium distribution function, which can be obtained analytically for Maxwell molecules. Several tests are performed to validate the scheme, including the shock structure problem under different Mach numbers and molar concentrations, the channel flow driven by a small gradient of pressure, temperature, or concentration, the plane Couette flow, and the shear driven cavity flow under different mass ratios and molar concentrations. The results are compared with those from other reliable numerical methods. The results show that the proposed scheme is an effective and reliable method for binary gas mixtures in all flow regimes.

Magnetic trapping of buffer-gas-cooled chromium atoms and prospects for the extension to paramagnetic molecules

NASA Astrophysics Data System (ADS)

Bakker, Joost M.; Stoll, Michael; Weise, Dennis R.; Vogelsang, Oliver; Meijer, Gerard; Peters, Achim

2006-10-01

We report the successful buffer-gas cooling and magnetic trapping of chromium atoms with densities exceeding 1012 atoms per cm3 at a temperature of 350 mK for the trapped sample. The possibilities of extending the method to buffer-gas cool and magnetically trap molecules are discussed. To minimize the most important loss mechanism in magnetic trapping, molecules with a small spin spin interaction and a large rotational constant are preferred. Both the CrH (6Σ+ ground state) and MnH (7Σ+) radicals appear to be suitable systems for future experiments.

A theoretical study on metal atom-modified BC3 sheets for effects of gas molecule adsorptions

NASA Astrophysics Data System (ADS)

Tang, Yanan; Cui, Xiao; Chen, Weiguang; Zhu, Dalei; Chai, Huaduo; Dai, Xianqi

2018-06-01

Based on the first-principle calculations, the chemical reactivity of transition metal (Fe, Co, Ni, and Cu) dopants within BC3 sheets toward toxic gas molecules (CO, NO, NO2, SO2, and HCN) is comparably investigated. First, the adsorbed gases on metal-modified BC3 sheets exhibit the different stability. Compared with other gases, the metal-modified BC3 substrates exhibit the stronger affinity toward the NO and NO2 molecules (> 1.0 eV), while the adsorbed HCN has the smallest adsorption energy, illustrating that the NO and NO2 as specific toxic gas molecule can be easily detected. Second, the adsorbed gas molecules can effectively regulate the electronic structure and magnetic property of BC3 systems. Fox example, the strong adsorption of NO and NO2 on Fe-modified BC3 systems exhibits non-magnetic property, yet these gases on Co modified BC3 systems exhibit the magnetic character. In addition, the adsorbed NO and SO2 can induce and turn the degree of magnetic moments of Ni- and Cu-modified BC3 systems. Therefore, the different kinds of adsorbed gases on metal-modified BC3 sheets can be distinguished through investigating the changed magnetic moments of system, which would provide important information for designing the functional BC3-based materials.

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.

Structural organization of surfactant aggregates in vacuo: a molecular dynamics and well-tempered metadynamics study.

PubMed

Longhi, Giovanna; Fornili, Sandro L; Turco Liveri, Vincenzo

2015-07-07

Experimental investigations using mass spectrometry have established that surfactant molecules are able to form aggregates in the gas phase. However, there is no general consensus on the organization of these aggregates and how it depends on the aggregation number and surfactant molecular structure. In the present paper we investigate the structural organization of some surfactants in vacuo by molecular dynamics and well-tempered metadynamics simulations to widely explore the space of their possible conformations in vacuo. To study how the specific molecular features of such compounds affect their organization, we have considered as paradigmatic surfactants, the anionic single-chain sodium dodecyl sulfate (SDS), the anionic double-chain sodium bis(2-ethylhexyl) sulfosuccinate (AOT) and the zwitterionic single-chain dodecyl phosphatidyl choline (DPC) within a wide aggregation number range (from 5 to 100). We observe that for low aggregation numbers the aggregates show in vacuo the typical structure of reverse micelles, while for large aggregation numbers a variety of globular aggregates occur that are characterized by the coexistence of interlaced domains formed by the polar or ionic heads and by the alkyl chains of the surfactants. Well-tempered metadynamics simulations allows us to confirm that the structural organizations obtained after 50 ns of molecular dynamics simulations are practically the equilibrium ones. Similarities and differences of surfactant aggregates in vacuo and in apolar media are also discussed.

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.

Polarized components of C=O vibrations Raman spectra for ethylacetate, acetone, and aggregation of molecules

NASA Astrophysics Data System (ADS)

Tukhvatullin, F. H.; Jumabaev, A.; Tashkenbaev, U. N.; Hushvaktov, H. A.; Absanov, A. A.

2002-11-01

For liquid ethylacetate the frequency maximums for parallel (I|| (v)) and perpendicular (I\\highmod(v)) polarized components of C=O vibrations band in Raman spectra are differed on 5.3 cm-1. At dilution ethylacetate in CCl4 and heptane or heating in this difference is decreased by displacement of I|| (v) maximum to the I\\highmod(v) maximum. In polar solvent, nitrometane, the picture is different - the frequency maxima difference is decreased though the displacement of I\\highmod(v) band maximum to the I|| (v)one. The results were explained by the complexity of C=O vibration bands, and existence within the band of two lines with the different depolarization ratio. The complexity of the band is the result existence in liquid ethylacetate the monomer molecules and molecular aggregations.

Doping and defect-induced germanene: A superior media for sensing H2S, SO2, and CO2 gas molecules

NASA Astrophysics Data System (ADS)

Monshi, M. M.; Aghaei, S. M.; Calizo, I.

2017-11-01

First-principles calculations based on density functional theory (DFT) have been employed to investigate the structural, electronic, and gas-sensing properties of pure, defected, and doped germanene nanosheets. Our calculations have revealed that while a pristine germanene nanosheet adsorbs CO2 weakly, H2S moderately, and SO2 strongly, the introduction of vacancy defects increases the sensitivity significantly which is promising for future gas-sensing applications. Mulliken population analysis imparts that an appreciable amount of charge transfer occurs between gas molecules and a germanene nanosheet which supports our results for adsorption energies of the systems. The enhancement of the interactions between gas molecules and the germanene nanosheet has been further investigated by density of states. Projected density of states provides detailed insight of the gas molecule's contribution in the gas-sensing system. Additionally, the influences of substituted dopant atoms such as B, N, and Al in the germanene nanosheet have also been considered to study the impact on its gas sensing ability. There was no significant improvement found in the doped gas sensing capability of germanene over the vacancy defects, except for CO2 upon adsorption on N-doped germanene.

Physics with Cold Molecules Using Buffer Gas Cooling: Precision Measurement, Collisions, and Laser Cooling

NASA Astrophysics Data System (ADS)

Hutzler, Nicholas R.; Doyle, John M.

2014-06-01

Cryogenic buffer gas cooled beams and cells can be used to study many species, from atoms and polar molecules to biomolecules. We report on recent applications of this technique to improve the limit on the electron electric dipole moment [1], load polar molecules into a magnetic trap through optical pumping [2], perform chirally sensitive microwave spectroscopy on polyatomic molecules [3], progress towards magneto-optical trapping of polar molecules [4], and studies of atom-molecule sticking [5]. [1] The ACME Collaboration: J. Baron et al., Science 343, p. 269 (2014) [2] B. Hemmerling et al., arXiv:1310.2669, to appear in Phys. Rev. Lett. [3] D. Patterson, M. Schnell, & J. M. Doyle, Nature 497, p. 475 (2013) [4] H. Lu et al., arXiv:1310.3239, to appear in New. J. Phys. [5] J. Piskorski et al., under preparation

Bistable aggregate of all-trans-astaxanthin in an aqueous solution

NASA Astrophysics Data System (ADS)

Mori, Yuso; Yamano, Kuniko; Hashimoto, Hideki

1996-05-01

The temperature dependence of the optical absorption spectra for astaxanthin aggregate has been studied between 2 and 32°C. Red-shifted absorption bands as compared to the monomer absorption band are found above 21°C in addition to the blue-shifted band of the aggregate. The spectra suggest that the molecular arrangement in the aggregate is a bistable one consisting of head-to-tail and card-packed arrangements. A diagram describing the bistability together with the monomer state is proposed in the space defined by the free energy and the quantity of Σi = 1 N< θ12 + < σθ12 for the ith molecule in the N-molecule aggregate.

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.

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

Graph Theory and Ion and Molecular Aggregation in Aqueous Solutions

NASA Astrophysics Data System (ADS)

Choi, Jun-Ho; Lee, Hochan; Choi, Hyung Ran; Cho, Minhaeng

2018-04-01

In molecular and cellular biology, dissolved ions and molecules have decisive effects on chemical and biological reactions, conformational stabilities, and functions of small to large biomolecules. Despite major efforts, the current state of understanding of the effects of specific ions, osmolytes, and bioprotecting sugars on the structure and dynamics of water H-bonding networks and proteins is not yet satisfactory. Recently, to gain deeper insight into this subject, we studied various aggregation processes of ions and molecules in high-concentration salt, osmolyte, and sugar solutions with time-resolved vibrational spectroscopy and molecular dynamics simulation methods. It turns out that ions (or solute molecules) have a strong propensity to self-assemble into large and polydisperse aggregates that affect both local and long-range water H-bonding structures. In particular, we have shown that graph-theoretical approaches can be used to elucidate morphological characteristics of large aggregates in various aqueous salt, osmolyte, and sugar solutions. When ion and molecular aggregates in such aqueous solutions are treated as graphs, a variety of graph-theoretical properties, such as graph spectrum, degree distribution, clustering coefficient, minimum path length, and graph entropy, can be directly calculated by considering an ensemble of configurations taken from molecular dynamics trajectories. Here we show percolating behavior exhibited by ion and molecular aggregates upon increase in solute concentration in high solute concentrations and discuss compelling evidence of the isomorphic relation between percolation transitions of ion and molecular aggregates and water H-bonding networks. We anticipate that the combination of graph theory and molecular dynamics simulation methods will be of exceptional use in achieving a deeper understanding of the fundamental physical chemistry of dissolution and in describing the interplay between the self-aggregation of solute

Graph Theory and Ion and Molecular Aggregation in Aqueous Solutions.

PubMed

Choi, Jun-Ho; Lee, Hochan; Choi, Hyung Ran; Cho, Minhaeng

2018-04-20

In molecular and cellular biology, dissolved ions and molecules have decisive effects on chemical and biological reactions, conformational stabilities, and functions of small to large biomolecules. Despite major efforts, the current state of understanding of the effects of specific ions, osmolytes, and bioprotecting sugars on the structure and dynamics of water H-bonding networks and proteins is not yet satisfactory. Recently, to gain deeper insight into this subject, we studied various aggregation processes of ions and molecules in high-concentration salt, osmolyte, and sugar solutions with time-resolved vibrational spectroscopy and molecular dynamics simulation methods. It turns out that ions (or solute molecules) have a strong propensity to self-assemble into large and polydisperse aggregates that affect both local and long-range water H-bonding structures. In particular, we have shown that graph-theoretical approaches can be used to elucidate morphological characteristics of large aggregates in various aqueous salt, osmolyte, and sugar solutions. When ion and molecular aggregates in such aqueous solutions are treated as graphs, a variety of graph-theoretical properties, such as graph spectrum, degree distribution, clustering coefficient, minimum path length, and graph entropy, can be directly calculated by considering an ensemble of configurations taken from molecular dynamics trajectories. Here we show percolating behavior exhibited by ion and molecular aggregates upon increase in solute concentration in high solute concentrations and discuss compelling evidence of the isomorphic relation between percolation transitions of ion and molecular aggregates and water H-bonding networks. We anticipate that the combination of graph theory and molecular dynamics simulation methods will be of exceptional use in achieving a deeper understanding of the fundamental physical chemistry of dissolution and in describing the interplay between the self-aggregation of solute

Characterization of Noble Gas Ion Beam Fabricated Single Molecule Nanopore Detectors

NASA Astrophysics Data System (ADS)

Rollings, Ryan; Ledden, Bradley; Shultz, John; Fologea, Daniel; Li, Jiali; Chervinsky, John; Golovchenko, Jene

2006-03-01

Nanopores fabricated with low energy noble gas ion beams in a silicon nitride membrane can be employed as the fundamental element of single biomolecule detection and characterization devices [1,2]. With the help of X-ray Photoelectron Spectroscopy (XPS) and Rutherford Backscattering (RBS), we demonstrate that the electrical noise properties, and hence ultimate sensitivity of nanopore single molecule detectors depends on ion beam species and nanopore annealing conditions. .1. Li, J., D. Stein, C. McMullan, D. Branton, M.J. Aziz, and J.A. Golovchenko, Ion-beam sculpting at nanometre length scales. Nature, 2001. 412(12 July): p. 166-169. 2. Li, J., M. Gershow, D. Stein, E. Brandin, and J.A. Golovchenko, DNA Molecules and Configurations in a Solid-state Nanopore Microscope. Nature Materials, 2003. 2: p. 611-615.

Small Molecule Acceptor and Polymer Donor Crystallinity and Aggregation Effects on Microstructure Templating: Understanding Photovoltaic Response in Fullerene-Free Solar Cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eastham, Nicholas D.; Dudnik, Alexander S.; Aldrich, Thomas J.

Perylenediimide (PDI) small molecule acceptor (SMA) crystallinity and donor polymer aggregation and crystallinity effects on bulk-heterojunction microstructure and polymer solar cell (PSC) performance are systematically investigated. Two highperformance polymers, semicrystalline poly[5-(2-hexyldodecyl)-4Hthieno[3,4-c]pyrrole-4,6(5H)-dione-1,3-yl-alt-4,4''dodecyl-2,2':5',2''- terthiophene-5,5''-diyl] (PTPD3T or D1) and amorphous poly{4,8- bis(5-(2-ethylhexyl)thiophen-2-yl)benzo[1,2-b:4,5-b']dithiophene- 2,6-diyl-alt-(4-(2-ethylhexyl)-3-fluorothieno[3,4-b]thiophene-2-carboxylate-2,6-diyl) (PBDTT-FTTE or D2), are paired with three PDI-based SMAs (A1-A3) of differing crystallinity (A1 is the most, A3 is the least crystalline). The resulting PSC performance trends are strikingly different from those of typical fullerene-based PSCs and are highly material-dependent. The present trends reflect synergistic aggregation propensities between the SMA and polymer components. Importantly, the active layer morphology is templatedmore » by the PDI in some blends and by the polymer in others, with the latter largely governed by the polymer aggregation. Thus, PTPD3T templating capacity increases as self-aggregation increases (greater Mn), optimizing PSC performance with A2, while A3-based cells exhibit an inverse relationship between polymer aggregation and performance, which is dramatically different from fullerene-based PSCs. For PBDTT-FTTE, A2-based cells again deliver the highest PCEs of ~5%, but here both A2 and PBDTT-FTTE (medium Mn) template the morphology. Overall, the present results underscore the importance of nonfullerene acceptor aggregation for optimizing PSC performance and offer guidelines for pairing SMAs with acceptable donor polymers.« less

π-π-Induced aggregation and single-crystal fluorescence anisotropy of 5,6,10b-tri-aza-acephenanthrylene.

PubMed

Ostrowska, Katarzyna; Ceresoli, Davide; Stadnicka, Katarzyna; Gryl, Marlena; Cazzaniga, Marco; Soave, Raffaella; Musielak, Bogdan; Witek, Łukasz J; Goszczycki, Piotr; Grolik, Jarosław; Turek, Andrzej M

2018-05-01

The structural origin of absorption and fluorescence anisotropy of the single crystal of the π-conjugated heterocyclic system 5,6,10b-tri-aza-acephenan-thrylene, TAAP, is presented in this study. X-ray analysis shows that the crystal framework in the space group P [Formula: see text] is formed by centrosymmetric dimers of face-to-face mutually oriented TAAP molecules joined by π-π non-covalent interactions. The conformation of the TAAP molecule is stabilized by intramolecular C-H⋯N( sp 2 ), N( sp 2 )H⋯π(CN), and C-H⋯O( sp 2 ) hydrogen bonds. The presence of weak π-π interactions is confirmed by quantum theory of atoms in molecules (QTAIM) and non-covalent interaction (NCI) analysis. The analysis of the optical spectra of TAAP in solution and in the solid state does not allow the specification of the aggregation type. DFT calculations for the dimer in the gas phase indicate that the lowest singlet excitation is forbidden by symmetry, suggesting H-type aggregation, even though the overall absorption spectrum is bathochromically shifted as for the J-type. The experimental determination of the permanent dipole moment of a TAAP molecule in 1,4-dioxane solution indicates the presence of the monomer form. The calculated absorption and emission spectra of the crystal in a simple approximation are consistent with the experimentally determined orientation of the absorption and emission transition dipole moments in TAAP single crystals. The electrostatic interaction between monomers with a permanent dipole moment ( ca 4 D each) could result in the unusual spectroscopic JH-aggregate behaviour of the TAAP dimer.

GEOMETRIC CROSS SECTIONS OF DUST AGGREGATES AND A COMPRESSION MODEL FOR AGGREGATE COLLISIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suyama, Toru; Wada, Koji; Tanaka, Hidekazu

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 wellmore » 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.« less

Spin-coated Films of Squarylium Dye J-Aggregates Exhibiting Ultrafast Optical Responses

NASA Astrophysics Data System (ADS)

Tatsuura, Satoshi; Tian, Minquan; Furuki, Makoto; Sato, Yasuhiro; Pu, Lyong Sun; Wada, Osamu

2000-08-01

The formation of J-aggregates of squarylium dye derivatives in spin-coated films is reported. Squarylium dye derivatives with dipropylamino bases are found to spontaneously aggregate in a spin-coated film. Aggregation is promoted when dye molecules are dispersed in a poly(vinyl alcohol) film, and when a spin-coated film of dye molecules is heated in the presence of acid vapor. In particular, J-aggregates formed by exposure to acetic acid vapor show the narrowest spectral width. J-aggregates formed by the acid treatment method are stable at room temperature and the spectral full-width at half maximum of the J-band is 20 nm. Optical response of the acid-treated film is confirmed to exhibit a short relaxation time of bleached absorption of 300 fs.

Adsorption Mechanism of Inhibitor and Guest Molecules on the Surface of Gas Hydrates.

PubMed

Yagasaki, Takuma; Matsumoto, Masakazu; Tanaka, Hideki

2015-09-23

The adsorption of guest and kinetic inhibitor molecules on the surface of methane hydrate is investigated by using molecular dynamics simulations. We calculate the free energy profile for transferring a solute molecule from bulk water to the hydrate surface for various molecules. Spherical solutes with a diameter of ∼0.5 nm are significantly stabilized at the hydrate surface, whereas smaller and larger solutes exhibit lower adsorption affinity than the solutes of intermediate size. The range of the attractive force is subnanoscale, implying that this force has no effect on the macroscopic mass transfer of guest molecules in crystal growth processes of gas hydrates. We also examine the adsorption mechanism of a kinetic hydrate inhibitor. It is found that a monomer of the kinetic hydrate inhibitor is strongly adsorbed on the hydrate surface. However, the hydrogen bonding between the amide group of the inhibitor and water molecules on the hydrate surface, which was believed to be the driving force for the adsorption, makes no contribution to the adsorption affinity. The preferential adsorption of both the kinetic inhibitor and the spherical molecules to the surface is mainly due to the entropic stabilization arising from the presence of cavities at the hydrate surface. The dependence of surface affinity on the size of adsorbed molecules is also explained by this mechanism.

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.

Adsorption of gas molecules on a manganese phthalocyanine molecular device and its possibility as a gas sensor.

PubMed

Zou, Dongqing; Zhao, Wenkai; Cui, Bin; Li, Dongmei; Liu, Desheng

2018-01-17

A theoretical investigation of the gas detection performance of manganese(ii) phthalocyanine (MnPc) molecular junctions for six different gases (NO, CO, O 2 , CO 2 , NO 2 , and NH 3 ) is executed through a non-equilibrium Green's function technique in combination with spin density functional theory. Herein, we systematically studied the adsorption structural configurations, the adsorption energy, the charge transfer, and the spin transport properties of the MnPc molecular junctions with these gas adsorbates. Remarkably, NO adsorption can achieve an off-state of the Mn spin; this may be an effective measure to switch the molecular spin. In addition, our results indicate that by measuring spin filter efficiency and the changes in total current through the molecular junctions, the CO, NO, O 2 , and NO 2 gas molecules can be detected selectively. However, the CO 2 and NH 3 gas adsorptions are difficult to be detected due to weak van der Waals interaction between these two gases and central Mn atom. Our findings provide important clues to the application of nanosensors for highly sensitive and selective based on MnPc molecular junction systems.

Aggregate nanostructures of organic molecular materials.

PubMed

Liu, Huibiao; Xu, Jialiang; Li, Yongjun; Li, Yuliang

2010-12-21

Conjugated organic molecules are interesting materials because of their structures and their electronic, electrical, magnetic, optical, biological, and chemical properties. However, researchers continue to face great challenges in the construction of well-defined organic compounds that aggregate into larger molecular materials such as nanowires, tubes, rods, particles, walls, films, and other structural arrays. Such nanoscale materials could serve as direct device components. In this Account, we describe our recent progress in the construction of nanostructures formed through the aggregation of organic conjugated molecules and in the investigation of the optical, electrical, and electronic properties that depend on the size or morphology of these nanostructures. We have designed and synthesized functional conjugated organic molecules with structural features that favor assembly into aggregate nanostructures via weak intermolecular interactions. These large-area ordered molecular aggregate nanostructures are based on a variety of simpler structures such as fullerenes, perylenes, anthracenes, porphyrins, polydiacetylenes, and their derivatives. We have developed new methods to construct these larger structures including organic vapor-solid phase reaction, natural growth, association via self-polymerization and self-organization, and a combination of self-assembly and electrochemical growth. These methods are both facile and reliable, allowing us to produce ordered and aligned aggregate nanostructures, such as large-area arrays of nanowires, nanorods, and nanotubes. In addition, we can synthesize nanoscale materials with controlled properties. Large-area ordered aggregate nanostructures exhibit interesting electrical, optical, and optoelectronic properties. We also describe the preparation of large-area aggregate nanostructures of charge transfer (CT) complexes using an organic solid-phase reaction technique. By this process, we can finely control the morphologies and

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.

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.

The formation of urea in space. I. Ion-molecule, neutral-neutral, and radical gas-phase reactions

NASA Astrophysics Data System (ADS)

Brigiano, Flavio Siro; Jeanvoine, Yannick; Largo, Antonio; Spezia, Riccardo

2018-02-01

Context. Many organic molecules have been observed in the interstellar medium thanks to advances in radioastronomy, and very recently the presence of urea was also suggested. While those molecules were observed, it is not clear what the mechanisms responsible to their formation are. In fact, if gas-phase reactions are responsible, they should occur through barrierless mechanisms (or with very low barriers). In the past, mechanisms for the formation of different organic molecules were studied, providing only in a few cases energetic conditions favorable to a synthesis at very low temperature. A particularly intriguing class of such molecules are those containing one N-C-O peptide bond, which could be a building block for the formation of biological molecules. Urea is a particular case because two nitrogen atoms are linked to the C-O moiety. Thus, motivated also by the recent tentative observation of urea, we have considered the synthetic pathways responsible to its formation. Aims: We have studied the possibility of forming urea in the gas phase via different kinds of bi-molecular reactions: ion-molecule, neutral, and radical. In particular we have focused on the activation energy of these reactions in order to find possible reactants that could be responsible for to barrierless (or very low energy) pathways. Methods: We have used very accurate, highly correlated quantum chemistry calculations to locate and characterize the reaction pathways in terms of minima and transition states connecting reactants to products. Results: Most of the reactions considered have an activation energy that is too high; but the ion-molecule reaction between NH2OHNH2OH2+ and formamide is not too high. These reactants could be responsible not only for the formation of urea but also of isocyanic acid, which is an organic molecule also observed in the interstellar medium.

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.

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

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

Lanosterol reverses protein aggregation in cataracts.

PubMed

Zhao, Ling; Chen, Xiang-Jun; Zhu, Jie; Xi, Yi-Bo; Yang, Xu; Hu, Li-Dan; Ouyang, Hong; Patel, Sherrina H; Jin, Xin; Lin, Danni; Wu, Frances; Flagg, Ken; Cai, Huimin; Li, Gen; Cao, Guiqun; Lin, Ying; Chen, Daniel; Wen, Cindy; Chung, Christopher; Wang, Yandong; Qiu, Austin; Yeh, Emily; Wang, Wenqiu; Hu, Xun; Grob, Seanna; Abagyan, Ruben; Su, Zhiguang; Tjondro, Harry Christianto; Zhao, Xi-Juan; Luo, Hongrong; Hou, Rui; Jefferson, J; Perry, P; Gao, Weiwei; Kozak, Igor; Granet, David; Li, Yingrui; Sun, Xiaodong; Wang, Jun; Zhang, Liangfang; Liu, Yizhi; Yan, Yong-Bin; Zhang, Kang

2015-07-30

The human lens is comprised largely of crystallin proteins assembled into a highly ordered, interactive macro-structure essential for lens transparency and refractive index. Any disruption of intra- or inter-protein interactions will alter this delicate structure, exposing hydrophobic surfaces, with consequent protein aggregation and cataract formation. Cataracts are the most common cause of blindness worldwide, affecting tens of millions of people, and currently the only treatment is surgical removal of cataractous lenses. The precise mechanisms by which lens proteins both prevent aggregation and maintain lens transparency are largely unknown. Lanosterol is an amphipathic molecule enriched in the lens. It is synthesized by lanosterol synthase (LSS) in a key cyclization reaction of a cholesterol synthesis pathway. Here we identify two distinct homozygous LSS missense mutations (W581R and G588S) in two families with extensive congenital cataracts. Both of these mutations affect highly conserved amino acid residues and impair key catalytic functions of LSS. Engineered expression of wild-type, but not mutant, LSS prevents intracellular protein aggregation of various cataract-causing mutant crystallins. Treatment by lanosterol, but not cholesterol, significantly decreased preformed protein aggregates both in vitro and in cell-transfection experiments. We further show that lanosterol treatment could reduce cataract severity and increase transparency in dissected rabbit cataractous lenses in vitro and cataract severity in vivo in dogs. Our study identifies lanosterol as a key molecule in the prevention of lens protein aggregation and points to a novel strategy for cataract prevention and treatment.

Orientation of surfactant self-assembled aggregates on graphite

NASA Astrophysics Data System (ADS)

Sammalkorpi, Maria; Hynninen, Antti-Pekka; Panagiotopoulos, Athanassios Z.; Haataja, Mikko

2007-03-01

Micellar aggregates on surfaces can provide a self-healing corrosion protection or lubrication layer. It has been observed experimentally that on a single crystal surface this layer often consists of oriented hemi-cylindrical micelles which are aligned with the underlying crystal lattice (``orientation effect''). A key feature of this self-assembly process is the interplay between detergent--detergent and detergent--surface interactions. Since the dimensions of the detergent molecules and the unit cell of the surface are typically quite different, the origins of this orientation effect remain unclear. Here we address the question and present the results of Molecular Dynamics simulations of sodium dodecyl sulfate (SDS) self-aggregation on graphite. We employ both single-molecule and multi-molecule simulations of SDS to unravel the origins of the orientation effect. We report that the underlying graphite surface is sufficient to impose orientational bias on individual SDS molecules diffusing on the surface. This produces collective effects that give rise to the oriented hemi-micelles.

Ion aggregation in high salt solutions. VII. The effect of cations on the structures of ion aggregates and water hydrogen-bonding network

NASA Astrophysics Data System (ADS)

Choi, Jun-Ho; Choi, Hyung Ran; Jeon, Jonggu; Cho, Minhaeng

2017-10-01

Ions in high salt solutions have a strong propensity to form polydisperse ion aggregates with broad size and shape distributions. In a series of previous comparative investigations using femtosecond IR pump-probe spectroscopy, molecular dynamics simulation, and graph theoretical analysis, we have shown that there exists a morphological difference in the structures of ion aggregates formed in various salt solutions. As salt concentration increases, the ions in high salt solutions form either cluster-like structures excluding water molecules or network-like structures entwined with water hydrogen-bonding networks. Interestingly, such morphological characteristics of the ion aggregates have been found to be in correlation with the solubility limits of salts. An important question that still remains unexplored is why certain salts with different cations have notably different solubility limits in water. Here, carrying out a series of molecular dynamics simulations of aqueous salt solutions and analyzing the distributions and connectivity patterns of ion aggregates with a spectral graph analysis method, we establish the relationship between the salt solubility and the ion aggregate morphology with a special emphasis on the cationic effects on water structures and ion aggregation. We anticipate that the understanding of large scale ion aggregate structures revealed in this study will be critical for elucidating the specific ion effects on the solubility and conformational stability of co-solute molecules such as proteins in water.

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 K 2 -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.

Model for fluorescence quenching in light harvesting complex II in different aggregation states.

PubMed

Andreeva, Atanaska; Abarova, Silvia; Stoitchkova, Katerina; Busheva, Mira

2009-02-01

Low-temperature (77 K) steady-state fluorescence emission spectroscopy and dynamic light scattering were applied to the main chlorophyll a/b protein light harvesting complex of photosystem II (LHC II) in different aggregation states to elucidate the mechanism of fluorescence quenching within LHC II oligomers. Evidences presented that LHC II oligomers are heterogeneous and consist of large and small particles with different fluorescence yield. At intermediate detergent concentrations the mean size of the small particles is similar to that of trimers, while the size of large particles is comparable to that of aggregated trimers without added detergent. It is suggested that in small particles and trimers the emitter is monomeric chlorophyll, whereas in large aggregates there is also another emitter, which is a poorly fluorescing chlorophyll associate. A model, describing populations of antenna chlorophyll molecules in small and large aggregates in their ground and first singlet excited states, is considered. The model enables us to obtain the ratio of the singlet excited-state lifetimes in small and large particles, the relative amount of chlorophyll molecules in large particles, and the amount of quenchers as a function of the degree of aggregation. These dependencies reveal that the quenching of the chl a fluorescence upon aggregation is due to the formation of large aggregates and the increasing of the amount of chlorophyll molecules forming these aggregates. As a consequence, the amount of quenchers, located in large aggregates, is increased, and their singlet excited-state lifetimes steeply decrease.

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 ...

Brome isotope selective control of CF3Br molecule clustering by IR laser radiation in gas-dynamic expansion of CF3Br - Ar mixture

NASA Astrophysics Data System (ADS)

Apatin, V. M.; Lokhman, V. N.; Makarov, G. N.; Ogurok, N.-D. D.; Ryabov, E. A.

2018-02-01

We report the results of research on the experimental control of CF3Br molecule clustering under gas-dynamic expansion of the CF3Br - Ar mixture at a nozzle exit by using IR laser radiation. A cw CO2 laser is used for exciting molecules and clusters in the beam and a time-of-flight mass-spectrometer with laser UV ionisation of particles for their detection. The parameters of the gas above the nozzle are determined (compositions and pressure) at which intensive molecule clustering occurs. It is found that in the case of the CF3Br gas without carrier when the pressure P0 above the nozzle does not exceed 4 atm, molecular clusters actually are not generated in the beam. If the gas mixture of CF3Br with argon is used at a pressure ratio 1 : N, where N >= 3, and the total pressure above the nozzle is P0 >= 2 atm, then there occurs molecule clustering. We study the dependences of the efficiency of suppressing the molecule clustering on parameters of the exciting pulse, gas parameters above the nozzle, and on a distance of the molecule irradiation zone from the nozzle exit section. It is shown that in the case of resonant vibrational excitation of gas-dynamically cooled CF3Br molecules at the nozzle exit one can realise isotope-selective suppression of molecule clustering with respect to bromine isotopes. With the CF3Br - Ar mixtures having the pressure ratio 1 : 3 and 1 : 15, the enrichment factors obtained with respect to bromine isotopes are kenr ≈ 1.05 ± 0.005 and kenr ≈ 1.06 ± 0.007, respectively, under jet irradiation by laser emission in the 9R(30) line (1084.635 cm-1). The results obtained let us assume that this method can be used to control clustering of molecules comprising heavy element isotopes, which have a small isotopic shift in IR absorption spectra.

Plasma based formation and deposition of metal and metal oxide nanoparticles using a gas aggregation source

NASA Astrophysics Data System (ADS)

Polonskyi, Oleksandr; Ahadi, Amir Mohammad; Peter, Tilo; Fujioka, Kenji; Abraham, Jan Willem; Vasiliauskaite, Egle; Hinz, Alexander; Strunskus, Thomas; Wolf, Sebastian; Bonitz, Michael; Kersten, Holger; Faupel, Franz

2018-05-01

Metal clusters and nanoparticles (NPs) have been studied intensively due to their unique chemical, physical, electrical, and optical properties, resulting from their dimensions, which provided host of applications in nanoscience and nanotechnology. Formation of new materials by embedding NPs into various matrices (i.e. formation of nanocomposites) further expands the horizon of possible application of such nanomaterials. In the last few decades, the focus was put on the formation of metallic and metal oxide NPs via a so-called gas aggregation nanoparticle source employing magnetron sputtering (i.e. Haberland concept). In this paper, an overview is given of the recent progress in formation and deposition of NPs by the gas aggregation method. Examples range from noble metals (Ag, Au) through reactive metals (Al, Ti) to Si and the respective oxides. Emphasis is placed on the mechanism of nanoparticle growth and the resulting properties. Moreover, kinetic Monte Carlo simulations were developed to explain the growth mechanism and dynamics of nanoparticle formation depending on the experimental conditions. In addition, the role of trace amounts of reactive gases and of pulsed operation of the plasma on the nucleation process is addressed. Finally, the treatment of the NPs in the plasma environment resulting in nanoparticle charging, morphological and chemical modifications is discussed. Contribution to the Topical Issue "Fundamentals of Complex Plasmas", edited by Jürgen Meichsner, Michael Bonitz, Holger Fehske, Alexander Piel.

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

Interactions of gaseous molecules with X-ray photons and photoelectrons in AP-XPS study of solid surface in gas phase.

PubMed

Tao, Franklin Feng; Nguyen, Luan

2018-04-18

Studies of the surface of a catalyst in the gas phase via photoelectron spectroscopy is an important approach to establish a correlation between the surface of a catalyst under reaction conditions or during catalysis and its corresponding catalytic performance. Unlike the well understood interactions between photoelectrons and the atomic layers of a surface in ultrahigh vacuum (UHV) and the well-developed method of quantitative analysis of a solid surface in UHV, a fundamental understanding of the interactions between X-ray photons and gaseous molecules and between photoelectrons and molecules of the gas phase in ambient pressure X-ray photoelectron spectroscopy (AP-XPS) is lacking. Through well designed experiments, here the impact of the interactions between photoelectrons and gaseous molecules and interactions between X-ray photons and gaseous molecules on the intensity of the collected photoelectrons have been explored. How the changes in photoelectron intensity resulting from these interactions influence measurement of the authentic atomic ratio of element M to A of a solid surface has been discussed herein, and methods to correct the measured nominal atomic ratio of two elements of a solid surface upon travelling through a gas phase to its authentic atomic ratio have been developed.

Aggregation-induced chemical reactions: acid dissociation in growing water clusters.

PubMed

Forbert, Harald; Masia, Marco; Kaczmarek-Kedziera, Anna; Nair, Nisanth N; Marx, Dominik

2011-03-23

Understanding chemical reactivity at ultracold conditions, thus enabling molecular syntheses via interstellar and atmospheric processes, is a key issue in cryochemistry. In particular, acid dissociation and proton transfer reactions are ubiquitous in aqueous microsolvation environments. Here, the full dissociation of a HCl molecule upon stepwise solvation by a small number of water molecules at low temperatures, as relevant to helium nanodroplet isolation (HENDI) spectroscopy, is analyzed in mechanistic detail. It is found that upon successive aggregation of HCl with H(2)O molecules, a series of cyclic heteromolecular structures, up to and including HCl(H(2)O)(3), are initially obtained before a precursor state for dissociation, HCl(H(2)O)(3)···H(2)O, is observed upon addition of a fourth water molecule. The latter partially aggregated structure can be viewed as an "activated species", which readily leads to dissociation of HCl and to the formation of a solvent-shared ion pair, H(3)O(+)(H(2)O)(3)Cl(-). Overall, the process is mostly downhill in potential energy, and, in addition, small remaining barriers are overcome by using kinetic energy released as a result of forming hydrogen bonds due to aggregation. The associated barrier is not ruled by thermal equilibrium but is generated by athermal non-equilibrium dynamics. These "aggregation-induced chemical reactions" are expected to be of broad relevance to chemistry at ultralow temperature much beyond HENDI spectroscopy.

Raman spectral signatures as conformational probes of gas phase flexible molecules

NASA Astrophysics Data System (ADS)

Golan, Amir; Mayorkas, Nitzan; Rosenwaks, Salman; Bar, Ilana

2009-07-01

A novel application of ionization-loss stimulated Raman spectroscopy (ILSRS) for monitoring the spectral features of four conformers of a gas phase flexible molecule is reported. The Raman spectral signatures of four conformers of 2-phenylethylamine are well matched by the results of density functional theory calculations, showing bands uniquely identifying the structures. The measurement of spectral signatures by ILSRS in an extended spectral range, with a conventional laser source, is instrumental in facilitating the unraveling of intra- and intermolecular interactions that are significant in biological structure and activity.

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.

Curcumin and kaempferol prevent lysozyme fibril formation by modulating aggregation kinetic parameters.

PubMed

Borana, Mohanish S; Mishra, Pushpa; Pissurlenkar, Raghuvir R S; Hosur, Ramakrishna V; Ahmad, Basir

2014-03-01

Interaction of small molecule inhibitors with protein aggregates has been studied extensively, but how these inhibitors modulate aggregation kinetic parameters is little understood. In this work, we investigated the ability of two potential aggregation inhibiting drugs, curcumin and kaempferol, to control the kinetic parameters of aggregation reaction. Using thioflavin T fluorescence and static light scattering, the kinetic parameters such as amplitude, elongation rate constant and lag time of guanidine hydrochloride-induced aggregation reactions of hen egg white lysozyme were studied. We observed a contrasting effect of inhibitors on the kinetic parameters when aggregation reactions were measured by these two probes. The interactions of these inhibitors with hen egg white lysozyme were investigated using fluorescence quench titration method and molecular dynamics simulations coupled with binding free energy calculations. We conclude that both the inhibitors prolong nucleation of amyloid aggregation through binding to region of the protein which is known to form the core of the protein fibril, but once the nucleus is formed the rate of elongation is not affected by the inhibitors. This work would provide insight into the mechanism of aggregation inhibition by these potential drug molecules. Copyright © 2014 Elsevier B.V. All rights reserved.

Communication: Gas-phase structural isomer identification by Coulomb explosion of aligned molecules

NASA Astrophysics Data System (ADS)

Burt, Michael; Amini, Kasra; Lee, Jason W. L.; Christiansen, Lars; Johansen, Rasmus R.; Kobayashi, Yuki; Pickering, James D.; Vallance, Claire; Brouard, Mark; Stapelfeldt, Henrik

2018-03-01

The gas-phase structures of four difluoroiodobenzene and two dihydroxybromobenzene isomers were identified by correlating the emission angles of atomic fragment ions created, following femtosecond laser-induced Coulomb explosion. The structural determinations were facilitated by confining the most polarizable axis of each molecule to the detection plane prior to the Coulomb explosion event using one-dimensional laser-induced adiabatic alignment. For a molecular target consisting of two difluoroiodobenzene isomers, each constituent structure could additionally be singled out and distinguished.

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.

Measurements of water molecule density by tunable diode laser absorption spectroscopy in dielectric barrier discharges with gas-water interface

NASA Astrophysics Data System (ADS)

Tachibana, Kunihide; Nakamura, Toshihiro; Kawasaki, Mitsuo; Morita, Tatsuo; Umekawa, Toyofumi; Kawasaki, Masahiro

2018-01-01

We measured water molecule (H2O) density by tunable diode-laser absorption spectroscopy (TDLAS) for applications in dielectric barrier discharges (DBDs) with a gas-water interface. First, the effects of water temperature and presence of gas flow were tested using a Petri dish filled with water and a gas injection nozzle. Second, the TDLAS system was applied to the measurements of H2O density in two types of DBDs; one was a normal (non-inverted) type with a dielectric-covered electrode above a water-filled counter electrode and the other was an inverted type with a water-suspending mesh electrode above a dielectric-covered counter electrode. The H2O density in the normal DBD was close to the density estimated from the saturated vapor pressure, whereas the density in the inverted DBD was about half of that in the former type. The difference is attributed to the upward gas flow in the latter type, that pushes the water molecules up towards the gas-water interface.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Ji-Min; School of Chemistry and Chemical Engineering, Linyi University, Linyi 276005; Liu, Qing

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 sizemore » 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.« less

Exploration of bulk and interface behavior of gas molecules and 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid using equilibrium and nonequilibrium molecular dynamics simulation and quantum chemical calculation.

PubMed

Yang, Quan; Achenie, Luke E K

2018-04-18

Ionic liquids (ILs) show brilliant performance in separating gas impurities, but few researchers have performed an in-depth exploration of the bulk and interface behavior of penetrants and ILs thoroughly. In this research, we have performed a study on both molecular dynamics (MD) simulation and quantum chemical (QC) calculation to explore the transport of acetylene and ethylene in the bulk and interface regions of 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM]-[BF4]). The diffusivity, solubility and permeability of gas molecules in the bulk were researched with MD simulation first. The subdiffusion behavior of gas molecules is induced by coupling between the motion of gas molecules and the ions, and the relaxation processes of the ions after the disturbance caused by gas molecules. Then, QC calculation was performed to explore the optical geometry of ions, ion pairs and complexes of ions and penetrants, and interaction potential for pairs and complexes. Finally, nonequilibrium MD simulation was performed to explore the interface structure and properties of the IL-gas system and gas molecule behavior in the interface region. The research results may be used in the design of IL separation media.

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 ...

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.

Profiles of equilibrium constants for self-association of aromatic molecules

NASA Astrophysics Data System (ADS)

Beshnova, Daria A.; Lantushenko, Anastasia O.; Davies, David B.; Evstigneev, Maxim P.

2009-04-01

Analysis of the noncovalent, noncooperative self-association of identical aromatic molecules assumes that the equilibrium self-association constants are either independent of the number of molecules (the EK-model) or change progressively with increasing aggregation (the AK-model). The dependence of the self-association constant on the number of molecules in the aggregate (i.e., the profile of the equilibrium constant) was empirically derived in the AK-model but, in order to provide some physical understanding of the profile, it is proposed that the sources for attenuation of the equilibrium constant are the loss of translational and rotational degrees of freedom, the ordering of molecules in the aggregates and the electrostatic contribution (for charged units). Expressions are derived for the profiles of the equilibrium constants for both neutral and charged molecules. Although the EK-model has been widely used in the analysis of experimental data, it is shown in this work that the derived equilibrium constant, KEK, depends on the concentration range used and hence, on the experimental method employed. The relationship has also been demonstrated between the equilibrium constant KEK and the real dimerization constant, KD, which shows that the value of KEK is always lower than KD.

Stacking and Branching in Self-Aggregation of Caffeine in Aqueous Solution: From the Supramolecular to Atomic Scale Clustering.

PubMed

Tavagnacco, Letizia; Gerelli, Yuri; Cesàro, Attilio; Brady, John W

2016-09-22

The dynamical and structural properties of caffeine solutions at the solubility limit have been investigated as a function of temperature by means of MD simulations, static and dynamic light scattering, and small angle neutron scattering experiments. A clear picture unambiguously supported by both experiment and simulation emerges: caffeine self-aggregation promotes the formation of two distinct types of clusters: linear aggregates of stacked molecules, formed by 2-14 caffeine molecules depending on the thermodynamic conditions and disordered branched aggregates with a size in the range 1000-3000 Å. While the first type of association is well-known to occur under room temperature conditions for both caffeine and other purine systems, such as nucleotides, the presence of the supramolecular aggregates has not been reported previously. MD simulations indicate that branched structures are formed by caffeine molecules in a T-shaped arrangement. An increase of the solubility limit (higher temperature but also higher concentration) broadens the distribution of cluster sizes, promoting the formation of stacked aggregates composed by a larger number of caffeine molecules. Surprisingly, the effect on the branched aggregates is rather limited. Their internal structure and size do not change considerably in the range of solubility limits investigated.

Construction of the Free Energy Landscape of Peptide Aggregation from Molecular Dynamics Simulations.

PubMed

Riccardi, Laura; Nguyen, Phuong H; Stock, Gerhard

2012-04-10

To describe the structure and dynamics of oligomers during peptide aggregation, a method is proposed that considers both the intramolecular and intermolecular structures of the multimolecule system and correctly accounts for its degeneracy. The approach is based on the "by-parts" strategy, which partitions a complex molecular system into parts, determines the metastable conformational states of each part, and describes the overall conformational state of the system in terms of a product basis of the states of the parts. Starting from a molecular dynamics simulation of n molecules, the method consists of three steps: (i) characterization of the intramolecular structure, that is, of the conformational states of a single molecule in the presence of the other molecules (e.g., β-strand or random coil); (ii) characterization of the intermolecular structure through the identification of all occurring aggregate states of the peptides (dimers, trimers, etc.); and (iii) construction of the overall conformational states of the system in terms of a product basis of the n "single-molecule" states and the aggregate states. Considering the Alzheimer β-amyloid peptide fragment Aβ16-22 as a first application, about 700 overall conformational states of the trimer (Aβ16-22)3 were constructed from all-atom molecular dynamics simulation in explicit water. Based on these states, a transition network reflecting the free energy landscape of the aggregation process can be constructed that facilitates the identification of the aggregation pathways.

Dis-aggregation of an insoluble porphyrin in a calixarene matrix: characterization of aggregate modes by extended dipole model.

PubMed

de Miguel, Gustavo; Martín-Romero, María T; Pedrosa, José M; Muñoz, Eulogia; Pérez-Morales, Marta; Richardson, Tim H; Camacho, Luis

2008-03-21

In this paper, the different aggregation modes of a water-insoluble porphyrin (EHO) mixed with an amphiphilic calix[8]arene (C8A), at the air-water interface and in Langmuir-Blodgett (LB) film form, are analyzed as a function of the mixed composition. The strategy used to control the EHO aggregation has consisted of preparing mixed thin films containing EHO and C8A, in different ratios, at the air-water interface. Therefore, the increase of the C8A molar ratio in the mixed film diminishes the aggregation of the EHO molecules, although such an effect must be exclusively related to the dilution of the porphyrin. The reflection spectra of the mixed C8A-EHO films registered at the air-water interface, show a complex Soret band exhibiting splitting, hypochromicity and broadening features. Also, during the transfer process at high surface pressure, it has been shown that the EHO molecules are ejected from the C8A monolayer and only a fraction of porphyrin is transferred to the solid support, in spite of a complete transfer for the C8A matrix. The complex structure of the reflection spectra at the air-water interface, as well as the polarization dependence of the absorption spectra for the mixed LB films, indicate the existence of four different arrangements for the EHO hosted in the C8A matrix. The aggregate formation is governed by two factors: the attraction between the porphyrin rings which minimizes their separation, and the alkyl chain interactions, that is, hydrophobic effect and/or steric hindrance which determine and restrict the possible aggregation structures. By using the extended dipole model, the assignment of the spectral peaks observed to different EHO aggregates is shown.

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

Structural characterization of astaxanthin aggregates as revealed by analysis and simulation of optical spectra

NASA Astrophysics Data System (ADS)

Lu, Liping; Hu, Taoping; Xu, Zhigang

2017-10-01

Carotenoids can self-assemble in hydrated polar solvents to form J- or H-type aggregates, inducing dramatic changes in photophysical properties. Here, we measured absorption and emission spectra of astaxanthin in ethanol-water solution using ultraviolet-visible and fluorescence spectrometers. Two types of aggregates were distinguished in mixed solution at different water contents by absorption spectra. After addition of water, all probed samples immediately formed H-aggregates with maximum blue shift of 31 nm. In addition, J-aggregate was formed in 1:3 ethanol-water solution measured after an hour. Based on Frenkel exciton model, we calculated linear absorption and emission spectra of these aggregates to describe aggregate structures in solution. For astaxanthin, experimental results agreed well with the fitted spectra of H-aggregate models, which consisted of tightly packed stacks of individual molecules, including hexamers, trimers, and dimers. Transition moment of single astaxanthin in ethanol was obtained by Gaussian 09 program package to estimate the distance between molecules in aggregates. Intermolecular distance of astaxanthin aggregates ranges from 0.45 nm to 0.9 nm. Fluorescence analysis showed that between subbands, strong exciton coupling induced rapid relaxation of H-aggregates. This coupling generated larger Stokes shift than monomers and J-aggregates.

Determining the Effect of Catechins on SOD1 Conformation and Aggregation by Ion Mobility Mass Spectrometry Combined with Optical Spectroscopy

NASA Astrophysics Data System (ADS)

Zhao, Bing; Zhuang, Xiaoyu; Pi, Zifeng; Liu, Shu; Liu, Zhiqiang; Song, Fengrui

2018-02-01

The aggregation of Cu,Zn-superoxide dismutase (SOD1) plays an important role in the etiology of amyotrophic lateral sclerosis (ALS). For the disruption of ALS progression, discovering new drugs or compounds that can prevent SOD1 aggregation is important. In this study, ESI-MS was used to investigate the interaction of catechins and SOD1. The noncovalent complex of catechins that interact with SOD1 was found and retained in the gas phase under native ESI-MS condition. The conformation changes of SOD1 after binding with catechins were also explored via traveling wave ion mobility (IM) spectrometry. Epigallocatechin gallate (EGCG) can stabilize SOD1 conformation against unfolding in three catechins. To further evaluate the efficacy of EGCG, we monitored the fluorescence changes of dimer E2,E2,-SOD1(apo-SOD1, E:empty) with and without ligands under denaturation conditions, and found that EGCG can inhibit apo-SOD1 aggregation. In addition, the circular dichroism spectra of the samples showed that EGCG can decrease the β-sheet content of SOD1, which can produce aggregates. These results indicated that orthogonal separation dimension in the gas-phase IM coupled with ESI-MS (ESI-IM-MS) can potentially provide insight into the interaction between SOD1 and small molecules. The advantage is that it dramatically decreases the analysis time. Meantime, optical spectroscopy techniques can be used to confirm ESI-IM-MS results. [Figure not available: see fulltext.

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steimle, Timothy

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), palladiummore » (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, μ m. In general terms, μ el, gives insight into the charge distribution and mm into the number

Inhibition of GNNQQNY prion peptide aggregation by trehalose: a mechanistic view.

PubMed

Katyal, Nidhi; Deep, Shashank

2017-07-26

Deposition of amyloid fibrils is the seminal event in the pathogenesis of numerous neurodegenerative diseases. The formation of this amyloid assembly is the manifestation of a cascade of structural transitions including toxic oligomer formation in the early stages of aggregation. Thus a viable therapeutic strategy involves the use of small molecular ligands to interfere with this assembly. In this perspective, we have explored the kinetics of aggregate formation of the fibril forming GNNQQNY peptide fragment from the yeast prion protein SUP35 using multiple all atom MD simulations with explicit solvent and provided mechanistic insights into the way trehalose, an experimentally known aggregation inhibitor, modulates the aggregation pathway. The results suggest that the assimilation process is impeded by different barriers at smaller and larger oligomeric sizes: the initial one being easily surpassed at higher temperatures and peptide concentrations. The kinetic profile demonstrates that trehalose delays the aggregation process by increasing both these activation barriers, specifically the latter one. It increases the sampling of small-sized aggregates that lack the beta sheet conformation. Analysis reveals that the barrier in the growth of larger stable oligomers causes the formation of multiple stable small oligomers which then fuse together bimolecularly. The PCA of 26 properties was carried out to deconvolute the events within the temporary lag phases, which suggested dynamism in lags involving an increase in interchain contacts and burial of SASA. The predominant growth route is monomer addition, which changes to condensation on account of a large number of depolymerisation events in the presence of trehalose. The favourable interaction of trehalose specifically with the sidechain of the peptide promotes crowding of trehalose molecules in its vicinity - the combination of both these factors imparts the observed behaviour. Furthermore, increasing trehalose

Conformation and Aggregation of LKα14 Peptide in Bulk Water and at the Air/Water Interface.

PubMed

Dalgicdir, Cahit; Sayar, Mehmet

2015-12-10

Historically, the protein folding problem has mainly been associated with understanding the relationship between amino acid sequence and structure. However, it is known that both the conformation of individual molecules and their aggregation strongly depend on the environmental conditions. Here, we study the aggregation behavior of the model peptide LKα14 (with amino acid sequence LKKLLKLLKKLLKL) in bulk water and at the air/water interface. We start by a quantitative analysis of the conformational space of a single LKα14 in bulk water. Next, in order to analyze the aggregation tendency of LKα14, by using the umbrella sampling technique we calculate the potential of mean force for pulling a single peptide from an n-molecule aggregate. In agreement with the experimental results, our calculations yield the optimal aggregate size as four. This equilibrium state is achieved by two opposing forces: Coulomb repulsion between the lysine side chains and the reduction of solvent accessible hydrophobic surface area upon aggregation. At the vacuum/water interface, however, even dimers of LKα14 become marginally stable, and any larger aggregate falls apart instantaneously. Our results indicate that even though the interface is highly influential in stabilizing the α-helix conformation for a single molecule, it significantly reduces the attraction between two LKα14 peptides, along with their aggregation tendency.

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.

Modulation of the aggregation properties of sodium deoxycholate in presence of hydrophilic imidazolium based ionic liquid: water dynamics study to probe the structural alteration of the aggregates.

PubMed

Kundu, Niloy; Banik, Debasis; Roy, Arpita; Kuchlyan, Jagannath; Sarkar, Nilmoni

2015-10-14

In this article, we have investigated the effect of a hydrophilic ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim]-BF4), on the aggregation properties of a biological surfactant, sodium deoxycholate (NaDC), in water. In solution, unlike conventional surfactants it shows stepwise aggregation and the effect of the conventional ionic liquid on the aggregation properties is rather interesting. We have observed concentration dependent dual role of the ionic liquid; at their low concentration, the aggregated structure of NaDC reorganizes itself into an elongated rod like structure. However, the aggregated network is disintegrated into small aggregates upon further addition of ionic liquid. TEM (Transmission Electron Microscopy), SEM (Scanning Electron Microscopy) and FLIM (Fluorescence Lifetime Imaging Microscopy) images also confirmed the structural alteration of NaDC upon varying the concentration of the ionic liquid. The proton NMR data indicate that hydrophobic as well as electrostatic interaction is solely responsible for such structural adaptation of NaDC in the presence of an ionic liquid. The host-guest interaction inside the aggregates is monitored using Coumarin-153 (C-153) and the location of C-153 is probed by varying the excitation wavelength from 375 nm to 440 nm and the two binding sites of the aggregates are affected in a different fashion in the presence of ionic liquid. Excitation in the blue region selects the fluorophores which preferably bind to the buried region of the aggregates, whereas 440 nm excitation corresponds to the guest molecules which are exposed to the solvent molecules. The average solvation time of C-153 is increased in the presence of 1.68 wt% [bmim]-BF4 at λexc = 440 nm i.e. the probe molecules relocate themselves to a more restricted region. However, the average solvation time became 2.6 times faster in the presence of 11.2 wt% [bmim]-BF4, which corresponds to a more polar and exposed region. The time resolved

Spectroscopic manifestations of hybrid association of CdS colloidal quantum dots with J-aggregates of a thiatrimethine cyanine dye

NASA Astrophysics Data System (ADS)

Ovchinnikov, O. V.; Smirnov, M. S.; Shapiro, B. I.; Dedikova, A. O.; Shatskikh, T. S.

2015-11-01

We have found spectroscopic manifestations of hybrid association in mixtures of CdS colloidal quantum dots with an average size of 2.5-4.2 nm with J-aggregates of pyridinium salt of the 3,3'-di-(γ- sulfopropyl)-9-ethyl-4,5,4',5'-dibenzo-thiacarbocyanine betaine dye that were prepared by the sol-gel method in gelatin. Observed changes of the spectral properties of J-aggregates of dye molecules due to their hybrid association with CdS quantum dots are ensured by steric transformations of dye molecules, which lead to the formation of luminescent trans-J-aggregates. The hybrid association is accompanied by the quenching of the recombination luminescence band of CdS quantum dots (540-640 nm) and by an increase in the luminescence intensity of J-aggregates of dye molecules (670-680 nm). This regularity becomes enhanced with an increase in the ratio of the number of dye molecules to the number of quantum dots [ n dye]: [ n QD] and in the degree of overlap between the luminescence spectrum of quantum dots and the absorption spectrum of J-aggregates, which indicates that there is a resonant nonradiative transfer of the electronic excitation energy from recombination luminescence centers in CdS quantum dots to trans-J-aggregates of dye molecules conjugated to them.

Aggregation and breakup of colloidal particle aggregates in shear flow, studied with video microscopy.

PubMed

Tolpekin, V A; Duits, M H G; van den Ende, D; Mellema, J

2004-03-30

We used video microscopy to study the behavior of aggregating suspensions in shear flow. Suspensions consisted of 920 nm diameter silica spheres, dispersed in a methanol/bromoform solvent, to which poly(ethylene glycol) (M = 35.000 g) was added to effect weak particle aggregation. With our solvent mixture, the refractive index of the particles could be closely matched, to allow microscopic observations up to 80 microm deep into the suspension. Also the mass density is nearly equal to that of the particles, thus allowing long observation times without problems due to aggregate sedimentation. Particles were visualized via fluorescent molecules incorporated into their cores. Using a fast confocal scanning laser microscope made it possible to characterize the (flowing) aggregates via their contour-area distributions as observed in the focal plane. The aggregation process was monitored from the initial state (just after adding the polymer), until a steady state was reached. The particle volume fraction was chosen at 0.001, to obtain a characteristic aggregation time of a few hundred seconds. On variation of polymer concentration, cP (2.2-12.0 g/L), and shear rate, gamma (3-6/s), it was observed that the volume-averaged size, Dv, in the steady state became larger with polymer concentration and smaller with shear rate. This demonstrates that the aggregate size is set by a competition between cohesive forces caused by the polymer and rupture forces caused by the flow. Also aggregate size distributions were be measured (semiquantitatively). Together with a description for the internal aggregate structure they allowed a modeling of the complete aggregation curve, from t = 0 up to the steady state. A satisfactory description could be obtained by describing the aggregates as fractal objects, with Df = 2.0, as measured from CSLM images after stopping the flow. In this modeling, the fitted characteristic breakup time was found to increase with cP.

Acid-induced aggregation propensity of nivolumab is dependent on the Fc.

PubMed

Liu, Boning; Guo, Huaizu; Xu, Jin; Qin, Ting; Xu, Lu; Zhang, Junjie; Guo, Qingcheng; Zhang, Dapeng; Qian, Weizhu; Li, Bohua; Dai, Jianxin; Hou, Sheng; Guo, Yajun; Wang, Hao

2016-01-01

Nivolumab, an anti-programmed death (PD)1 IgG4 antibody, has shown notable success as a cancer treatment. Here, we report that nivolumab was susceptible to aggregation during manufacturing, particularly in routine purification steps. Our experimental results showed that exposure to low pH caused aggregation of nivolumab, and the Fc was primarily responsible for an acid-induced unfolding phenomenon. To compare the intrinsic propensity of acid-induced aggregation for other IgGs subclasses, tocilizumab (IgG1), panitumumab (IgG2) and atezolizumab (aglyco-IgG1) were also investigated. The accurate pH threshold of acid-induced aggregation for individual IgG Fc subclasses was identified and ranked as: IgG1 < aglyco-IgG1 < IgG2 < IgG4. This result was cross-validated by thermostability and conformation analysis. We also assessed the effect of several protein stabilizers on nivolumab, and found mannitol ameliorated the acid-induced aggregation of the molecule. Our results provide valuable insight into downstream manufacturing process development, especially for immune checkpoint modulating molecules with a human IgG4 backbone.

Acid-induced aggregation propensity of nivolumab is dependent on the Fc

PubMed Central

Liu, Boning; Guo, Huaizu; Xu, Jin; Qin, Ting; Xu, Lu; Zhang, Junjie; Guo, Qingcheng; Zhang, Dapeng; Qian, Weizhu; Li, Bohua; Dai, Jianxin; Hou, Sheng; Guo, Yajun; Wang, Hao

2016-01-01

ABSTRACT Nivolumab, an anti-programmed death (PD)1 IgG4 antibody, has shown notable success as a cancer treatment. Here, we report that nivolumab was susceptible to aggregation during manufacturing, particularly in routine purification steps. Our experimental results showed that exposure to low pH caused aggregation of nivolumab, and the Fc was primarily responsible for an acid-induced unfolding phenomenon. To compare the intrinsic propensity of acid-induced aggregation for other IgGs subclasses, tocilizumab (IgG1), panitumumab (IgG2) and atezolizumab (aglyco-IgG1) were also investigated. The accurate pH threshold of acid-induced aggregation for individual IgG Fc subclasses was identified and ranked as: IgG1 < aglyco-IgG1 < IgG2 < IgG4. This result was cross-validated by thermostability and conformation analysis. We also assessed the effect of several protein stabilizers on nivolumab, and found mannitol ameliorated the acid-induced aggregation of the molecule. Our results provide valuable insight into downstream manufacturing process development, especially for immune checkpoint modulating molecules with a human IgG4 backbone. PMID:27310175

HIGH RESOLUTION SPECTROSCOPY IN THE GAS PHASE: Even Large Molecules Have Well-Defined Shapes

NASA Astrophysics Data System (ADS)

Pratt, David W.

1998-10-01

A review of recent high-resolution microwave, infrared, and optical spectroscopy experiments demonstrates that remarkable progress has been made in the past 20 years in determining the equilibrium geometries of large polyatomic molecules and their clusters in the gas phase, and how these geometries change when the photon is absorbed. A special focus is on the dynamical information that can be obtained from such studies, particularly of electronically excited states.

Morphological study on small molecule acceptor-based organic solar cells with efficiencies beyond 7% (Presentation Recording)

NASA Astrophysics Data System (ADS)

Ma, Wei; Yan, He

2015-10-01

Despite the essential role of fullerenes in achieving best-performance organic solar cells (OSCs), fullerene acceptors have several drawbacks including poor light absorption, high-cost production and purification. For this reason, small molecule acceptor (SMA)-based OSCs have attracted much attention due to the easy tunability of electronic and optical properties of SMA materials. In this study, polymers with temperature dependent aggregation behaviors are combined with various small molecule acceptor materials, which lead to impressive power conversion efficiencies of up to 7.3%. The morphological and aggregation properties of the polymer:small molecule blends are studied in details. It is found that the temperature-dependent aggregation behavior of polymers allows for the processing of the polymer solutions at moderately elevated temperature, and more importantly, controlled aggregation and strong crystallization of the polymer during the film cooling and drying process. This results in a well-controlled and near-ideal polymer:small molecule morphology that is controlled by polymer aggregation during warm casting and thus insensitive to the choice of small molecules. As a result, several cases of highly efficient (PCE between 6-7.3%) SMA OSCs are achieved. The second part of this presentation will describe the morphology of a new small molecule acceptor with a unique 3D structure. The relationship between molecular structure and morphology is revealed.

Enhanced Optical and Electric Manipulation of a Quantum Gas of KRb Molecules

NASA Astrophysics Data System (ADS)

Covey, Jacob P.

Polar molecules are an ideal platform for studying quantum information and quantum simulation due to their long-range dipolar interactions. However, they have many degrees of freedom at disparate energy scales and thus are difficult to cool. Ultracold KRb molecules near quantum degeneracy were first produced in 2008. Nevertheless, it was found that even when prepared in the absolute lowest state chemical reactions can make the gas unstable. During my PhD we worked to mitigate these limitations by loading molecules into an optical lattice where the tunneling rates, and thus the chemistry, can be exquisitely controlled. This setting allowed us to start using the rotational degree of freedom as a pseudo-spin, and paved the way for studying models of quantum magnetism, such as the t-J model and the XXZ model. Further, by allowing molecules of two "spin''-states to tunnel in the lattice, we were able to observe a continuous manifestion of the quantum Zeno effect, where increased mobility counterintuitively suppresses dissipation from inelastic collisions. In a deep lattice we observed dipolar spin-exchange interactions, and we were able to elucidate their truly many-body nature. These two sets of experiments informed us that the filling fraction of the molecules in the lattice was only 5-10%, and so we implemented a quantum synthesis approach where atomic insulators were used to maximize the number of sites with one K and one Rb, and then these "doublons'' were converted to molecules with a filling of 30%. Despite these successes, a number of tools such as high resolution detection and addressing as well as large, stable electric fields were unavailable. Also during my PhD I led efforts to design, build, test, and implement a new apparatus which provides access to these tools and more. We have successfully produced ultracold molecules in this new apparatus, and we are now applying AC and DC electric fields with in vacuum electrodes. This apparatus will allow us to study

Mechanism of charge transfer and its impacts on Fermi-level pinning for gas molecules adsorbed on monolayer WS2.

PubMed

Zhou, Changjie; Yang, Weihuang; Zhu, Huili

2015-06-07

Density functional theory calculations were performed to assess changes in the geometric and electronic structures of monolayer WS2 upon adsorption of various gas molecules (H2, O2, H2O, NH3, NO, NO2, and CO). The most stable configuration of the adsorbed molecules, the adsorption energy, and the degree of charge transfer between adsorbate and substrate were determined. All evaluated molecules were physisorbed on monolayer WS2 with a low degree of charge transfer and accept charge from the monolayer, except for NH3, which is a charge donor. Band structure calculations showed that the valence and conduction bands of monolayer WS2 are not significantly altered upon adsorption of H2, H2O, NH3, and CO, whereas the lowest unoccupied molecular orbitals of O2, NO, and NO2 are pinned around the Fermi-level when these molecules are adsorbed on monolayer WS2. The phenomenon of Fermi-level pinning was discussed in light of the traditional and orbital mixing charge transfer theories. The impacts of the charge transfer mechanism on Fermi-level pinning were confirmed for the gas molecules adsorbed on monolayer WS2. The proposed mechanism governing Fermi-level pinning is applicable to the systems of adsorbates on recently developed two-dimensional materials, such as graphene and transition metal dichalcogenides.

Interference between Coulombic and CT-mediated couplings in molecular aggregates: H- to J-aggregate transformation in perylene-based π-stacks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hestand, Nicholas J.; Spano, Frank C.

2015-12-28

The spectroscopic differences between J and H-aggregates are traditionally attributed to the spatial dependence of the Coulombic coupling, as originally proposed by Kasha. However, in tightly packed molecular aggregates wave functions on neighboring molecules overlap, leading to an additional charge transfer (CT) mediated exciton coupling with a vastly different spatial dependence. The latter is governed by the nodal patterns of the molecular LUMOs and HOMOs from which the electron (t{sub e}) and hole (t{sub h}) transfer integrals derive. The sign of the CT-mediated coupling depends on the sign of the product t{sub e}t{sub h} and is therefore highly sensitive tomore » small (sub-Angstrom) transverse displacements or slips. Given that Coulombic and CT-mediated couplings exist simultaneously in tightly packed molecular systems, the interference between the two must be considered when defining J and H-aggregates. Generally, such π-stacked aggregates do not abide by the traditional classification scheme of Kasha: for example, even when the Coulomb coupling is strong the presence of a similarly strong but destructively interfering CT-mediated coupling results in “null-aggregates” which spectroscopically resemble uncoupled molecules. Based on a Frenkel/CT Holstein Hamiltonian that takes into account both sources of electronic coupling as well as intramolecular vibrations, vibronic spectral signatures are developed for integrated Frenkel/CT systems in both the perturbative and resonance regimes. In the perturbative regime, the sign of the lowest exciton band curvature, which rigorously defines J and H-aggregation, is directly tracked by the ratio of the first two vibronic peak intensities. Even in the resonance regime, the vibronic ratio remains a useful tool to evaluate the J or H nature of the system. The theory developed is applied to the reversible H to J-aggregate transformations recently observed in several perylene bisimide systems.« less

Electrostatic interactions lead to the formation of asymmetric collagen-phosphophoryn aggregates.

PubMed

Dahl, Thomas; Veis, Arthur

2003-01-01

In bone and dentin the formation and mineralization of the extra cellular matrix structure is a complex process highly dependent on intermolecular interactions. In dentin, the phosphophoryns (PP) and type I collagen (COL1) are the major constituents implicated in mineralization. Thus, as a first step in understanding the tissue organization, we have initiated a study of their interaction as a function of pH, ionic strength, and relative concentrations or mixing ratios. Complex formation has been analyzed by dynamic light scattering to detect aggregate formation and by rotary shadowing electron microscopy (EM) to determine aggregate shape. The EM data showed that at the pH values studied, the PP-COL1 interaction leads to the formation of large fibrillar aggregates in which the PP are present along the fibril surfaces. The quantitative phase distribution data showed a 1/1 molar equivalence at the maximum aggregation point, not at electrostatic PP-COL1 equivalence. As the ionic strength was raised, the PP-COL1 aggregates became smaller but the binding and asymmetric fibrillar aggregation persisted. In EM, the PP appear as dense spheres. Along the surfaces of the collagen aggregates, the PP are larger and more open or extended, suggesting that COL1-bound PP may undergo a conformational change, opening up so that a single PP molecule might interact with and electrostatically link several COL1 molecules. This might have important implications for dentin structure, stability, and mineralization.

A small molecule chemical chaperone optimizes its unfolded state contraction and denaturant like properties

NASA Astrophysics Data System (ADS)

Sharma, Sunny; Sarkar, Suparna; Paul, Simanta Sarani; Roy, Syamal; Chattopadhyay, Krishnananda

2013-12-01

Protein aggregation is believed to occur through the formation of misfolded conformations. It is expected that, in order to minimize aggregation, an effective small molecule chaperone would destabilize these intermediates. To study the mechanism of a chemical chaperone, we have designed a series of mutant proteins in which a tryptophan residue experiences different local environments and solvent exposures. We show that these mutants correspond to a series of conformationally altered proteins with varying degree of misfolding stress and aggregation propensities. Using arginine as a model small molecule, we show that a combination of unfolded state contraction and denaturant like properties results in selective targeting and destabilization of the partially folded proteins. In comparison, the effect of arginine towards the folded like control mutant, which is not aggregation prone, is significantly less. Other small molecules, lacking either of the above two properties, do not offer any specificity towards the misfolded proteins.

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.

Impact of Supramolecular Aggregation on the Crystallization Kinetics of Organic Compounds from the Supercooled Liquid State.

PubMed

Kalra, Arjun; Tishmack, Patrick; Lubach, Joseph W; Munson, Eric J; Taylor, Lynne S; Byrn, Stephen R; Li, Tonglei

2017-06-05

Despite numerous challenges in their theoretical description and practical implementation, amorphous drugs are of growing importance to the pharmaceutical industry. One such challenge is to gain molecular level understanding of the propensity of a molecule to form and remain as a glassy solid. In this study, a series of structurally similar diarylamine compounds was examined to elucidate the role of supramolecular aggregation on crystallization kinetics from supercooled liquid state. The structural similarity of the compounds makes it easier to isolate the molecular features that affect crystallization kinetics and glass forming ability of these compounds. To examine the role of hydrogen-bonded aggregation and motifs on crystallization kinetics, a combination of thermal and spectroscopic techniques was employed. Using variable temperature FTIR, Raman, and solid-state NMR spectroscopies, the presence of hydrogen bonding in the melt and glassy state was examined and correlated with observed phase transition behaviors. Spectroscopic results revealed that the formation of hydrogen-bonded aggregates involving carboxylic acid and pyridine nitrogen (acid-pyridine aggregates) between neighboring molecules in the melt state impedes crystallization, while the presence of carboxylic acid dimers (acid-acid dimers) in the melt favors crystallization. This study suggests that glass formation of small molecules is influenced by the type of intermolecular interactions present in the melt state and the kinetics associated with the molecules to assemble into a crystalline lattice. For the compounds that form acid-pyridine aggregates, the formation of energy degenerate chains, produced due to conformational flexibility of the molecules, presents a kinetic barrier to crystallization. The poor crystallization tendency of these aggregates stems from the highly directional hydrogen-bonding interactions needed to form the acid-pyridine chains. Conversely, for the compounds that form acid

Isothermal evaporation of ethanol in a dynamic gas atmosphere.

PubMed

Milev, Adriyan S; Wilson, Michael A; Kannangara, G S Kamali; Feng, Hai; Newman, Phillip A

2012-01-12

Optimization of evaporation and pyrolysis conditions for ethanol are important in carbon nanotube (CNT) synthesis. The activation enthalpy (ΔH(‡)), the activation entropy (ΔS(‡)), and the free energy barrier (ΔG(‡)) to evaporation have been determined by measuring the molar coefficient of evaporation, k(evap), at nine different temperatures (30-70 °C) and four gas flow rates (25-200 mL/min) using nitrogen and argon as carrier gases. At 70 °C in argon, the effect of the gas flow rate on k(evap) and ΔG(‡) is small. However, this is not true at temperatures as low as 30 °C, where the increase of the gas flow rate from 25 to 200 mL/min results in a nearly 6 times increase of k(evap) and decrease of ΔG(‡) by ~5 kJ/mol. Therefore, at 30 °C, the effect of the gas flow rate on the ethanol evaporation rate is attributed to interactions of ethanol with argon molecules. This is supported by simultaneous infrared spectroscopic analysis of the evolved vapors, which demonstrates the presence of different amounts of linear and cyclic hydrogen bonded ethanol aggregates. While the amount of these aggregates at 30 °C depends upon the gas flow rate, no such dependence was observed during evaporation at 70 °C. When the evaporation was carried out in nitrogen, ΔG(‡) was almost independent of the evaporation temperature (30-70 °C) and the gas flow rate (25-200 mL/min). Thus the evaporation of ethanol in a dynamic gas atmosphere at different temperatures may go via different mechanisms depending on the nature of the carrier gas.

Effects of adatom and gas molecule adsorption on the physical properties of tellurene: a first principles investigation.

PubMed

Wang, Xiao Hua; Wang, Da Wei; Yang, Ai Jun; Koratkar, Nikhil; Chu, Ji Feng; Lv, Pin Lei; Rong, Ming Zhe

2018-02-07

Tellurene is a new member of the two-dimensional (2D) materials' family, whose existence has been recently confirmed by first principles calculation and experimental work. Tellurene is also the first 2D mono-elemental material of group-VI predicted by scientists, and investigations of its basic properties are still in their infancy. In this study, we use first principles calculation based on density functional theory to investigate the adsorption of nineteen typical adatoms (Li, Na, K, Ca, Fe, Co, Ni, Cu, Zn, Ag, Au, Pd, Pt, B, N, O, Si, Cl, and Al), and five typical gas molecules (H 2 , O 2 , H 2 O, NO 2 , and NH 3 ) on α-phase as well as β-phase tellurene sheets. Our calculations shows that most adatoms are chemisorbed on tellurene sheets with large adsorption energies. Moreover, some of the adatoms are observed to give rise to distinct structural deformations and even local reconstructions. We report that a variety of electronic states are induced by the adatoms, which implies that different electronic structures can be engineered by the adsorption of adatoms. In fact, n-type doping, p-type doping, half-metal, and spin-gapless semiconductor features can be acquired by doping adatoms on tellurene sheets. Our calculations also show that the five gas molecules are all physisorbed on tellurene sheets, and no splitting behaviors are observed. Therefore, the adsorption of the five gas molecules has a weak effect on the electronic properties of tellurene. To conclude, our results indicate that adatom engineering may be used to greatly expand the potential applications of 2D tellurene.

Control of Porosity in Ladder Polymers by Solvent-induced Aggregation

NASA Astrophysics Data System (ADS)

Brady, Michael; Gamo, Eri; Wang, Cheng; Xia, Yan

Porous polymers hold promise as materials for gas absorption, membranes, and organic electronics. In all of these applications, attaining in-plane ordering of backbones and thus porous free volume impacts the ability to adsorb gas, selectively filter molecules, and conduct charges. In this work, hard and soft x-ray scattering and soft x-ray spectroscopy are of focus to study the pore structure, induced by the solution-driven aggregation of ladder polymer thin films made of LP-1 and LP-2. Using GISAXS and AFM it is shown that thermal annealing drives the growth of crystallites in thin films. Due to the completely sp2nature of the ladder polymer backbones, it is expected that backbones are extremely stiff and thus preventing them from packing once left in a metastable state following casting. Therefore, the combination of GIWAXS and GISAXS will be shown to be critical in correctly understanding how pores develop in this 700 m2/g sorbent (N2). Finally, application in CO2/N2 separation membranes towards carbon sequestration will be presented that show gas selectivity is achieved through heteroatom incorporation and polymer blending. In this talk, focus will be placed on state-of-the-art x-ray scattering and spectroscopy, highlighting the importance of chemically sensitive structural information enabled by the combination of spectroscopy and scattering at play with the use of resonant soft x-rays.

Optical characteristics of the nanoparticle coupled to a quantum molecular aggregate

NASA Astrophysics Data System (ADS)

Ropakova, I. Yu.; Zvyagin, A. A.

2017-11-01

Optical characteristics of a single nanoparticle, coupled to the one-dimensional quantum molecular aggregate is studied. Depending on the values of the coupling of the particle and its own frequency, with respect to the own frequency of the aggregated molecules, and the strength of the aggregation, the dynamical relative permittivity of the nanoparticle manifests the contribution from the exciton band, or/and the ones from the local level(s) caused by the particle. The refractive index and the extinction coefficient of the nanoparticle is also calculated.

Engineering cell aggregates through incorporated polymeric microparticles.

PubMed

Ahrens, Caroline C; Dong, Ziye; Li, Wei

2017-10-15

Ex vivo cell aggregates must overcome significant limitations in the transport of nutrients, drugs, and signaling proteins compared to vascularized native tissue. Further, engineered extracellular environments often fail to sufficiently replicate tethered signaling cues and the complex architecture of native tissue. Co-cultures of cells with microparticles (MPs) is a growing field directed towards overcoming many of these challenges by providing local and controlled presentation of both soluble and tethered proteins and small molecules. Further, co-cultured MPs offer a mechanism to better control aggregate architecture and even to report key characteristics of the local microenvironment such as pH or oxygen levels. Herein, we provide a brief introduction to established and developing strategies for MP production including the choice of MP materials, fabrication techniques, and techniques for incorporating additional functionality. In all cases, we emphasize the specific utility of each approach to form MPs useful for applications in cell aggregate co-culture. We review established techniques to integrate cells and MPs. We highlight those strategies that promote targeted heterogeneity or homogeneity, and we describe approaches to engineer cell-particle and particle-particle interactions that enhance aggregate stability and biological response. Finally, we review advances in key application areas of MP aggregates and future areas of development. Cell-scaled polymer microparticles (MPs) integrated into cellular aggregates have been shown to be a powerful tool to direct cell response. MPs have supported the development of healthy cartilage, islets, nerves, and vasculature by the maintenance of soluble gradients as well as by the local presentation of tethered cues and diffusing proteins and small molecules. MPs integrated with pluripotent stem cells have directed in vivo expansion and differentiation. Looking forward, MPs are expected to support both the

An advanced molecule-surface scattering instrument for study of vibrational energy transfer in gas-solid collisions.

PubMed

Ran, Qin; Matsiev, Daniel; Wodtke, Alec M; Auerbach, Daniel J

2007-10-01

We describe an advanced and highly sensitive instrument for quantum state-resolved molecule-surface energy transfer studies under ultrahigh vacuum (UHV) conditions. The apparatus includes a beam source chamber, two differential pumping chambers, and a UHV chamber for surface preparation, surface characterization, and molecular beam scattering. Pulsed and collimated supersonic molecular beams are generated by expanding target molecule mixtures through a home-built pulsed nozzle, and excited quantum state-selected molecules were prepared via tunable, narrow-band laser overtone pumping. Detection systems have been designed to measure specific vibrational-rotational state, time-of-flight, angular and velocity distributions of molecular beams coming to and scattered off the surface. Facilities are provided to clean and characterize the surface under UHV conditions. Initial experiments on the scattering of HCl(v = 0) from Au(111) show many advantages of this new instrument for fundamental studies of the energy transfer at the gas-surface interface.

Formation of novel rare-gas-containing molecules by molecular photodissociation in clusters.

PubMed

Cohen, A; Niv, M Y; Gerber, R B

2001-01-01

Recent work by Räsänen and coworkers showed that photolysis of hydrides in rare-gas matrices results in part in formation of novel, rare-gas-containing molecules. Thus, photolysis of HCl in Xe and of H2O in Xe result respectively in formation of HXeCl and HXeOH in the Xe matrices. Ab initio calculations show that the compounds HRgY so formed are stable in isolation, and that by the strength and nature of the bonding these are molecules, very different from the corresponding weakly bound clusters Rg...HY. This paper presents a study of the formation mechanism of HRgY following the photolysis of HY in clusters Rgn(HY). Calculations are described for HXeCl, as a representative example. Potential energy surfaces that govern the formation of HXeCl in the photolysis of HCl in xenon clusters are obtained, and the dynamics on these surfaces is analyzed, partly with insight from trajectories of molecular dynamics simulations. The potential surfaces are obtained by a new variant of the DIM (diatomics in molecules) and DIIS (diatomics in ionic systems) models. Non-adiabatic couplings are also obtained. The main results are: (1) Properties of HXeCl predicted by the DIM-DIIS model are in reasonable accord with results of ab initio calculations. (2) The potential along the isomerization path HXeCl-->Xe...HCl predicted by DIM is in semiquantitative accord with the ab initio results. (3) Surface-hopping molecular dynamics simulations of the process in clusters, with "on the fly" calculations of the DIM-DIIS potentials and non-adiabatic couplings are computationally feasible. (4) Formation of HXeCl, following photolysis of HCl in Xe54(HCl), requires cage-exit of the H atom as a precondition. The H atom and the Cl can then attack the same Xe atom on opposite sides, leading to charge transfer and production of the ionic HXeCl. (5) Non-adiabatic processes play an important role, both in the reagent configurations, and at the charge-transfer stage. The results open the way to

Phase Transitions in a Model of Y-Molecules Abstract

NASA Astrophysics Data System (ADS)

Holz, Danielle; Ruth, Donovan; Toral, Raul; Gunton, James

Immunoglobulin is a Y-shaped molecule that functions as an antibody to neutralize pathogens. In special cases where there is a high concentration of immunoglobulin molecules, self-aggregation can occur and the molecules undergo phase transitions. This prevents the molecules from completing their function. We used a simplified model of 2-Dimensional Y-molecules with three identical arms on a triangular lattice with 2-dimensional Grand Canonical Ensemble. The molecules were permitted to be placed, removed, rotated or moved on the lattice. Once phase coexistence was found, we used histogram reweighting and multicanonical sampling to calculate our phase diagram.

A Colloidal Route to Detection of Organic Molecules Based on Surface-Enhanced Raman Spectroscopy Using Nanostructured Substrate Derived from Aerosols

NASA Astrophysics Data System (ADS)

Gen, Masao; Kakuta, Hideo; Kamimoto, Yoshihito; Wuled Lenggoro, I.

2011-06-01

A detection method based on the surface-enhanced Raman spectroscopy (SERS)-active substrate derived from aerosol nanoparticles and a colloidal suspension for detecting organic molecules of a model analyte (a pesticide) is proposed. This approach can detect the molecules of the derived from its solution with the concentration levels of ppb. For substrate fabrication, a gas-phase method is used to directly deposit Ag nanoparticles on to a silicon substrate having pyramidal structures. By mixing the target analyte with a suspension of Ag colloids purchased in advance, clotianidin analyte on Ag colloid can exist in junctions of co-aggregated Ag colloids. Using (i) a nanostructured substrate made from aerosol nanoparticles and (ii) colloidal suspension can increase the number of activity spots.

Comparing the energy landscapes for native folding and aggregation of PrP

PubMed Central

Dee, Derek R.; Woodside, Michael T.

2016-01-01

ABSTRACT Protein sequences are evolved to encode generally one folded structure, out of a nearly infinite array of possible folds. Underlying this code is a funneled free energy landscape that guides folding to the native conformation. Protein misfolding and aggregation are also a manifestation of free-energy landscapes. The detailed mechanisms of these processes are poorly understood, but often involve rare, transient species and a variety of different pathways. The inherent complexity of misfolding has hampered efforts to measure aggregation pathways and the underlying energy landscape, especially using traditional methods where ensemble averaging obscures important rare and transient events. We recently studied the misfolding and aggregation of prion protein by examining 2 monomers tethered in close proximity as a dimer, showing how the steps leading to the formation of a stable aggregated state can be resolved in the single-molecule limit and the underlying energy landscape thereby reconstructed. This approach allows a more quantitative comparison of native folding versus misfolding, including fundamental differences in the dynamics for misfolding. By identifying key steps and interactions leading to misfolding, it should help to identify potential drug targets. Here we describe the importance of characterizing free-energy landscapes for aggregation and the challenges involved in doing so, and we discuss how single-molecule studies can help test proposed structural models for PrP aggregates. PMID:27191683

Optical and Electron Spin Resonance Studies of Destruction of Porous Structures Formed by Nitrogen-Rare Gas Nanoclusters in Bulk Superfluid Helium

NASA Astrophysics Data System (ADS)

McColgan, Patrick T.; Meraki, Adil; Boltnev, Roman E.; Lee, David M.; Khmelenko, Vladimir V.

2017-04-01

We studied optical and electron spin resonance spectra during destruction of porous structures formed by nitrogen-rare gas (RG) nanoclusters in bulk superfluid helium containing high concentrations of stabilized nitrogen atoms. Samples were created by injecting products of a radio frequency discharge of nitrogen-rare gas-helium gas mixtures into bulk superfluid helium. These samples have a high energy density allowing the study of energy release in chemical processes inside of nanocluster aggregates. The rare gases used in the studies were neon, argon, and krypton. We also studied the effects of changing the relative concentrations between nitrogen and rare gas on thermoluminescence spectra during destruction of the samples. At the beginning of the destructions, α -group of nitrogen atoms, Vegard-Kaplan bands of N_2 molecules, and β -group of O atoms were observed. The final destruction of the samples were characterized by a series bright flashes. Spectra obtained during these flashes contain M- and β -bands of NO molecules, the intensities of which depend on the concentration of molecular nitrogen in the gas mixture as well as the type of rare gas present in the gas mixture.

Inhibition of copper-mediated aggregation of human γD-crystallin by Schiff bases.

PubMed

Chauhan, Priyanka; Muralidharan, Sai Brinda; Velappan, Anand Babu; Datta, Dhrubajyoti; Pratihar, Sanjay; Debnath, Joy; Ghosh, Kalyan Sundar

2017-06-01

Protein aggregation, due to the imbalance in the concentration of Cu 2+ and Zn 2+ ions is found to be allied with various physiological disorders. Copper is known to promote the oxidative damage of β/γ-crystallins in aged eye lens and causes their aggregation leading to cataract. Therefore, synthesis of a small-molecule 'chelator' for Cu 2+ with complementary antioxidant effect will find potential applications against aggregation of β/γ-crystallins. In this paper, we have reported the synthesis of different Schiff bases and studied their Cu 2+ complexation ability (using UV-Vis, FT-IR and ESI-MS) and antioxidant activity. Further based on their copper complexation efficiency, Schiff bases were used to inhibit Cu 2+ -mediated aggregation of recombinant human γD-crystallin (HGD) and β/γ-crystallins (isolated from cataractous human eye lens). Among these synthesized molecules, compound 8 at a concentration of 100 μM had shown ~95% inhibition of copper (100 μM)-induced aggregation. Compound 8 also showed a positive cooperative effect at a concentration of 5-15 μM on the inhibitory activity of human αA-crystallin (HAA) during Cu 2+ -induced aggregation of HGD. It eventually inhibited the aggregation process by additional ~20%. However, ~50% inhibition of copper-mediated aggregation of β/γ-crystallins (isolated from cataractous human eye lens) was recorded by compound 8 (100 μM). Although the reductive aminated products of the imines showed better antioxidant activity due to their lower copper complexing ability, they were found to be non-effective against Cu 2+ -mediated aggregation of HGD.

Photodissociation and caging of HBr and HI molecules on the surface of large rare gas clusters.

PubMed

Baumfalk, R; Nahler, N H; Buck, U

2001-01-01

Photodissociation experiments were carried out at a wavelength of 243 nm for single HBr and HI molecules adsorbed on the surface of large Nen, Arn, Krn and Xen clusters. The average size is about = 130; the size ranges = 62-139 for the system HBr-Arn and = 110-830 for HI-Xen were covered. In this way the dependence of the photodissociation dynamics on both the size and the rare gas host cluster was investigated. The main observable is the kinetic energy distribution of the outgoing H atoms. The key results are that we do not find any size dependence for either system but that we observe a strong dependence on the rare gas clusters. All systems exhibit H atoms with no energy loss that indicate direct cage exit and those with nearly zero energy that are an indication of complete caging. The intensity ratio of caged to uncaged H atoms is largest for Nen, decreases with increasing mass of the cage atoms, and is weakest for Xen. On the basis of accompanying calculations this behaviour is attributed to the large amplitude motion of the light H atom. This leads to direct cage exit and penetration of the atom through the cluster with different energy transfer per collision depending on the rare gas atoms. The differences between HBr and HI molecules are attributed to different surface states, a flat and an encapsulated site.

Two-Step Amyloid Aggregation: Sequential Lag Phase Intermediates

NASA Astrophysics Data System (ADS)

Castello, Fabio; Paredes, Jose M.; Ruedas-Rama, Maria J.; Martin, Miguel; Roldan, Mar; Casares, Salvador; Orte, Angel

2017-01-01

The self-assembly of proteins into fibrillar structures called amyloid fibrils underlies the onset and symptoms of neurodegenerative diseases, such as Alzheimer’s and Parkinson’s. However, the molecular basis and mechanism of amyloid aggregation are not completely understood. For many amyloidogenic proteins, certain oligomeric intermediates that form in the early aggregation phase appear to be the principal cause of cellular toxicity. Recent computational studies have suggested the importance of nonspecific interactions for the initiation of the oligomerization process prior to the structural conversion steps and template seeding, particularly at low protein concentrations. Here, using advanced single-molecule fluorescence spectroscopy and imaging of a model SH3 domain, we obtained direct evidence that nonspecific aggregates are required in a two-step nucleation mechanism of amyloid aggregation. We identified three different oligomeric types according to their sizes and compactness and performed a full mechanistic study that revealed a mandatory rate-limiting conformational conversion step. We also identified the most cytotoxic species, which may be possible targets for inhibiting and preventing amyloid aggregation.

Effects of Inter- and Intra-aggregate Pore Space on the Soil-Gas Diffusivity Behavior in Unsaturated, Undisturbed Volcanic Ash Soils

NASA Astrophysics Data System (ADS)

Resurreccion, A. C.; Kawamoto, K.; Komatsu, T.; Moldrup, P.

2006-12-01

Volcanic ash soils (Andisols) have a unique dual porosity structure that results in good drainage and high soil- water retention. Despite of the complicated and highly developed soil structure, recent studies have reported a simple, highly linear relation between the soil-gas diffusion coefficient, Dp, and the soil-air content, ɛ, for several Japanese Andisols. In this study, we explain the linear Dp(ɛ) behavior from the effects of the inter- and intra-aggregate pore-size distributions. We couple the bimodal van Genuchten soil-water retention model with a general Dp(ɛ) model, ɛ^{X}, allowing the tortuosity- connectivity factor X to vary with pF (= log(-ψ; the soil-water matric potential in cm H2O)). Measured data suggest that the tortuosity-connectivity parameter X is at the minimum at pF 3 (where X ~ 2, following Buckingham, 1904), equal to the water retention point where a separation of inter- and intra-aggregate effects on Dp is observed. At pF < 3, the X values increased as pF decreased because of inactive/remote air-filled pore space entrapped by the inter-connected water films between inter-aggregate pore spaces. At pF > 3, X increased to a high value at very dry conditions due to remote air-filled space inside the intra-aggregate pores. By combining the complex dual porosity soil-water retention model with the power- law gas diffusivity model using a parabolic X(pF) function, the surprisingly simple linear behavior of Dp with ɛ was captured while the variation of Dp with pF followed a dual s-shaped curve similar to the water retention curve. A simple linear model to predict Dp(ɛ) is suggested, with slope C and threshold soil-air content, ɛth, calculated from the power-law model ɛ^{X} at pF 2 (near field capacity) and at pF 4.1 (near wilting point) using the same X value (= 2.3) at both pF in agreement with measured data. This linear Dp(ɛ) model performed better, especially at dry conditions, compared to the traditionally-used predictive models when

Competition between protein folding and aggregation: A three-dimensional lattice-model simulation

NASA Astrophysics Data System (ADS)

Bratko, D.; Blanch, H. W.

2001-01-01

Aggregation of protein molecules resulting in the loss of biological activity and the formation of insoluble deposits represents a serious problem for the biotechnology and pharmaceutical industries and in medicine. Considerable experimental and theoretical efforts are being made in order to improve our understanding of, and ability to control, the process. In the present work, we describe a Monte Carlo study of a multichain system of coarse-grained model proteins akin to lattice models developed for simulations of protein folding. The model is designed to examine the competition between intramolecular interactions leading to the native protein structure, and intermolecular association, resulting in the formation of aggregates of misfolded chains. Interactions between the segments are described by a variation of the Go potential [N. Go and H. Abe, Biopolymers 20, 1013 (1981)] that extends the recognition between attracting types of segments to pairs on distinct chains. For the particular model we adopt, the global free energy minimum of a pair of protein molecules corresponds to a dimer of native proteins. When three or more molecules interact, clusters of misfolded chains can be more stable than aggregates of native folds. A considerable fraction of native structure, however, is preserved in these cases. Rates of conformational changes rapidly decrease with the size of the protein cluster. Within the timescale accessible to computer simulations, the folding-aggregation balance is strongly affected by kinetic considerations. Both the native form and aggregates can persist in metastable states, even if conditions such as temperature or concentration favor a transition to an alternative form. Refolding yield can be affected by the presence of an additional polymer species mimicking the function of a molecular chaperone.

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)

Cytotoxicity Assessment of Some Carbon Nanotubes and Related Carbon Nanoparticle Aggregates and the Implications for Anthropogenic Carbon Nanotube Aggregates in the Environment

PubMed Central

Murr, L. E.; Garza, K. M.; Soto, K. F.; Carrasco, A.; Powell, T. G.; Ramirez, D. A.; Guerrero, P. A.; Lopez, D. A.; Venzor, J.

2005-01-01

Nanotechnology and nanomaterials have become the new frontier world-wide over the past few years and prospects for the production and novel uses of large quantities of carbon nanotubes in particular are becoming an increasing reality. Correspondingly, the potential health risks for these and other nanoparticulate materials have been of considerable concern. Toxicological studies, while sparse, have been concerned with virtually uncharacterized, single wall carbon nanotubes, and the conclusions have been conflicting and uncertain. In this research we performed viability assays on a murine lung macrophage cell line to assess the comparative cytotoxicity of commercial, single wall carbon nanotubes (ropes) and two different multiwall carbon nanotube samples; utilizing chrysotile asbestos nanotubes and black carbon nanoaggregates as toxicity standards. These nanotube materials were completely characterized by transmission electron microscopy and observed to be aggregates ranging from 1 to 2 μm in mean diameter, with closed ends. The cytotoxicity data indicated a strong concentration relationship and toxicity for all the carbon nanotube materials relative to the asbestos nanotubes and black carbon. A commercial multiwall carbon nanotube aggregate exhibiting this significant cell response was observed to be identical in structure to multiwall carbon nanotube aggregates demonstrated to be ubiquitous in the environment, and especially in indoor environments, where natural gas or propane cooking stoves exist. Correspondingly, preliminary epidemiological data, although sparse, indicate a correlation between asthma incidence or classification, and exposure to gas stoves. These results suggest a number of novel epidemiological and etiological avenues for asthma triggers and related respiratory or other environmental health effects, especially since indoor number concentrations for multiwall carbon nanotube aggregates is at least 10 times the outdoor concentration, and

The use of native cation-exchange chromatography to study aggregation and phase separation of monoclonal antibodies

PubMed Central

Chen, Shuang; Lau, Hollis; Brodsky, Yan; Kleemann, Gerd R; Latypov, Ramil F

2010-01-01

This study introduces a novel analytical approach for studying aggregation and phase separation of monoclonal antibodies (mAbs). The approach is based on using analytical scale cation-exchange chromatography (CEX) for measuring the loss of soluble monomer in the case of individual and mixed protein solutions. Native CEX outperforms traditional size-exclusion chromatography in separating complex protein mixtures, offering an easy way to assess mAb aggregation propensity. Different IgG1 and IgG2 molecules were tested individually and in mixtures consisting of up to four protein molecules. Antibody aggregation was induced by four different stress factors: high temperature, low pH, addition of fatty acids, and rigorous agitation. The extent of aggregation was determined from the amount of monomeric protein remaining in solution after stress. Consequently, it was possible to address the role of specific mAb regions in antibody aggregation by co-incubating Fab and Fc fragments with their respective full-length molecules. Our results revealed that the relative contribution of Fab and Fc regions in mAb aggregation is strongly dependent on pH and the stress factor applied. In addition, the CEX-based approach was used to study reversible protein precipitation due to phase separation, which demonstrated its use for a broader range of protein–protein association phenomena. In all cases, the role of Fab and Fc was clearly dissected, providing important information for engineering more stable mAb-based therapeutics. PMID:20512972

Calculation of ground state rotational populations for kinetic gas homonuclear diatomic molecules including electron-impact excitation and wall collisions.

PubMed

Farley, David R

2010-09-07

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 nonequilibrating 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.

Complex Behavior of Aqueous α-Cyclodextrin Solutions. Interfacial Morphologies Resulting from Bulk Aggregation.

PubMed

Hernandez-Pascacio, Jorge; Piñeiro, Ángel; Ruso, Juan M; Hassan, Natalia; Campbell, Richard A; Campos-Terán, José; Costas, Miguel

2016-07-05

The spontaneous aggregation of α-cyclodextrin (α-CD) molecules in the bulk aqueous solution and the interactions of the resulting aggregates at the liquid/air interface have been studied at 283 K using a battery of techniques: transmission electron microscopy, dynamic light scattering, dynamic surface tensiometry, Brewster angle microscopy, neutron reflectometry, and ellipsometry. We show that α-CD molecules spontaneously form aggregates in the bulk that grow in size with time. These aggregates adsorb to the liquid/air interface with their size in the bulk determining the adsorption rate. The material that reaches the interface coalesces laterally to form two-dimensional domains on the micrometer scale with a layer thickness on the nanometer scale. These processes are affected by the ages of both the bulk and the interface. The interfacial layer formed is not in fast dynamic equilibrium with the subphase as the resulting morphology is locked in a kinetically trapped state. These results reveal a surprising complexity of the parallel physical processes taking place in the bulk and at the interface of what might have seemed initially like a simple system.

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

Tunneling electron induced molecular electroluminescence from individual porphyrin J-aggregates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Qiushi; Zhang, Chao; Zhang, Yang, E-mail: zhyangnano@ustc.edu.cn, E-mail: zcdong@ustc.edu.cn

2015-07-27

We investigate molecular electroluminescence from individual tubular porphyrin J-aggregates on Au(111) by tunneling electron excitations in an ultrahigh-vacuum scanning tunneling microscope (STM). High-resolution STM images suggest a spiral tubular structure for the porphyrin J-aggregate with highly ordered “brickwork”-like arrangements. Such aggregated nanotube is found to behave like a self-decoupled molecular architecture and shows red-shifted electroluminescence characteristics of J-aggregates originated from the delocalized excitons. The positions of the emission peaks are found to shift slightly depending on the excitation sites, which, together with the changes in the observed spectral profiles with vibronic progressions, suggest a limited exciton coherence number within severalmore » molecules. The J-aggregate electroluminescence is also found unipolar, occurring only at negative sample voltages, which is presumably related to the junction asymmetry in the context of molecular excitations via the carrier injection mechanism.« less

Pulse gas chromatographic study of adsorption of substituted aromatics and heterocyclic molecules on MIL-47 at zero coverage.

PubMed

Duerinck, Tim; Couck, Sarah; Vermoortele, Frederik; De Vos, Dirk E; Baron, Gino V; Denayer, Joeri F M

2012-10-02

The low coverage adsorptive properties of the MIL-47 metal organic framework toward aromatic and heterocyclic molecules are reported in this paper. The effect of molecular functionality and size on Henry adsorption constants and adsorption enthalpies of alkyl and heteroatom functionalized benzene derivates and heterocyclic molecules was studied using pulse gas chromatography. By means of statistical analysis, experimental data was analyzed and modeled using principal component analysis and partial least-squares regression. Structure-property relationships were established, revealing and confirming several trends. Among the molecular properties governing the adsorption process, vapor pressure, mean polarizability, and dipole moment play a determining role.

Isolation and purification of an early pregnancy factor-like molecule from culture supernatants obtained from lymphocytes of pregnant women: II. Identification of the molecule as a Fc-receptor-like molecule: a preliminary report.

PubMed

Aranha, C; Bordekar, A; Shahani, S

1998-11-01

Early pregnancy factor (EPF)-like activity from culture supernatants obtained from stimulated lymphocytes of pregnant women was characterized and identified. The enzyme-linked immunosorbent assay depending on the presence of "Fc" receptors on bovine spermatozoa was used to identify the EPF-like molecule purified by gel filtration and reverse-phase high-performance liquid chromatography. The results indicated that the crude lymphocyte culture supernatant, the EPF-positive G IV fraction obtained on gel filtration, and the EPF-positive reverse-phase high-performance liquid chromatography protein readily bound with the different concentrations of aggregated human gamma-globulin in a manner similar to that in which the standard control of aggregated human gamma-globulin binds to the bovine spermatozoa. EPF-like activity synthesized and secreted by lymphocytes during pregnancy may be a Fc-receptor-like molecule.

Small Angle X-Ray Scattering Study of Meso-Tetrakis (4-Sulfonatophenyl) Porphyrin in Aqueous Solution: A Self-Aggregation Model

PubMed Central

Gandini, S.C.M.; Gelamo, E.L.; Itri, R.; Tabak, M.

2003-01-01

The aggregate morphology of meso-tetrakis(4-sulfonatophenyl) porphyrin (TPPS4) in aqueous solution is investigated by using small angle x-ray scattering (SAXS) technique. Measurements were performed at pH 4.0 and 9.0 to monitor the pH influence on the structural parameters of the aggregates. Radii of gyration were obtained from distance distribution functions p(r) analysis. The experimental data of TPPS4 at pH 4.0 showed well-defined oscillations characteristic of large aggregates in contrast to the SAXS curve of 5 mM TPPS4 at pH 9.0, where both a significant decrease in the intensity and the disappearance of the oscillation peaks suggest the dissociation of the aggregate. A 340-Å long “hollow” cylinder with shell thickness of 20 Å, compatible to the porphyrin molecule dimension, represents well the scattering curve of the aggregates at pH 4.0. According to the fitting parameters, 26 porphyrin molecules self-associate into a ringlike configuration in the plane of the cylinder cross-section. The total number of porphyrin molecules in the whole aggregate was also estimated as ∼3000. The model compatible to SAXS data of a hollow cylinder with J-aggregation in the cross-section and H-aggregation (columnar stacking) between the cylinder layers is consistent with optical absorption spectroscopic data both in the literature and obtained in this work. PMID:12885669

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.

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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Diffusion Monte Carlo simulations of gas phase and adsorbed D2-(H2)n clusters

NASA Astrophysics Data System (ADS)

Curotto, E.; Mella, M.

2018-03-01

We have computed ground state energies and analyzed radial distributions for several gas phase and adsorbed D2(H2)n and HD(H2)n clusters. An external model potential designed to mimic ionic adsorption sites inside porous materials is used [M. Mella and E. Curotto, J. Phys. Chem. A 121, 5005 (2017)]. The isotopic substitution lowers the ground state energies by the expected amount based on the mass differences when these are compared with the energies of the pure clusters in the gas phase. A similar impact is found for adsorbed aggregates. The dissociation energy of D2 from the adsorbed clusters is always much higher than that of H2 from both pure and doped aggregates. Radial distributions of D2 and H2 are compared for both the gas phase and adsorbed species. For the gas phase clusters, two types of hydrogen-hydrogen interactions are considered: one based on the assumption that rotations and translations are adiabatically decoupled and the other based on nonisotropic four-dimensional potential. In the gas phase clusters of sufficiently large size, we find the heavier isotopomer more likely to be near the center of mass. However, there is a considerable overlap among the radial distributions of the two species. For the adsorbed clusters, we invariably find the heavy isotope located closer to the attractive interaction source than H2, and at the periphery of the aggregate, H2 molecules being substantially excluded from the interaction with the source. This finding rationalizes the dissociation energy results. For D2-(H2)n clusters with n ≥12 , such preference leads to the desorption of D2 from the aggregate, a phenomenon driven by the minimization of the total energy that can be obtained by reducing the confinement of (H2)12. The same happens for (H2)13, indicating that such an effect may be quite general and impact on the absorption of quantum species inside porous materials.

A highly sensitive nanoscale pH-sensor using Au nanoparticles linked by a multifunctional Raman-active reporter molecule

NASA Astrophysics Data System (ADS)

Lawson, Latevi S.; Chan, James W.; Huser, Thomas

2014-06-01

Chemical sensing on the nanoscale has been breaking new ground since the discovery of surface enhanced Raman scattering (SERS). For nanoparticles, controlled particle aggregation is necessary to achieve the largest SERS enhancements. Therefore, aggregating agents such as salts or linker molecules are used in conjunction with chemically sensitive reporters in order to develop robust environmentally sensitive SERS probes. While salt-induced colloidal nanosphere aggregates have produced robust SERS signals, their variability in aggregate size contributes significantly to poor SERS signal reproducibility, which can complicate their use in in vitro cellular studies. Such systems often also lack reproducibility in spectral measurements between different nanoparticle clusters. Preaggregation of colloids via linkers followed by surface functionalization with reporter molecules results in the linker occupying valuable SERS hotspot volume which could otherwise be utilized by additional reporter molecules. Ideally, both functionalities should be obtained from a single molecule. Here, we report the use of 3,5-dimercaptobenzoic acid, a single multifunctional molecule that creates SERS hotspots via the controlled aggregation of nanoparticles, and also reports pH values. We show that 3,5-dimercaptobenzoic acid bound to Au nanospheres results in an excellent pH nanoprobe, producing very robust, and highly reproducible SERS signals that can report pH across the entire physiological range with excellent pH resolution. To demonstrate the efficacy of our novel pH reporters, these probes were also used to image both the particle and pH distribution in the cytoplasm of human induced pluripotent stem cells (hiPSCs).Chemical sensing on the nanoscale has been breaking new ground since the discovery of surface enhanced Raman scattering (SERS). For nanoparticles, controlled particle aggregation is necessary to achieve the largest SERS enhancements. Therefore, aggregating agents such as salts

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. )

Influence of aggregate size on the binding and activation of the first component of human complement by soluble IgG aggregates.

PubMed Central

Doekes, G; Vanes, L A; Daha, M R

1982-01-01

The interaction between small aggregates of human IgG and the first component of human complement was studied. Stabilized soluble IgG aggregates of restricted size were prepared by heat aggregation of human IgG, followed by sucrose-density ultracentrifugation. Human C1 was isolated in its precursor form by euglobulin precipitation, followed by gel filtration and immunoadsorption. A C1 preparation was obtained of which more than 90% was still in its unactivated form. Soluble aggregates containing 20, 10 or 5 molecules IgG, and monomeric IgG were tested for their ability to bind and to activate C1. The binding of C1 was determined by C1 consumption, whereas the activation of C1 was measured as the increased ability of the C1 preparation to consume purified human C4 after the incubation with the aggregates. The three aggregates tested and monomeric IgG were all able to bind and to activate C1, but the efficiency of both processes markedly increased with increasing aggregate-size. Furthermore, it was found that all four preparations activated an appreciable amount of C1 at concentrations that did not result in any detectable C1 fixation. These results confirm earlier suggestion that C1 can be activated during a short, transient binding to small aggregates or immune complexes that have a low avidity for C1, after which the activated form, C1, is released into the medium. PMID:7068172

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

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.

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.

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.

On the Relative "Transparency" of Gas-phase Coronene Molecules to Low-energy Electrons: Effects on the Interstellar Medium

NASA Astrophysics Data System (ADS)

Carelli, F.; Gianturco, F. A.

2011-12-01

Free, gas-phase polycyclic aromatic hydrocarbons (PAHs) are understood to play an important role in the interstellar medium (ISM), as they are thought to significantly contribute to both diffused and unidentified infrared interstellar bands. They are also considered fundamental blocks of the interstellar dust, whose nature has important implications for a plethora of physical and chemical nanoscopic processes within the ISM. Since free electrons represent a versatile alternative way to transport energy in the interstellar space, in this paper we compute from quantum scattering methods the angular redistributions of free electrons by gas-phase coronene molecules, the latter of which are believed to be one of the most representative PAHs, in order to assess their role in describing the efficiency of electron deflection by this molecule. The associated rates can provide useful information about the coupling mechanism between external radio-frequency fields and complex molecular plasmas containing neutral and ionized PAHs. They can also yield information on the possible presence of such species in the dust phase of the medium.

Clay induced aggregation of a tetra-cationic metalloporphyrin in Layer by Layer self assembled film

NASA Astrophysics Data System (ADS)

Banik, Soma; Bhattacharjee, J.; Hussain, S. A.; Bhattacharjee, D.

2015-12-01

Porphyrins have a general tendency to form aggregates in ultrathin films. Also electrostatic adsorption of cationic porphyrins onto anionic nano clay platelets results in the flattening of porphyrin moieties. The flattening is evidenced by the red-shifting of Soret band with respect to the aqueous solution. In the present communication, we have studied the clay induced aggregation behaviour of a tetra-cationic metalloporphyrin Manganese (III) 5, 10, 15, 20-tetra (4 pyridyl)-21 H, 23 H-porphine chloride tetrakis (methochloride) (MnTMPyP) in Layer-by-Layer (LbL) self assembled film. The adsorption of dye molecules onto nano clay platelets resulted in the flattening of the meso substituent groups of the dye chromophore. In Layer-by-Layer ultrathin film, the flattened porphyrin molecules tagged nano clay platelets were further associated to form porphyrin aggregates. This has been clearly demonstrated from the UV-vis absorption spectroscopic studies. Atomic Force Microscopic (AFM) studies gave visual evidence of the association of organo-clay hybrid molecules in the LbL film.

Conformational Equilibria in Monomeric α-Synuclein at the Single-Molecule Level

PubMed Central

Tessari, Isabella; Mammi, Stefano; Bergantino, Elisabetta; Musiani, Francesco; Brucale, Marco; Bubacco, Luigi; Samorì, Bruno

2008-01-01

Human α-Synuclein (αSyn) is a natively unfolded protein whose aggregation into amyloid fibrils is involved in the pathology of Parkinson disease. A full comprehension of the structure and dynamics of early intermediates leading to the aggregated states is an unsolved problem of essential importance to researchers attempting to decipher the molecular mechanisms of αSyn aggregation and formation of fibrils. Traditional bulk techniques used so far to solve this problem point to a direct correlation between αSyn's unique conformational properties and its propensity to aggregate, but these techniques can only provide ensemble-averaged information for monomers and oligomers alike. They therefore cannot characterize the full complexity of the conformational equilibria that trigger the aggregation process. We applied atomic force microscopy–based single-molecule mechanical unfolding methodology to study the conformational equilibrium of human wild-type and mutant αSyn. The conformational heterogeneity of monomeric αSyn was characterized at the single-molecule level. Three main classes of conformations, including disordered and “β-like” structures, were directly observed and quantified without any interference from oligomeric soluble forms. The relative abundance of the “β-like” structures significantly increased in different conditions promoting the aggregation of αSyn: the presence of Cu2+, the pathogenic A30P mutation, and high ionic strength. This methodology can explore the full conformational space of a protein at the single-molecule level, detecting even poorly populated conformers and measuring their distribution in a variety of biologically important conditions. To the best of our knowledge, we present for the first time evidence of a conformational equilibrium that controls the population of a specific class of monomeric αSyn conformers, positively correlated with conditions known to promote the formation of aggregates. A new tool is thus made

Spherical and hyperspherical harmonics representation of van der Waals aggregates

NASA Astrophysics Data System (ADS)

Lombardi, Andrea; Palazzetti, Federico; Aquilanti, Vincenzo; Grossi, Gaia; Albernaz, Alessandra F.; Barreto, Patricia R. P.; Cruz, Ana Claudia P. S.

2016-12-01

The representation of the potential energy surfaces of atom-molecule or molecular dimers interactions should account faithfully for the symmetry properties of the systems, preserving at the same time a compact analytical form. To this aim, the choice of a proper set of coordinates is a necessary precondition. Here we illustrate a description in terms of hyperspherical coordinates and the expansion of the intermolecular interaction energy in terms of hypersherical harmonics, as a general method for building potential energy surfaces suitable for molecular dynamics simulations of van der Waals aggregates. Examples for the prototypical case diatomic-molecule-diatomic-molecule interactions are shown.

Adsorption and dissociation of sulfur-based toxic gas molecules on silicene nanoribbons: a quest for high-performance gas sensors and catalysts.

PubMed

Walia, Gurleen Kaur; Randhawa, Deep Kamal Kaur

2018-03-16

The adsorption behavior of sulfur-based toxic gases (H 2 S and SO 2 ) on armchair silicene nanoribbons (ASiNRs) was investigated using first-principles density functional theory (DFT). Being a zero band gap material, application of bulk silicene is limited in nanoelectronics, despite its high carrier mobility. By restricting its dimensions into one dimension, construction of nanoribbons, and by introduction of a defect, its band gap can be tuned. Pristine armchair silicene nanoribbons (P-ASiNRs) have a very low sensitivity to gas molecules. Therefore, a defect was introduced by removal of one Si atom, leading to increased sensitivity. To deeply understand the impact of the aforementioned gases on silicene nanoribbons, electronic band structures, density of states, charge transfers, adsorption energies, electron densities, current-voltage characteristics and most stable adsorption configurations were calculated. H 2 S is dissociated completely into HS and H species when adsorbed onto defective armchair silicene nanoribbons (D-ASiNRs). Thus, D-ASiNR is a likely catalyst for dissociation of the H 2 S gas molecule. Conversely, upon SO 2 adsorption, P-ASiNR acts as a suitable sensor, whereas D-ASiNR provides enhanced sensitivity compared with P-ASiNR. On the basis of these results, D-ASiNR can be expected to be a disposable sensor for SO 2 detection as well as a catalyst for H 2 S reduction. Graphical abstract Comparison of I-V characteristics of pristine and defective armchair silicene nanoribbons with H 2 S and SO 2 adsorbed on them.

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 Office of Scientific and Technical Information (OSTI.GOV)

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

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, generatesmore » 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.« less

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 Office of Scientific and Technical Information (OSTI.GOV)

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

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 viamore » 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.« less

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, generatesmore » 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.« less

Radiation-induced transformations of isolated CH3CN molecules in noble gas matrices

NASA Astrophysics Data System (ADS)

Kameneva, Svetlana V.; Volosatova, Anastasia D.; Feldman, Vladimir I.

2017-12-01

The transformations of isolated CH3CN molecules in various solid noble-gas matrices (Ne, Ar, Kr, and Xe) under the action of X-ray irradiation at 5 K were investigated by FTIR spectroscopy. The main products are CH3NC, CH2CNH and CH2NCH molecular isomers as well as CH2CN and CH2NC radicals. The matrix has a strong effect on the distribution of reaction channels. In particular, the highest relative yield of keteneimine (CH2CNH) was found in Ne matrix, whereas the formation of CH3NC predominates in xenon. It was explained by differences in the matrix ionization energy (IE) resulting in different distributions of hot ionic reactions. The reactions of neutral excited states are mainly involved in Xe matrix with low IE, while the isomerization of the primary acetonitrile positive ions may be quite effective in Ne and Ar. Annealing of the irradiated samples results in mobilization of trapped hydrogen atoms followed by their reactions with radicals to yield parent molecule and its isomers. The scheme of the radiation-induced processes and its implications for the acetonitrile chemistry in cosmic ices are discussed.

Giant Raman scattering from J-aggregated dyes inside carbon nanotubes for multispectral imaging

NASA Astrophysics Data System (ADS)

Gaufrès, E.; Tang, N. Y.-Wa; Lapointe, F.; Cabana, J.; Nadon, M.-A.; Cottenye, N.; Raymond, F.; Szkopek, T.; Martel, R.

2014-01-01

Raman spectroscopy uses visible light to acquire vibrational fingerprints of molecules, thus making it a powerful tool for chemical analysis in a wide range of media. However, its potential for optical imaging at high resolution is severely limited by the fact that the Raman effect is weak. Here, we report the discovery of a giant Raman scattering effect from encapsulated and aggregated dye molecules inside single-walled carbon nanotubes. Measurements performed on rod-like dyes such as α-sexithiophene and β-carotene, assembled inside single-walled carbon nanotubes as highly polarizable J-aggregates, indicate a resonant Raman cross-section of (3 +/- 2) × 10-21 cm2 sr-1, which is well above the cross-section required for detecting individual aggregates at the highest optical resolution. Free from fluorescence background and photobleaching, this giant Raman effect allows the realization of a library of functionalized nanoprobe labels for Raman imaging with robust detection using multispectral analysis.

Interaction of a single acetophenone molecule with group III-IV elements mediated by Si(001)

NASA Astrophysics Data System (ADS)

Racis, A.; Jurczyszyn, L.; Radny, M. W.

2018-03-01

A theoretical study of an influence of the acetophenone molecule adsorbed on the Si(001) on the local chemical reactivity of silicon surface is presented. The obtained results indicate that the interaction of the molecule with silicon substrate breaks the intra-dimer π bonds in four surface silicon dimers interacting directly with adsorbed molecule. This leads to the formation of two pairs of unpaired dangling bonds at two opposite sides of the molecule. It is demonstrated that these dangling bonds increase considerably the local chemical reactivity of the silicon substrate in the vicinity of the adsorbed molecule. Consequently, it is shown that such molecule bonded with Si(001) can stabilize the position of In and Pb adatoms diffusing on silicon substrate at two sides and initiate the one-dimensional aggregation of the metallic adatoms on the Si(001) substrate anchored at both sides of the adsorbed molecule. This type of aggregation leads to the growth of chain-like atomic structures in opposite directions, pinned to adsorbed molecule and oriented perpendicular to the rows of surface silicon dimers.

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.

Interaction and Aggregation of Colloidal Biological Particles and Droplets in Electrically-Driven Flows

NASA Technical Reports Server (NTRS)

Davis, Robert H.; Loewenberg, Michael

1997-01-01

The primary objective of this research was to develop a fundamental understanding of aggregation and coalescence processes during electrically-driven migration of cells, particles and droplets. The process by which charged cells, particles, molecules, or drops migrate in a weak electric field is known as electrophoresis. If the migrating species have different charges or surface potentials, they will migrate at different speeds and thus may collide and aggregate or coalesce. Aggregation and coalescence are undesirable, if the goal is to separate the different species on the basis of their different electrophoretic mobilities.

Cholesterol catalyses Aβ42 aggregation through a heterogeneous nucleation pathway in the presence of lipid membranes

NASA Astrophysics Data System (ADS)

Habchi, Johnny; Chia, Sean; Galvagnion, Céline; Michaels, Thomas C. T.; Bellaiche, Mathias M. J.; Ruggeri, Francesco Simone; Sanguanini, Michele; Idini, Ilaria; Kumita, Janet R.; Sparr, Emma; Linse, Sara; Dobson, Christopher M.; Knowles, Tuomas P. J.; Vendruscolo, Michele

2018-06-01

Alzheimer's disease is a neurodegenerative disorder associated with the aberrant aggregation of the amyloid-β peptide. Although increasing evidence implicates cholesterol in the pathogenesis of Alzheimer's disease, the detailed mechanistic link between this lipid molecule and the disease process remains to be fully established. To address this problem, we adopt a kinetics-based strategy that reveals a specific catalytic role of cholesterol in the aggregation of Aβ42 (the 42-residue form of the amyloid-β peptide). More specifically, we demonstrate that lipid membranes containing cholesterol promote Aβ42 aggregation by enhancing its primary nucleation rate by up to 20-fold through a heterogeneous nucleation pathway. We further show that this process occurs as a result of cooperativity in the interaction of multiple cholesterol molecules with Aβ42. These results identify a specific microscopic pathway by which cholesterol dramatically enhances the onset of Aβ42 aggregation, thereby helping rationalize the link between Alzheimer's disease and the impairment of cholesterol homeostasis.

Salt-induced aggregation of lysozyme: Implications for crystal growth

NASA Technical Reports Server (NTRS)

Wilson, Lori J.

1994-01-01

Crystallization of proteins is a prerequisite for structural analysis by x-ray crystallography. While improvements in protein crystals have been obtained in microgravity onboard the U.S. Space Shuttle, attempts to improve the crystal growth process both on the ground and in space have been limited by our lack of understanding of the mechanisms involved. Almost all proteins are crystallized with the aid of a precipitating agent. Many of the common precipitating agents are inorganic salts. An understanding of the role of salts on the aggregation of protein monomers is the key to the elucidation of the mechanisms involved in protein crystallization. In order for crystallization to occur individual molecules must self-associate into aggregates. Detection and characterization of aggregates in supersaturated protein solutions is the first step in understanding salt-induced crystallization.

Phthalocyanines as Molecular Scaffolds to Block Disease-Associated Protein Aggregation.

PubMed

Valiente-Gabioud, Ariel A; Miotto, Marco C; Chesta, María E; Lombardo, Verónica; Binolfi, Andres; Fernández, Claudio O

2016-05-17

The aggregation of proteins into toxic conformations plays a critical role in the development of different neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), and Creutzfled-Jakob's disease (CJD). These disorders share a common pathological mechanism that involves the formation of aggregated protein species including toxic oligomers and amyloid fibrils. The aggregation of alpha-synuclein (αS) in PD and the amyloid beta peptide (Aβ) and tau protein in AD results in neuronal death and disease onset. In the case of CJD, the misfolding of the physiological prion protein (PrP) induces a chain reaction that results in accumulation of particles that elicit brain damage. Currently, there is no preventive therapy for these diseases and the available therapeutic approaches are based on the treatment of the symptoms rather than the underlying causes of the disease. Accordingly, the aggregation pathway of these proteins represents a useful target for therapeutic intervention. Therefore, understanding the mechanism of amyloid formation and its inhibition is of high clinical importance. The design of small molecules that efficiently inhibit the aggregation process and/or neutralize its associated toxicity constitutes a promising tool for the development of therapeutic strategies against these disorders. In this accounts, we discuss current knowledge on the anti-amyloid activity of phthalocyanines and their potential use as drug candidates in neurodegeneration. These tetrapyrrolic compounds modulate the amyloid assembly of αS, tau, Aβ, and the PrP in vitro, and protect cells from the toxic effects of amyloid aggregates. In addition, in scrapie-infected mice, these compounds showed important prophylactic antiscrapie properties. The structural basis for the inhibitory effect of phthalocyanines on amyloid filament assembly relies on specific π-π interactions between the aromatic ring system of these molecules and aromatic residues in the

Screening the sequence selectivity of DNA-binding molecules using a gold nanoparticle-based colorimetric approach.

PubMed

Hurst, Sarah J; Han, Min Su; Lytton-Jean, Abigail K R; Mirkin, Chad A

2007-09-15

We have developed a novel competition assay that uses a gold nanoparticle (Au NP)-based, high-throughput colorimetric approach to screen the sequence selectivity of DNA-binding molecules. This assay hinges on the observation that the melting behavior of DNA-functionalized Au NP aggregates is sensitive to the concentration of the DNA-binding molecule in solution. When short, oligomeric hairpin DNA sequences were added to a reaction solution consisting of DNA-functionalized Au NP aggregates and DNA-binding molecules, these molecules may either bind to the Au NP aggregate interconnects or the hairpin stems based on their relative affinity for each. This relative affinity can be measured as a change in the melting temperature (Tm) of the DNA-modified Au NP aggregates in solution. As a proof of concept, we evaluated the selectivity of 4',6-diamidino-2-phenylindone (an AT-specific binder), ethidium bromide (a nonspecific binder), and chromomycin A (a GC-specific binder) for six sequences of hairpin DNA having different numbers of AT pairs in a five-base pair variable stem region. Our assay accurately and easily confirmed the known trends in selectivity for the DNA binders in question without the use of complicated instrumentation. This novel assay will be useful in assessing large libraries of potential drug candidates that work by binding DNA to form a drug/DNA complex.

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.

Heat-Induced Soluble Protein Aggregates from Mixed Pea Globulins and β-Lactoglobulin.

PubMed

Chihi, Mohamed-Lazhar; Mession, Jean-luc; Sok, Nicolas; Saurel, Rémi

2016-04-06

The present work investigates the formation of protein aggregates (85 °C, 60 min incubation) upon heat treatment of β-lactoglobulin (βlg)-pea globulins (Glob) mixtures at pH 7.2 and 5 mM NaCl from laboratory-prepared protein isolates. Various βlg/Glob weight ratios were applied, for a total protein concentration of 2 wt % in admixture. Different analytical methods were used to determine the aggregation behavior of "mixed" aggregates, that is, surface hydrophobicity and also sulfhydryl content, protein interactions by means of SDS-PAGE electrophoresis, and molecule size distribution by DLS and gel filtration. The production of "mixed" thermal aggregates would involve both the formation of new disulfide bonds and noncovalent interactions between the denatured βlg and Glob subunits. The majority of "mixed" soluble aggregates displayed higher molecular weight and smaller diameter than those for Glob heated in isolation. The development of pea-whey protein "mixed" aggregates may help to design new ingredients for the control of innovative food textures.

Aggregate-based sub-CMC Solubilization of Hexadecane by Surfactants.

PubMed

Zhong, Hua; Yang, Lei; Zeng, Guangming; Brusseau, Mark L; Wang, Yake; Li, Yang; Liu, Zhifeng; Yuan, Xingzhong; Tan, Fei

Solubilization of hexadecane by two surfactants, SDBS and Triton X-100, at concentrations near the critical micelle concentration (CMC) and the related aggregation behavior was investigated in this study. Solubilization was observed at surfactant concentrations lower than CMC, and the apparent solubility of hexadecane increased linearly with surfactant concentration for both surfactants. The capacity of SDBS to solubilize hexadecane is stronger at concentrations below CMC than above CMC. In contrast, Triton X-100 shows no difference. The results of dynamic light scattering (DLS) and cryogenic TEM analysis show aggregate formation at surfactant concentrations lower than CMC. DLS-based size of the aggregates ( d ) decreases with increasing surfactant concentration. Zeta potential of the SDBS aggregates decreases with increasing SDBS concentration, whereas it increases for Triton X-100. The surface excess (Γ) of SDBS calculated based on hexadecane solubility and aggregate size data increases rapidly with increasing bulk concentration, and then asymptotically approaches the maximum surface excess (Γ max ). Conversely, there is only a minor increase in Γ for Triton X-100. Comparison of Γ and d indicates that excess of surfactant molecules at aggregate surface has great impact on surface curvature. The results of this study demonstrate formation of aggregates at surfactant concentrations below CMC for hexadecane solubilization, and indicate the potential of employing low-concentration strategy for surfactant application such as remediation of HOC contaminated sites.

Thermally controlled preferential molecular aggregation state in a thiacarbocyanine dye

NASA Astrophysics Data System (ADS)

Passier, Rémy; Ritchie, James P.; Toro, Carlos; Diaz, Carlos; Masunov, Artëm E.; Belfield, Kevin D.; Hernandez, Florencio E.

2010-10-01

Herein we report the experimental and theoretical study of the temperature dependence of a thiacarbocyanine dye in its monomer, H- and J-aggregates states. We demonstrate the ability to control the ratio of monomer, H- and/or J-aggregates with heat. We link such a control to the conformation dependence of the molecule. An alternative way to gain access to the dominating species without changing the concentration as a complete switching mechanism between all the present species is proposed. The results presented in this work lead to a better understanding of thiacarbocyanine dye's behavior.

Contrasting self-aggregation over land and ocean surfaces

NASA Astrophysics Data System (ADS)

Inda Diaz, H. A.; O'Brien, T. A.

2017-12-01

The spontaneous organization of convection into clusters, or self-aggregation, demonstrably changes the nature and statistics of precipitation. While there has been much recent progress in this area, the processes that control self-aggregation are still poorly understood. Most of the work to date has focused on self-aggregation over ocean-like surfaces, but it is particularly pressing to understand what controls convective aggregation over land, since the associated change in precipitation statistics—between non-aggregated and aggregated convection—could have huge impacts on society and infrastructure. Radiative-convective equilibrium (RCE), has been extensively used as an idealized framework to study the tropical atmosphere. Self-aggregation manifests in numerous numerical models of RCE, nevertheless, there is still a lack of understanding in how it relates to convective organization in the observed world. Numerous studies have examined self-aggregation using idealized Cloud Resolving Models (CRMs) and General Circulation Models over the ocean, however very little work has been done on RCE and self-aggregation over land. Idealized models of RCE over ocean have shown that aggregation is sensitive to sea surface temperature (SST), more intense precipitation occurs in aggregated systems, and a variety of feedbacks—such as surface flux, cloud radiative, and upgradient moisture transport— contribute to the maintenance of aggregation, however it is not clear if these results apply over land. Progress in this area could help relate understanding of self-aggregation in idealized simulations to observations. In order to explore the behavior of self-aggregation over land, we use a CRM to simulate idealized RCE over land. In particular, we examine the aggregation of convection and how it compares with aggregation over ocean. Based on previous studies, where a variety of different CRMs exhibit a SST threshold below which self-aggregation does not occur, we hypothesize

A highly sensitive nanoscale pH-sensor using Au nanoparticles linked by a multifunctional Raman-active reporter molecule.

PubMed

Lawson, Latevi S; Chan, James W; Huser, Thomas

2014-07-21

Chemical sensing on the nanoscale has been breaking new ground since the discovery of surface enhanced Raman scattering (SERS). For nanoparticles, controlled particle aggregation is necessary to achieve the largest SERS enhancements. Therefore, aggregating agents such as salts or linker molecules are used in conjunction with chemically sensitive reporters in order to develop robust environmentally sensitive SERS probes. While salt-induced colloidal nanosphere aggregates have produced robust SERS signals, their variability in aggregate size contributes significantly to poor SERS signal reproducibility, which can complicate their use in in vitro cellular studies. Such systems often also lack reproducibility in spectral measurements between different nanoparticle clusters. Preaggregation of colloids via linkers followed by surface functionalization with reporter molecules results in the linker occupying valuable SERS hotspot volume which could otherwise be utilized by additional reporter molecules. Ideally, both functionalities should be obtained from a single molecule. Here, we report the use of 3,5-dimercaptobenzoic acid, a single multifunctional molecule that creates SERS hotspots via the controlled aggregation of nanoparticles, and also reports pH values. We show that 3,5-dimercaptobenzoic acid bound to Au nanospheres results in an excellent pH nanoprobe, producing very robust, and highly reproducible SERS signals that can report pH across the entire physiological range with excellent pH resolution. To demonstrate the efficacy of our novel pH reporters, these probes were also used to image both the particle and pH distribution in the cytoplasm of human induced pluripotent stem cells (hiPSCs).

A mechanistic model of tau amyloid aggregation based on direct observation of oligomers

NASA Astrophysics Data System (ADS)

Shammas, Sarah L.; Garcia, Gonzalo A.; Kumar, Satish; Kjaergaard, Magnus; Horrocks, Mathew H.; Shivji, Nadia; Mandelkow, Eva; Knowles, Tuomas P. J.; Mandelkow, Eckhard; Klenerman, David

2015-04-01

Protein aggregation plays a key role in neurodegenerative disease, giving rise to small oligomers that may become cytotoxic to cells. The fundamental microscopic reactions taking place during aggregation, and their rate constants, have been difficult to determine due to lack of suitable methods to identify and follow the low concentration of oligomers over time. Here we use single-molecule fluorescence to study the aggregation of the repeat domain of tau (K18), and two mutant forms linked with familial frontotemporal dementia, the deletion mutant ΔK280 and the point mutant P301L. Our kinetic analysis reveals that aggregation proceeds via monomeric assembly into small oligomers, and a subsequent slow structural conversion step before fibril formation. Using this approach, we have been able to quantitatively determine how these mutations alter the aggregation energy landscape.

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.

Platelet aggregation inhibitors from Philippine marine invertebrate samples screened in a new microplate assay.

PubMed

Pimentel, Sheila Marie V; Bojo, Zenaida P; Roberto, Amy V D; Lazaro, Jose Enrico H; Mangalindan, Gina C; Florentino, Leila M; Lim-Navarro, Pilar; Tasdemir, Deniz; Ireland, Chris M; Concepcion, Gisela P

2003-01-01

A new microplate assay for Ca(2+)-induced platelet aggregation as detected by Giemsa dye was used to screen marine invertebrate samples from the Philippines for inhibitors of human platelet aggregation. Out of 261 crude methanol extracts of marine sponges and tunicates, 25 inhibited aggregation at 2 mg/ml. Inhibition of agonist-induced aggregation in an aggregometer was used to confirm results of the microplate assay and to determine the specific mode of inhibition of 2 samples. The marine sponge Xestospongia sp. yielded a xestospongin/araguspongine-type molecule that inhibited collagen-induced aggregation by 87% at 2 micro g/ml, and epinephrine-induced aggregation by 78% at 20 micro g/ml, while the marine sponge Aplysina sp. yielded 5,6-dibromotryptamine, which inhibited epinephrine-induced aggregation by 51% at 20 micro g/ml. In this study we have found that the microplate assay is a simple, inexpensive, yet useful preliminary tool to qualitatively screen a large number of marine samples for antiplatelet aggregation activity.

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.

Dye-sensitized solar cell employing zinc oxide aggregates grown in the presence of lithium

DOEpatents

Zhang, Qifeng; Cao, Guozhong

2013-10-15

Provided are a novel ZnO dye-sensitized solar cell and method of fabricating the same. In one embodiment, deliberately added lithium ions are used to mediate the growth of ZnO aggregates. The use of lithium provides ZnO aggregates that have advantageous microstructure, morphology, crystallinity, and operational characteristics. Employing lithium during aggregate synthesis results in a polydisperse collection of ZnO aggregates favorable for porosity and light scattering. The resulting nanocrystallites forming the aggregates have improved crystallinity and more favorable facets for dye molecule absorption. The lithium synthesis improves the surface stability of ZnO in acidic dyes. The procedures developed and disclosed herein also help ensure the formation of an aggregate film that has a high homogeneity of thickness, a high packing density, a high specific surface area, and good electrical contact between the film and the fluorine-doped tin oxide electrode and among the aggregate particles.

Ballistic aggregation in systems of inelastic particles: Cluster growth, structure, and aging

NASA Astrophysics Data System (ADS)

Paul, Subhajit; Das, Subir K.

2017-07-01

We study far-from-equilibrium dynamics in models of freely cooling granular gas and ballistically aggregating compact clusters. For both the cases, from event-driven molecular dynamics simulations, we have presented detailed results on structure and dynamics in space dimensions d =1 and 2. Via appropriate analyses it has been confirmed that the ballistic aggregation mechanism applies in d =1 granular gases as well. Aging phenomena for this mechanism, in both the dimensions, have been studied via the two-time density autocorrelation function. This quantity is demonstrated to exhibit scaling property similar to that in the standard phase transition kinetics. The corresponding functional forms have been quantified and the outcomes have been discussed in connection with the structural properties. Our results on aging establish a more complete equivalence between the granular gas and the ballistic aggregation models in d =1 .

Tyrosine- and tryptophan-coated gold nanoparticles inhibit amyloid aggregation of insulin.

PubMed

Dubey, Kriti; Anand, Bibin G; Badhwar, Rahul; Bagler, Ganesh; Navya, P N; Daima, Hemant Kumar; Kar, Karunakar

2015-12-01

Here, we have strategically synthesized stable gold (AuNPs(Tyr), AuNPs(Trp)) and silver (AgNPs(Tyr)) nanoparticles which are surface functionalized with either tyrosine or tryptophan residues and have examined their potential to inhibit amyloid aggregation of insulin. Inhibition of both spontaneous and seed-induced aggregation of insulin was observed in the presence of AuNPs(Tyr), AgNPs(Tyr), and AuNPs(Trp) nanoparticles. These nanoparticles also triggered the disassembly of insulin amyloid fibrils. Surface functionalization of amino acids appears to be important for the inhibition effect since isolated tryptophan and tyrosine molecules did not prevent insulin aggregation. Bioinformatics analysis predicts involvement of tyrosine in H-bonding interactions mediated by its C=O, -NH2, and aromatic moiety. These results offer significant opportunities for developing nanoparticle-based therapeutics against diseases related to protein aggregation.

Aggregation-induced emission—fluorophores and applications

NASA Astrophysics Data System (ADS)

Hong, Yuning

2016-06-01

Aggregation-induced emission (AIE) is a novel photophysical phenomenon found in a group of luminogens that are not fluorescent in solution but are highly emissive in the aggregate or solid state. Since the first publication of AIE luminogens in 2001, AIE has become a hot research area in which the number of research papers regarding new AIE molecules and their applications has been increasing in an exponential manner. Thomson Reuters Essential Science Indicators ranked AIE no.3 among the Top 100 Research Frontiers in the field of Chemistry and Materials Science in 2013. In this review, I will give a general introduction of the AIE phenomenon, discuss the structure-property relationship of the AIE lumingens and summarize the recent progress in the applications including as light-emitting materials in optoelectronics, as chemosensors and bioprobes, and for bioimaging (total 69 references cited).

Attogram detection of picric acid by hexa-peri-hexabenzocoronene-based chemosensors by controlled aggregation-induced emission enhancement.

PubMed

Vij, Varun; Bhalla, Vandana; Kumar, Manoj

2013-06-12

Hexa-peri-hexabenzocoronene (HBC) based molecules 5 and 6 have been designed and synthesized. These planar coronenes are appended with rotors to invoke aggregation induced emission enhancement (AIEE) phenomenon by controlling the ratio of H2O in solutions of aggregates. These aggregates of HBC derivatives serve as highly selective chemosensors for picric acid (PA) in mixed aqueous solution. These aggregates are also able to detect PA in vapor phase. In addition, fluorescent test strips have been prepared by dip-coating the Whatman paper with aggregates of both compounds for trace detection of PA in contact mode with detection limits in attograms.

Microbial Ecology of Soil Aggregation in Agroecosystems

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bell, S.; Tfailly, M.; Thompson, A.; Callister, S.

2017-12-01

Crop selection and soil texture influence the physicochemical attributes of the soil, which structures microbial communities and influences soil C cycling storage. At the molecular scale, microbial metabolites and necromass alter the soil environment, which creates feedbacks that influence ecosystem functions, including soil C accumulation. By integrating lab to field studies we aim to identify the molecules, organisms and metabolic pathways that control carbon cycling and stabilization in bioenergy soils. We investigated the relative influence of plants, microbes, and minerals on soil aggregate ecology at the Great Lakes Bioenergy Research experiment. Sites in WI and MI, USA have been in corn and switchgrass cropping systems for a decade. By comparing soil aggregate ecology across sites and cropping systems we are able to test the relative importance of plant, microbe, mineral influences on soil aggregate dynamics. Soil microbial communities (16S) differ in diversity and phylogeny among sites and cropping systems. FT-ICR MS revealed differences in the molecular composition of water-soluble fraction of soil organic matter for cropping systems and soil origin for both relative abundance of assigned formulas and biogeochemical classes of compounds. We found the degree of aggregation, measured by mean weighted diameter of aggregate fractions, is influenced by plant-soil interactions. Similarly, the proportion of soil aggregate fractions varied by both soil and plant factors. Differences in aggregation were reflected in differences in bacterial, but not fungal community composition across aggregate fractions, within each soil. Scanning electron microscopy revealed stark differences in mineral-organic interactions that influence the microbial niche and the accessibility of substrates within the soil. The clay soils show greater surface heterogeneity, enabling interactions with organic fraction of the soil. This is consistent with molecular data that reveal differences

Attractive interactions between reverse aggregates and phase separation in concentrated malonamide extractant solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Erlinger, C.; Belloni, L.; Zemb, T.

1999-03-30

Using small angle X-ray scattering, conductivity, and phase behavior determination, the authors show that concentrated solutions of malonamide extractants, dimethyldibutyltetradecylmalonamide (DMDBTDMA), are organized in reverse oligomeric aggregates which have many features in common with reverse micelles. The aggregation numbers of these reverse globular aggregates as well as their interaction potential are determined from absolute scattering curves. An attractive interaction is responsible for the demixing of the oil phase when in equilibrium with excess oil. Prediction of conductivity as well as the formation conditions for the third phase is possible using standard liquid theory applied to the extractant aggregates. The interactions,more » modeled with the sticky sphere model proposed by Baster, are shown to be due to steric interactions resulting from the hydrophobic tails of the extractant molecule and van der Waals forces between the highly polarizable water core of the reverse micelles. The attractive interaction in the oil phase, equilibrated with water, is determined as a function of temperature, extractant molecule concentration, and proton and neodynium(III) cation concentration. It is shown that van der Waals interactions, with an effective Hamaker constant of 3kT, quantitatively explain the behavior of DMDBTDMA in n-dodecane in terms of scattering as well as phase stability limits.« less

J-aggregation in porphyrin nanoparticles induced by diphenylalanine

NASA Astrophysics Data System (ADS)

Li, Fengqing; Liu, Dongzhi; Wang, Tianyang; Hu, Jianxin; Meng, Fancui; Sun, Haiya; Shang, Zhi; Li, Pingan; Feng, Wenhui; Li, Wei; Zhou, Xueqin

2017-08-01

In this report, L-diphenylalanine-decorated tetraphenylporphyrin (TPPtFFC) was synthesized and self-assembled into regular nano-architechtures. The morphology of the assemblies varied with the concentration of TPPtFFC. The absorption spectra of the nanoparticles show the Soret band merges with the Q bands and redistributes with great red-shift, indicative of the formation of J-aggregates of the porphyrin molecules. The fluorescence emission of the nanoparticles is merged and red-shifted to near-infrared region. Studies of absorption and fluorescence spectra reveal an indispensible role of diphenylalanine group in the formation of J-aggregates. The Raman spectra disclose that diprotonation of the porphyrin core contributes to delocalized coherent excited states in the nanoparticles. The positive cotton effect in circular dichroism spectra corresponding to the Soret band of TPPtFFC in solution confirms the formation of J-aggregates with right-handed chirality of the dipole moment. This report will shed light on the rational design of porphyrin-peptide conjugates to mimic naturally light-harvesting complexes.

Disrupting beta-amyloid aggregation for Alzheimer disease treatment.

PubMed

Estrada, L D; Soto, C

2007-01-01

Alzheimer's disease is a devastating degenerative disorder for which there is no cure or effective treatment. Although the etiology of Alzheimer's disease is not fully understood, compelling evidence indicates that deposition of aggregates composed by a misfolded form of the amyloid beta peptide (Abeta) is the central event in the disease pathogenesis. Therefore, an attractive therapeutic strategy is to prevent or reverse Abeta misfolding and aggregation. Diverse strategies have been described to identify inhibitors of this process, including screening of libraries of small molecules chemical compounds, rational design of synthetic peptides, assessment of natural Abeta-binding proteins and stimulation of the immune system by vaccination. In this article we describe these different approaches, their principles and their potential strengths and weaknesses. Overall the available data suggest that the development of drugs to interfere with Abeta misfolding and aggregation is a feasible target that hold great promise for the treatment of Alzheimer's disease.

Exchange and correlation in positronium-molecule scattering

NASA Astrophysics Data System (ADS)

Fabrikant, I. I.; Wilde, R. S.

2018-05-01

Exchange and correlations play a particularly important role in positronium (Ps) collisions with atoms and molecules, since the static potential for Ps interaction with a neutral system is zero. Theoretical description of both effects is a very challenging task. In the present work we use the free-electron-gas model to describe exchange and correlations in Ps collisions with molecules similar to the approach widely used in the theory of electron-molecule collisions. The results for exchange and correlation energies are presented as functions of the Fermi momentum of the electron gas and the Ps incident energy. Using the Thomas-Fermi model, these functions can be converted into exchange and correlation potentials for Ps interaction with molecules as functions of the distance between the projectile and the target.

A new understanding of inert gas narcosis

NASA Astrophysics Data System (ADS)

Meng, Zhang; Yi, Gao; Haiping, Fang

2016-01-01

Anesthetics are extremely important in modern surgery to greatly reduce the patient’s pain. The understanding of anesthesia at molecular level is the preliminary step for the application of anesthetics in clinic safely and effectively. Inert gases, with low chemical activity, have been found to cause anesthesia for centuries, but the mechanism is unclear yet. In this review, we first summarize the progress of theories about general anesthesia, especially for inert gas narcosis, and then propose a new hypothesis that the aggregated rather than the dispersed inert gas molecules are the key to trigger the narcosis to explain the steep dose-response relationship of anesthesia. Project supported by the Supercomputing Center of Chinese Academy of Sciences in Beijing, China, the Shanghai Supercomputer Center, China, the National Natural Science Foundation of China (Grant Nos. 21273268, 11290164, and 11175230), the Startup Funding from Shanghai Institute of Applied Physics, Chinese Academy of Sciences (Grant No. Y290011011), “Hundred People Project” from Chinese Academy of Sciences, and “Pu-jiang Rencai Project” from Science and Technology Commission of Shanghai Municipality, China (Grant No. 13PJ1410400).

The ongoing search for small molecules to study metal-associated amyloid-β species in Alzheimer's disease.

PubMed

Savelieff, Masha G; DeToma, Alaina S; Derrick, Jeffrey S; Lim, Mi Hee

2014-08-19

The development of a cure for Alzheimer's disease (AD) has been impeded by an inability to pinpoint the root cause of this disorder. Although numerous potential pathological factors have been indicated, acting either individually or mutually, the molecular mechanisms leading to disease onset and progression have not been clear. Amyloid-β (Aβ), generated from proteolytic processing of the amyloid precursor protein (APP), and its aggregated forms, particularly oligomers, are suggested as key pathological features in AD-affected brains. Historically, highly concentrated metals are found colocalized within Aβ plaques. Metal binding to Aβ (metal-Aβ) generates/stabilizes potentially toxic Aβ oligomers, and produces reactive oxygen species (ROS) in vitro (redox active metal ions; plausible contribution to oxidative stress). Consequently, clarification of the relationship between Aβ, metal ions, and toxicity, including oxidative stress via metal-Aβ, can lead to a deeper understanding of AD development. To probe the involvement of metal-Aβ in AD pathogenesis, rationally designed and naturally occurring molecules have been examined as chemical tools to target metal-Aβ species, modulate the interaction between the metal and Aβ, and subsequently redirect their aggregation into nontoxic, off-pathway unstructured aggregates. These ligands are also capable of attenuating the generation of redox active metal-Aβ-induced ROS to mitigate oxidative stress. One rational design concept, the incorporation approach, installs a metal binding site into a framework known to interact with Aβ. This approach affords compounds with the simultaneous ability to chelate metal ions and interact with Aβ. Natural products capable of Aβ interaction have been investigated for their influence on metal-induced Aβ aggregation and have inspired the construction of synthetic analogues. Systematic studies of these synthetic or natural molecules could uncover relationships between chemical

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.

Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.

PubMed

Pradhan, Mohan R; Pal, Arumay; Hu, Zhongqiao; Kannan, Srinivasaraghavan; Chee Keong, Kwoh; Lane, David P; Verma, Chandra S

2016-02-01

Aggregation is an irreversible form of protein complexation and often toxic to cells. The process entails partial or major unfolding that is largely driven by hydration. We model the role of hydration in aggregation using "Dehydrons." "Dehydrons" are unsatisfied backbone hydrogen bonds in proteins that seek shielding from water molecules by associating with ligands or proteins. We find that the residues at aggregation interfaces have hydrated backbones, and in contrast to other forms of protein-protein interactions, are under less evolutionary pressure to be conserved. Combining evolutionary conservation of residues and extent of backbone hydration allows us to distinguish regions on proteins associated with aggregation (non-conserved dehydron-residues) from other interaction interfaces (conserved dehydron-residues). This novel feature can complement the existing strategies used to investigate protein aggregation/complexation. © 2015 Wiley Periodicals, Inc.

Molecular simulations of micellar aggregation of polysorbate 20 ester fractions and their interaction with N-phenyl-1-naphthylamine dye.

PubMed

Lapelosa, Mauro; Patapoff, Thomas W; Zarraga, Isidro E

2016-06-01

Micellar aggregation behavior of polysorbate 20 (PS20) has generated significant interest because of the wide use of PS20 as a surfactant to minimize protein surface adsorption and mitigate protein aggregation. Thus, there is a need for better molecular understanding of what drives the biophysical behavior of PS20 in solution. We observe that a complex amphipathic PS20 molecule, which contains both hydrophobic tail and relatively large hydrophilic head, self-associates strongly within the course of a molecular dynamics simulation performed with a fully atomistic representation of the molecule and an explicit water solvent model. The in silico behavior is consistent with micellar models of PS20 in solution. The dynamics of this self-association is rather complex involving both internal reorganization of the molecule and diffusion to form stable micelle-like aggregates. The micellar aggregates of PS20 are long-lived and are formed by the balance between the large hydrophobic interactions associated with the aliphatic tail of PS20, and the steric repulsion of the hydrophilic sorbitan head structure. In the present work, molecular models of PS20 that represent naturally occurring PS20 fractions were produced and characterized in silico. The study investigated the monoester and diester fractions: PS20M, and PS20D. These fractions present differences in the strength of their hydrophobic effect, which influences the aggregation behavior. Adaptive biasing force (ABF) simulations were carried out with the PS20M and PS20D molecular constructs to calculate the free energy of their pairwise interaction. The free energy barrier for the dissociation is higher for PS20D compared with PS20M. The results show that hydrogen bonds can form when head groups are in close proximity, such as in the PS20 aggregate assembly, and the free energy of interaction can be used to predict the morphology of the micellar aggregate for the different PS20 fractions. We were also able to simulate PS20

Gravitational Instability of a Dust Layer Composed of Porous Silicate Dust Aggregates in a Protoplanetary Disk

NASA Astrophysics Data System (ADS)

Tatsuuma, Misako; Michikoshi, Shugo; Kokubo, Eiichiro

2018-03-01

Planetesimal formation is one of the most important unsolved problems in planet formation theory. In particular, rocky planetesimal formation is difficult because silicate dust grains are easily broken when they collide. It has recently been proposed that they can grow as porous aggregates when their monomer radius is smaller than ∼10 nm, which can also avoid the radial drift toward the central star. However, the stability of a layer composed of such porous silicate dust aggregates has not been investigated. Therefore, we investigate the gravitational instability (GI) of this dust layer. To evaluate the disk stability, we calculate Toomre’s stability parameter Q, for which we need to evaluate the equilibrium random velocity of dust aggregates. We calculate the equilibrium random velocity considering gravitational scattering and collisions between dust aggregates, drag by mean flow of gas, stirring by gas turbulence, and gravitational scattering by gas density fluctuation due to turbulence. We derive the condition of the GI using the disk mass, dust-to-gas ratio, turbulent strength, orbital radius, and dust monomer radius. We find that, for the minimum mass solar nebula model at 1 au, the dust layer becomes gravitationally unstable when the turbulent strength α ≲ 10‑5. If the dust-to-gas ratio is increased twice, the GI occurs for α ≲ 10‑4. We also find that the dust layer is more unstable in disks with larger mass, higher dust-to-gas ratio, and weaker turbulent strength, at larger orbital radius, and with a larger monomer radius.

Archean Earth Atmosphere Fractal Haze Aggregates: Light Scattering Calculations and the Faint Young Sun Paradox

NASA Astrophysics Data System (ADS)

Boness, D. A.; Terrell-Martinez, B.

2010-12-01

As part of an ongoing undergraduate research project of light scattering calculations involving fractal carbonaceous soot aggregates relevant to current anthropogenic and natural sources in Earth's atmosphere, we have read with interest a recent paper [E.T. Wolf and O.B Toon,Science 328, 1266 (2010)] claiming that the Faint Young Sun paradox discussed four decades ago by Carl Sagan and others can be resolved without invoking heavy CO2 concentrations as a greenhouse gas warming the early Earth enough to sustain liquid water and hence allow the origin of life. Wolf and Toon report that a Titan-like Archean Earth haze, with a fractal haze aggregate nature due to nitrogen-methane photochemistry at high altitudes, should block enough UV light to protect the warming greenhouse gas NH3 while allowing enough visible light to reach the surface of the Earth. To test this hypothesis, we have employed a rigorous T-Matrix arbitrary-particle light scattering technique, to avoid the simplifications inherent in Mie-sphere scattering, on haze fractal aggregates at UV and visible wavelenths of incident light. We generate these model aggregates using diffusion-limited cluster aggregation (DLCA) algorithms, which much more closely fit actual haze fractal aggregates than do diffusion-limited aggregation (DLA) algorithms.

Real-time imaging of Huntingtin aggregates diverting target search and gene transcription

PubMed Central

Li, Li; Liu, Hui; Dong, Peng; Li, Dong; Legant, Wesley R; Grimm, Jonathan B; Lavis, Luke D; Betzig, Eric; Tjian, Robert; Liu, Zhe

2016-01-01

The presumptive altered dynamics of transient molecular interactions in vivo contributing to neurodegenerative diseases have remained elusive. Here, using single-molecule localization microscopy, we show that disease-inducing Huntingtin (mHtt) protein fragments display three distinct dynamic states in living cells – 1) fast diffusion, 2) dynamic clustering and 3) stable aggregation. Large, stable aggregates of mHtt exclude chromatin and form 'sticky' decoy traps that impede target search processes of key regulators involved in neurological disorders. Functional domain mapping based on super-resolution imaging reveals an unexpected role of aromatic amino acids in promoting protein-mHtt aggregate interactions. Genome-wide expression analysis and numerical simulation experiments suggest mHtt aggregates reduce transcription factor target site sampling frequency and impair critical gene expression programs in striatal neurons. Together, our results provide insights into how mHtt dynamically forms aggregates and disrupts the finely-balanced gene control mechanisms in neuronal cells. DOI: http://dx.doi.org/10.7554/eLife.17056.001 PMID:27484239

Modeling the reversible kinetics of neutrophil aggregation under hydrodynamic shear.

PubMed Central

Neelamegham, S; Taylor, A D; Hellums, J D; Dembo, M; Smith, C W; Simon, S I

1997-01-01

Neutrophil emigration into inflamed tissue is mediated by beta 2-integrin and L-selectin adhesion receptors. Homotypic neutrophil aggregation is also dependent on these molecules, and it provides a model system in which to study adhesion dynamics. In the current study we formulated a mathematical model for cellular aggregation in a linear shear field based on Smoluchowski's two-body collision theory. Neutrophil suspensions activated with chemotactic stimulus and sheared in a cone-plate viscometer rapidly aggregate. Over a range of shear rates (400-800 s-1), approximately 90% of the single cells were recruited into aggregates ranging from doublets to groupings larger than sextuplets. The adhesion efficiency fit to these kinetics reached maximum levels of > 70%. Formed aggregates remained intact and resistant to shear up to 120 s, at which time they spontaneously dissociated back to singlets. The rate of cell disaggregation was linearly proportional to the applied shear rate, and it was approximately 60% lower for doublets as compared to larger aggregates. By accounting for the time-dependent changes in adhesion efficiency, disaggregation rate, and the effects of aggregate geometry, we succeeded in predicting the reversible kinetics of aggregation over a wide range of shear rates and cell concentrations. The combination of viscometry with flow cytometry and mathematical analysis as presented here represents a novel approach to differentiating between the effects of hydrodynamics and the intrinsic biological processes that control cell adhesion. Images FIGURE 3 FIGURE 5 PMID:9083659

Protein particulates: another generic form of protein aggregation?

PubMed

Krebs, Mark R H; Devlin, Glyn L; Donald, A M

2007-02-15

Protein aggregation is a problem with a multitude of consequences, ranging from affecting protein expression to its implication in many diseases. Of recent interest is the specific form of aggregation leading to the formation of amyloid fibrils, structures associated with diseases such as Alzheimer's disease. The ability to form amyloid fibrils is now regarded as a property generic to all polypeptide chains. Here we show that around the isoelectric point a different generic form of aggregation can also occur by studying seven widely different, nonrelated proteins that are also all known to form amyloid fibrils. Under these conditions gels consisting of relatively monodisperse spherical particulates are formed. Although these gels have been described before for beta-lactoglobulin, our results suggest that the formation of particulates in the regime where charge on the molecules is minimal is a common property of all proteins. Because the proteins used here also form amyloid fibrils, we further propose that protein misfolding into clearly defined aggregates is a generic process whose outcome depends solely on the general properties of the state the protein is in when aggregation occurs, rather than the specific amino acid sequence. Thus under conditions of high net charge, amyloid fibrils form, whereas under conditions of low net charge, particulates form. This observation furthermore suggests that the rules of soft matter physics apply to these systems.

Photonic molecules for improving the optical response of macroporous silicon photonic crystals for gas sensing purposes.

PubMed

Cardador, D; Segura, D; Rodríguez, A

2018-02-19

In this paper, we report the benefits of working with photonic molecules in macroporous silicon photonic crystals. In particular, we theoretically and experimentally demonstrate that the optical properties of a resonant peak produced by a single photonic atom of 2.6 µm wide can be sequentially improved if a second and a third cavity of the same length are introduced in the structure. As a consequence of that, the base of the peak is reduced from 500 nm to 100 nm, while its amplitude remains constant, increasing its Q-factor from its initial value of 25 up to 175. In addition, the bandgap is enlarged almost twice and the noise within it is mostly eliminated. In this study we also provide a way of reducing the amplitude of one or two peaks, depending whether we are in the two- or three-cavity case, by modifying the length of the involved photonic molecules so that the remainder can be used to measure gas by spectroscopic methods.

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.

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.

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

Sulfur mustard induces the formation of keratin aggregates in human epidermal keratinocytes.

PubMed

Dillman, James F; McGary, Kriston L; Schlager, John J

2003-12-01

The vesicant sulfur mustard is an alkylating agent that has the capacity to cross-link biological molecules. We are interested in identifying specific proteins that are altered upon sulfur mustard exposure. Keratins are particularly important for the structural integrity of skin, and several genetically inherited blistering diseases have been linked to mutations in keratin 5 and keratin 14. We examined whether sulfur mustard exposure alters keratin biochemistry in cultured human epidermal keratinocytes. Western blotting with specific monoclonal antibodies revealed the formation of stable high-molecular-weight "aggregates" containing keratin 14 and/or keratin 5. These aggregates begin to form within 15 min after sulfur mustard exposure. These aggregates display a complex gel electrophoresis pattern between approximately 100 and approximately 200 kDa. Purification and analysis of these aggregates by one- and two-dimensional gel electrophoresis and mass spectrometry confirmed the presence of keratin 14 and keratin 5 and indicate that at least some of the aggregates are composed of keratin 14-keratin 14, keratin 14-keratin 5, or keratin 5-keratin 5 dimers. These studies demonstrate that sulfur mustard induces keratin aggregation in keratinocytes and support further investigation into the role of keratin aggregation in sulfur mustard-induced vesication.

Interaction between phases in the liquid–gas system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berry, R. S., E-mail: bmsmirnov@gmail.com; Smirnov, B. M.

This work analyzes the equilibrium between a liquid and a gas over this liquid separated by an interface. Various gas forms exist inside the liquid: dissolved gas molecules attached to solvent molecules, free gas molecules, and gaseous bubbles. Thermodynamic equilibrium is maintained between two phases; the first phase is the liquid containing dissolved and free molecules, and the second phase is the gas over the liquid and bubbles inside it. Kinetics of gas transition between the internal and external gas proceeds through bubbles and includes the processes of bubbles floating up and bubble growth as a result of association duemore » to the Smoluchowski mechanism. Evolution of a gas in the liquid is considered using the example of oxygen in water, and numerical parameters of this system are given. In the regime under consideration for an oxygen–water system, transport of oxygen into the surrounding air proceeds through micron-size bubbles with lifetimes of hours. This regime is realized if the total number of oxygen molecules in water is small compared with the numbers of solvated and free molecules in the liquid.« less

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

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.

Dye-Binding Assays for Evaluation of the Effects of Small Molecule Inhibitors on Amyloid (Aβ) Self-Assembly

PubMed Central

2012-01-01

Dye-binding assays, such as those utilizing Congo red and thioflavin T, are among the most widely used tools to probe the aggregation of amyloidogenic biomolecules and for the evaluation of small molecule inhibitors of amyloid aggregation and fibrillization. A number of recent reports have indicated that these dye-binding assays could be prone to false positive effects when assessing inhibitors’ potential toward Aβ peptides, species involved in Alzheimer’s disease. Specifically, this review focuses on the application of thioflavin T for determining the efficiency of small molecule inhibitors of Aβ aggregation and addresses potential reasons that might be associated with the false positive effects in an effort to increase reliability of dye-binding assays. PMID:23173064

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

Intramolecular π-π Interactions in Flexibly Linked Partially Fluorinated Bisarenes in the Gas Phase.

PubMed

Blomeyer, Sebastian; Linnemannstöns, Marvin; Nissen, Jan Hendrick; Paulus, Jannik; Neumann, Beate; Stammler, Hans-Georg; Mitzel, Norbert W

2017-10-16

Three compounds with phenyl and pentafluorophenyl rings bridged by (CH 2 ) 3 and (CH 2 ) 2 SiMe 2 units were synthesized by hydrosilylation and C-C coupling reactions. Their solid-state structures are dominated by intermolecular π stacking interactions, primarily leading to dimeric or chain-type aggregates. Analysis of free molecules in the gas phase by electron diffraction revealed the most abundant conformer to be significantly stabilized by intramolecular π-π interactions. For the silicon compounds, structures characterized by σ-π interactions between methyl and pentafluorophenyl groups are second lowest in energy and cannot be excluded completely by the gas electron diffraction experiments. C 6 H 5 (CH 2 ) 3 C 6 F 5 , in contrast, is present as a single conformer. The gas-phase structures served as a reference for the evaluation of a series of (dispersion-corrected) quantum-chemical calculations. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Experimental aggregation of volcanic ash: the role of liquid bonding

NASA Astrophysics Data System (ADS)

Mueller, S.; Kueppers, U.; Jacob, M.; Ayris, P. M.; Dingwell, D. B.

2015-12-01

Explosive volcanic eruptions may release vast quantities of ash. Because of its size, it has the greatest dispersal potential and can be distributed globally. Ash may pose severe risks for 1) air traffic, 2) human and animal health, 3) agriculture and 4) infrastructure. Such ash particles can however cluster and form ash aggregates that range in size from millimeters to centimeters. During their growth, weight and aerodynamic properties change. This leads to significantly changed transport and settling behavior. The physico-chemical processes involved in aggregation are quantitatively poorly constrained. We have performed laboratory ash aggregation experiments using the ProCell Lab System® of Glatt Ingenieurtechnik GmbH. Solid particles are set into motion in a fluidized bed over a range of well-controlled boundary conditions (e.g., air flow rate, gas temperature, humidity, liquid composition). In this manner we simulate the variable gas-particle flow conditions expected in eruption plumes and pyroclastic density currents. We have used 1) soda-lime glass beads as an analogue material and 2) natural volcanic ash from Laacher See Volcano (Germany). In order to influence form, size, stability and the production rate of aggregates, a range of experimental conditions (e.g., particle concentration, degree of turbulence, temperature and moisture in the process chamber and the composition of the liquid phase) have been employed. We have successfully reproduced several features of natural ash aggregates, including round, internally structured ash pellets up to 3 mm in diameter. These experimental results help to constrain the boundary conditions required for the generation of spherical, internally-structured ash aggregates that survive deposition and are preserved in the volcanological record. These results should also serve as input parameters for models of ash transport and ash mass distribution.

A new interstellar molecule - Tricarbon monoxide

NASA Technical Reports Server (NTRS)

Matthews, H. E.; Irvine, W. M.; Friberg, P.; Brown, R. D.; Godfrey, P. D.

1984-01-01

The C3O molecule, whose pure rotational spectrum has only recently been studied in the laboratory, has been detected in the cold, dark interstellar Taurus Molecular Cloud 1. Since C3O is the first interstelar carbon chain molecule to contain oxygen, its existence places an important new constraint on chemical schemes for cold interstellar clouds. The abundance of C3O can be understood in terms of purely gas-phase ion-molecule chemistry.

Quantum mechanical computations and spectroscopy: from small rigid molecules in the gas phase to large flexible molecules in solution.

PubMed

Barone, Vincenzo; Improta, Roberto; Rega, Nadia

2008-05-01

Interpretation of structural properties and dynamic behavior of molecules in solution is of fundamental importance to understand their stability, chemical reactivity, and catalytic action. While information can be gained, in principle, by a variety of spectroscopic techniques, the interpretation of the rich indirect information that can be inferred from the analysis of experimental spectra is seldom straightforward because of the subtle interplay of several different effects, whose specific role is not easy to separate and evaluate. In such a complex scenario, theoretical studies can be very helpful at two different levels: (i) supporting and complementing experimental results to determine the structure of the target molecule starting from its spectral properties; (ii) dissecting and evaluating the role of different effects in determining the observed spectroscopic properties. This is the reason why computational spectroscopy is rapidly evolving from a highly specialized research field into a versatile and widespread tool for the assignment of experimental spectra and their interpretation in terms of chemical physical effects. In such a situation, it becomes important that both computationally and experimentally oriented chemists are aware that new methodological advances and integrated computational strategies are available, providing reliable estimates of fundamental spectral parameters not only for relatively small molecules in the gas phase but also for large and flexible molecules in condensed phases. In this Account, we review the most significant methodological contributions from our research group in this field, and by exploiting some recent results of their application to the computation of IR, UV-vis, NMR, and EPR spectral parameters, we discuss the microscopic mechanisms underlying solvent and vibrational effects on the spectral parameters. After reporting some recent achievements for the study of excited states by first principle quantum mechanical

Sugar-Terminated Nanoparticle Chaperones Are 102-105 Times Better Than Molecular Sugars in Inhibiting Protein Aggregation and Reducing Amyloidogenic Cytotoxicity.

PubMed

Pradhan, Nibedita; Shekhar, Shashi; Jana, Nihar R; Jana, Nikhil R

2017-03-29

Sugar-based osmolyte molecules are known to stabilize proteins under stress, but usually they have poor chaperone performance in inhibiting protein aggregation. Here, we show that the nanoparticle form of sugars molecule can enhance their chaperone performance typically by 10 2 -10 5 times, compared to molecular sugar. Sugar-based plate-like nanoparticles of 20-40 nm hydrodynamic size have been synthesized by simple heating of acidic aqueous solution of glucose/sucrose/maltose/trehalose. These nanoparticles have excitation-dependent green/yellow/orange emission and surface chemistry identical to the respective sugar molecule. Fibrillation of lysozyme/insulin/amyloid beta in extracellular space, aggregation of mutant huntingtin protein inside model neuronal cell, and cytotoxic effect of fibrils are investigated in the presence of these sugar nanoparticles. We found that sugar nanoparticles are 10 2 -10 5 times efficient than respective sugar molecules in inhibiting protein fibrillation and preventing cytotoxicity arising of fibrils. We propose that better performance of the nanoparticle form is linked to its stronger binding with fibril structure and enhanced cell uptake. This result suggests that nanoparticle form of osmolyte can be an attractive option in prevention and curing of protein aggregation-derived diseases.

Investigation of molecule-adsorption kinetics by a pulsed laser desorption technique

NASA Astrophysics Data System (ADS)

Varakin, V. N.; Lozovskii, A. D.; Panesh, A. M.; Simonov, A. P.

1987-02-01

The laser thermal desorption technique is used to measure the adsorption kinetics of SO2 and CO molecules on stainless steel with the aim of investigating the initial stage of oxidation of the steel by adsorbed CO molecules. Attention is given to the dependence of the rate of establishment of the equilibrium concentration of adsorbed molecules on SO2-gas pressure; CO adsorption kinetics on stainless steel at a gas pressure of 9 x 10 to the -8th torr; and the dependence of the concentration of adsorbed CO molecules on exposure in the gas at a pressure of 9 x 10 to the -8th torr under irradiation by laser pulses with repetition periods of 1-2, 2-4, 3-6, and 4-8 min.

MBAR-enhanced lattice Monte Carlo simulation of the effect of helices on membrane protein aggregation

NASA Astrophysics Data System (ADS)

Xu, Yuanwei; Rodger, P. Mark

2017-03-01

We study the effect of helical structure on the aggregation of proteins using a simplified lattice protein model with an implicit membrane environment. A recently proposed Monte Carlo approach, which exploits the proven statistical optimality of the MBAR estimator in order to improve simulation efficiency, was used. The results show that with both two and four proteins present, the tendency to aggregate is strongly expedited by the presence of amphipathic helix (APH), whereas a transmembrane helix (TMH) slightly disfavours aggregation. When four protein molecules are present, partially aggregated states (dimers and trimers) were more common when the APH was present, compared with the cases where no helices or only the TMH is present.

Gas phase basicities of polyfunctional molecules. Part 5: Non-aromatic sp2 nitrogen containing compounds.

PubMed

Bouchoux, Guy; Eckert-Maksic, Mirjana

2018-03-01

This paper constitutes the fifth part of a general review of the gas-phase protonation thermochemistry of polyfunctional molecules (Part 1: Theory and methods, Mass Spectrom Rev 2007, 26:775-835, Part 2: Saturated basic sites, Mass Spectrom Rev 2012, 31:353-390, Part 3: Amino acids, Mass Spectrom Rev 2012, 31:391-435, Part 4: Carbonyl as basic site, Mass Spectrom Rev 2015, 34:493-534). This part is devoted to non-aromatic molecules characterized by a lone pair located on a sp 2 nitrogen atom, it embraces functional groups such as imines, amidines, guanidines, diazenes, hydrazines, oximes, and phosphazenes. Specific examples are examined under five major chapters. In the first one, aliphatic and unsaturated (conjugated and cyclic) imines, hydrazones, and oximes are considered. A second chapter describes the protonation energetic of aliphatic, conjugated, or cyclic amidines. Guanidines, polyguanides, and biomolecules containing guanidine were examined in the third chapter. A fourth chapter describes the particular case of the phosphazene molecules. Finally, diazenes and azides were considered in the last chapter. Experimental data were re-evaluated according to the presently adopted basicity scale, i.e., PA(NH 3 ) = 853.6 kJ/mol, GB (NH 3 ) = 819 kJ/mol. Structural and energetic information given by G4MP2 quantum chemistry computations on typical systems are presented. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:139-170, 2018. © 2016 Wiley Periodicals, Inc.

Relaxation times and modes of disturbed aggregate distribution in micellar solutions with fusion and fission of micelles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zakharov, Anatoly I.; Adzhemyan, Loran Ts.; Shchekin, Alexander K., E-mail: akshch@list.ru

2015-09-28

We have performed direct numerical calculations of the kinetics of relaxation in the system of surfactant spherical micelles under joint action of the molecular mechanism with capture and emission of individual surfactant molecules by molecular aggregates and the mechanism of fusion and fission of the aggregates. As a basis, we have taken the difference equations of aggregation and fragmentation in the form of the generalized kinetic Smoluchowski equations for aggregate concentrations. The calculations have been made with using the droplet model of molecular surfactant aggregates and two modified Smoluchowski models for the coefficients of aggregate-monomer and aggregate-aggregate fusions which takemore » into account the effects of the aggregate size and presence of hydrophobic spots on the aggregate surface. A full set of relaxation times and corresponding relaxation modes for nonequilibrium aggregate distribution in the aggregation number has been found. The dependencies of these relaxation times and modes on the total concentration of surfactant in the solution and the special parameter controlling the probability of fusion in collisions of micelles with other micelles have been studied.« less

Nucleation of Organic Molecules via a Hot Precursor State: Pentacene on Amorphous Mica

PubMed Central

2013-01-01

Organic thin films have attracted considerable interest due to their applicability in organic electronics. The classical scenario for thin film nucleation is the diffusion-limited aggregation (DLA). Recently, it has been shown that organic thin film growth is better described by attachment-limited aggregation (ALA). However, in both cases, an unusual relationship between the island density and the substrate temperature was observed. Here, we present an aggregation model that goes beyond the classical DLA or ALA models to explain this behavior. We propose that the (hot) molecules impinging on the surface cannot immediately equilibrate to the substrate temperature but remain in a hot precursor state. In this state, the molecules can migrate considerable distances before attaching to a stable or unstable island. This results in a significantly smaller island density than expected by assuming fast equilibration and random diffusion. We have applied our model to pentacene film growth on amorphous Muscovite mica. PMID:24340130

From particle condensation to polymer aggregation

NASA Astrophysics Data System (ADS)

Janke, Wolfhard; Zierenberg, Johannes

2018-01-01

We draw an analogy between droplet formation in dilute particle and polymer systems. Our arguments are based on finite-size scaling results from studies of a two-dimensional lattice gas to three-dimensional bead-spring polymers. To set the results in perspective, we compare with in part rigorous theoretical scaling laws for canonical condensation in a supersaturated gas at fixed temperature, and derive corresponding scaling predictions for an undercooled gas at fixed density. The latter allows one to efficiently employ parallel multicanonical simulations and to reach previously not accessible scaling regimes. While the asymptotic scaling can not be observed for the comparably small polymer system sizes, they demonstrate an intermediate scaling regime also observable for particle condensation. Altogether, our extensive results from computer simulations provide clear evidence for the close analogy between particle condensation and polymer aggregation in dilute systems.

Oriented Polar Molecules in a Solid Inert-Gas Matrix: A Proposed Method for Measuring the Electric Dipole Moment of the Electron

NASA Astrophysics Data System (ADS)

Vutha, A.; Horbatsch, M.; Hessels, E.

2018-01-01

We propose a very sensitive method for measuring the electric dipole moment of the electron using polar molecules embedded in a cryogenic solid matrix of inert-gas atoms. The polar molecules can be oriented in the $\\hat{\\rm{z}}$ direction by an applied electric field, as has recently been demonstrated by Park, et al. [Angewandte Chemie {\\bf 129}, 1066 (2017)]. The trapped molecules are prepared into a state which has its electron spin perpendicular to $\\hat{\\rm{z}}$, and a magnetic field along $\\hat{\\rm{z}}$ causes precession of this spin. An electron electric dipole moment $d_e$ would affect this precession due to the up to 100~GV/cm effective electric field produced by the polar molecule. The large number of polar molecules that can be embedded in a matrix, along with the expected long coherence times for the precession, allows for the possibility of measuring $d_e$ to an accuracy that surpasses current measurements by many orders of magnitude. Because the matrix can inhibit molecular rotations and lock the orientation of the polar molecules, it may not be necessary to have an electric field present during the precession. The proposed technique can be applied using a variety of polar molecules and inert gases, which, along with other experimental variables, should allow for careful study of systematic uncertainties in the measurement.

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.

Beam-induced graphitic carbon cage transformation from sumanene aggregates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fujita, Jun-ichi, E-mail: fujita@bk.tsukuba.ac.jp; Tachi, Masashi; Murakami, Katsuhisa

2014-01-27

We found that electron-beam irradiation of sumanene aggregates strongly enhanced their transformation into a graphitic carbon cage, having a diameter of about 20 nm. The threshold electron dose was about 32 mC/cm{sup 2} at 200 keV, but the transformation is still induced at 20 keV. The transformation sequence suggested that the cage was constructed accompanied by the dynamical movement of the transiently linked sumanene molecules in order to pile up inside the shell. Thus, bond excitation in the sumanene molecules rather than a knock-on of carbon atoms seems to be the main cause of the cage transformation.

Dye-binding assays for evaluation of the effects of small molecule inhibitors on amyloid (aβ) self-assembly.

PubMed

Jameson, Laramie P; Smith, Nicholas W; Dzyuba, Sergei V

2012-11-21

Dye-binding assays, such as those utilizing Congo red and thioflavin T, are among the most widely used tools to probe the aggregation of amyloidogenic biomolecules and for the evaluation of small molecule inhibitors of amyloid aggregation and fibrillization. A number of recent reports have indicated that these dye-binding assays could be prone to false positive effects when assessing inhibitors' potential toward Aβ peptides, species involved in Alzheimer's disease. Specifically, this review focuses on the application of thioflavin T for determining the efficiency of small molecule inhibitors of Aβ aggregation and addresses potential reasons that might be associated with the false positive effects in an effort to increase reliability of dye-binding assays.

Thermodynamics and kinetics of gas storage in porous liquids

DOE PAGES

Zhang, Fei; Yang, Fengchang; Huang, Jingsong; ...

2016-07-05

The recent synthesis of organic molecular liquids with permanent porosity (Giri et al., Nature, 2015, 527, 216) opens up exciting new avenues for gas capture, storage, and separation. Using molecular dynamics simulations, we study the thermodynamics and kinetics for the storage of CH 4, CO 2, and N 2 molecules in porous liquids consisting of crown-ether substituted cage molecules in a 15-crown-5 solvent. It is found that the gas storage capacity per cage molecule follows the order of CH 4 > CO 2 > N 2, which does not correlate simply with the size of gas molecules. Different gas moleculesmore » are stored inside the cage differently, e.g., CO 2 molecules prefer the cage s core while CH 4 molecules favor both the core and the branch regions. All gas molecules considered can enter the cage essentially without energy barriers, and their dynamics inside the cage are only slightly hindered by the nanoscale confinement. In addition, all gas molecules can leave the cage on nanosecond time scale by overcoming a modest energy penalty. The molecular mechanisms of these observations are clarified.« less

Thermodynamics and kinetics of gas storage in porous liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Fei; Yang, Fengchang; Huang, Jingsong

The recent synthesis of organic molecular liquids with permanent porosity (Giri et al., Nature, 2015, 527, 216) opens up exciting new avenues for gas capture, storage, and separation. Using molecular dynamics simulations, we study the thermodynamics and kinetics for the storage of CH 4, CO 2, and N 2 molecules in porous liquids consisting of crown-ether substituted cage molecules in a 15-crown-5 solvent. It is found that the gas storage capacity per cage molecule follows the order of CH 4 > CO 2 > N 2, which does not correlate simply with the size of gas molecules. Different gas moleculesmore » are stored inside the cage differently, e.g., CO 2 molecules prefer the cage s core while CH 4 molecules favor both the core and the branch regions. All gas molecules considered can enter the cage essentially without energy barriers, and their dynamics inside the cage are only slightly hindered by the nanoscale confinement. In addition, all gas molecules can leave the cage on nanosecond time scale by overcoming a modest energy penalty. The molecular mechanisms of these observations are clarified.« less

Effect of Aggregation on Squaraine Fullerene Bulk-Heterojunction Organic Photovoltaic Devices

NASA Astrophysics Data System (ADS)

Jalan, Ishita

Organic photovoltaics (OPV) offer great promise as a low-cost renewable energy source, the relative low efficiency still challenges its commercialization potential. Small conjugated molecules like Squaraine (SQ) molecules show promising advancement in organic photovoltaics (OPV). Advantages of SQ over other materials is that it has a high extinction coefficient (>105), decent photo-stability, good synthetic reproducibility, and tunable molecular structure. With small chemical modifications, the squaraines can have substantial impact on photophysical properties and aggregation pattern, and thus on operational OPV efficiency. The squaraine molecule that will be studied in this work is a symmetric aniline-based squaraine with n-hexyl chain on the molecular arm with di hydroxyl substituents on the aniline, this will be referred to DHSQ(OH) 2. In this work, the assignment of the monomer and aggregate peak is discussed. It is known that crystallinity is important for efficient charge transport and exciton diffusion in the BHJ, this thesis focuses on thermal and solvent vapor annealing the as-cast films to reduce the amorphous regions. It is observed that crystallinity is improved but often at the expense of larger crystal size. Therefore, to achieve optimal OPV efficiency, this tradeoff is controlled to improve the crystallinity while maintaining a small, highly mixed BHJ morphology.

Hsp70 and Antifibrillogenic Peptides Promote Degradation and Inhibit Intracellular Aggregation of Amyloidogenic Light Chains

PubMed Central

Dul, Jeanne L.; Davis, David P.; Williamson, Edward K.; Stevens, Fred J.; Argon, Yair

2001-01-01

In light chain (LC) amyloidosis an immunoglobulin LC assembles into fibrils that are deposited in various tissues. Little is known about how these fibrils form in vivo. We previously showed that a known amyloidogenic LC, SMA, can give rise to amyloid fibrils in vitro when a segment of one of its β sheets undergoes a conformational change, exposing an Hsp70 binding site. To examine SMA aggregation in vivo, we expressed it and its wild-type counterpart, LEN, in COS cells. While LEN is rapidly oxidized and subsequently secreted, newly synthesized SMA remains in the reduced state. Most SMA molecules are dislocated out of the ER into the cytosol, where they are ubiquitinylated and degraded by proteasomes. A parallel pathway for molecules that are not degraded is condensation into perinuclear aggresomes that are surrounded by vimentin-containing intermediate filaments and are dependent upon intact microtubules. Inhibition of proteasome activity shifts the balance toward aggresome formation. Intracellular aggregation is decreased and targeting to proteasomes improved by overexpression of the cytosolic chaperone Hsp70. Importantly, transduction into the cell of an Hsp70 target peptide, derived from the LC sequence, also reduces aggresome formation and increases SMA degradation. These results demonstrate that an amyloidogenic LC can aggregate intracellularly despite the common presentation of extracellular aggregates, and that a similar molecular surface mediates both in vitro fibril formation and in vivo aggregation. Furthermore, rationally designed peptides can be used to suppress this aggregation and may provide a feasible therapeutic approach. PMID:11266462

Hsp70 and antifibrillogenic peptides promote degradation and inhibit intracellular aggregation of amyloidogenic light chains.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dul, J. L.; Davis, D. P.; Williamson, E. K.

2001-02-19

In light chain (LC) amyloidosis an immunoglobulin LC assembles into fibrils that are deposited in various tissues. Little is known about how these fibrils form in vivo. We previously showed that a known amyloidogenic LC, SMA, can give rise to amyloid fibrils in vitro when a segment of one of its {beta} sheets undergoes a conformational change, exposing an Hsp70 binding site. To examine SMA aggregation in vivo, we expressed it and its wild-type counterpart, LEN, in COS cells. While LEN is rapidly oxidized and subsequently secreted, newly synthesized SMA remains in the reduced state. Most SMA molecules are dislocatedmore » out of the ER into the cytosol, where they are ubiquitinylated and degraded by proteasomes. A parallel pathway for molecules that are not degraded is condensation into perinuclear aggresomes that are surrounded by vimentin-containing intermediate filaments and are dependent upon intact microtubules. Inhibition of proteasome activity shifts the balance toward aggresome formation. Intracellular aggregation is decreased and targeting to proteasomes improved by overexpression of the cytosolic chaperone Hsp70. Importantly, transduction into the cell of an Hsp70 target peptide, derived from the LC sequence, also reduces aggresome formation and increases SMA degradation. These results demonstrate that an amyloidogenic LC can aggregate intracellularly despite the common presentation of extracellular aggregates, and that a similar molecular surface mediates both in vitro fibril formation and in vivo aggregation. Furthermore, rationally designed peptides can be used to suppress this aggregation and may provide a feasible therapeutic approach.« less

[Effect of dilution on aggregation of nanoparticles of polycarboxylic derivative of fullerene C60].

PubMed

Bobylev, A G; Pen'kov, N V; Troshin, P A; Gudkov, S V

2015-01-01

In this work, we investigated the effect of dilution on aggregation of nanoparticles of the polycarboxylic derivative of fullerene C60. It is shown that the diminution of the concentration of PCDF-1 in aqueous medium leads to a decreased amount of aggregates of fullerene and an increased amount of single molecules. This can potentially interfere with the biological activity of a compound on one molecule basis. Addition of organic and inorganic salts to the aqueous medium with fullerene derivative leads to intense disaggregation of PCDF-1. The data obtained suggest an explanation of non-stoichiometric nature of neutralization of reactive oxygen species by derivatives of fullerenes, as well as provide new insight into the physical meaning of the work on the impact of nanoparticles at ultra-low concentrations on biological objects.

Effect of physicochemical action on the aggregative properties of detonation-synthesized nanodiamonds

NASA Astrophysics Data System (ADS)

Fan, Z. W.; Ilnitska, H.; Lysakovskyi, V.; Ivakhnenko, S.; Kovalenko, T.

2018-01-01

The results of researches of physicochemical action on aggregate properties of nanodiamond are presented. The kinetics of aggregation of nanodiamond powder was studied as a function of time, temperature, and pH of the solution. The effect of the sp2-sp3 hybridization ratio of carbon in nanodiamond powders on their aggregation was studied. It is shown that the presence of non-diamond carbon in detonation synthesis nanodiamond powders leads to the increase of the mean diameters of particles, i.e., their agglomeration. The theoretical justification of the aggregation mechanism is proposed. It is shown that it is possible to control aggregative properties of nanodiamond powders by physicochemical influences, e.g., gas-phase thermal treatment to reduce the size of agglomerates and to create a well-developed reconstructed surface of diamond particles with a low content of functional groups on their surface.

Acceleration of individual, decimetre-sized aggregates in the lower coma of comet 67P/Churyumov-Gerasimenko

NASA Astrophysics Data System (ADS)

Agarwal, Jessica; A'Hearn, M. F.; Vincent, J.-B.; Güttler, C.; Höfner, S.; Sierks, H.; Tubiana, C.; Barbieri, C.; Lamy, P. L.; Rodrigo, R.; Koschny, D.; Rickman, H.; Barucci, M. A.; Bertaux, J.-L.; Bertini, I.; Boudreault, S.; Cremonese, G.; Da Deppo, V.; Davidsson, B.; Debei, S.; De Cecco, M.; Deller, J.; Fornasier, S.; Fulle, M.; Gicquel, A.; Groussin, O.; Gutiérrez, P. J.; Hofmann, M.; Hviid, S. F.; Ip, W.-H.; Jorda, L.; Keller, H. U.; Knollenberg, J.; Kramm, J.-R.; Kührt, E.; Küppers, M.; Lara, L. M.; Lazzarin, M.; Lopez Moreno, J. J.; Marzari, F.; Naletto, G.; Oklay, N.; Shi, X.; Thomas, N.

2016-11-01

We present observations of decimetre-sized, likely ice-containing aggregates ejected from a confined region on the surface of comet 67P/Churyumov-Gerasimenko. The images were obtained with the narrow angle camera of the Optical, Spectroscopic, and Infrared Remote Imaging System on board the Rosetta spacecraft in 2016 January when the comet was at 2 au from the Sun outbound from perihelion. We measure the acceleration of individual aggregates through a 2 h image series. Approximately 50 per cent of the aggregates are accelerated away from the nucleus, and 50 per cent towards it, and likewise towards either horizontal direction. The accelerations are up to one order of magnitude stronger than local gravity, and are most simply explained by the combined effect of gas drag accelerating all aggregates upwards, and the recoil force from asymmetric outgassing, either from rotating aggregates with randomly oriented spin axes and sufficient thermal inertia to shift the temperature maximum away from an aggregate's subsolar region, or from aggregates with variable ice content. At least 10 per cent of the aggregates will escape the gravity field of the nucleus and feed the comet's debris trail, while others may fall back to the surface and contribute to the deposits covering parts of the Northern hemisphere. The rocket force plays a crucial role in pushing these aggregates back towards the surface. Our observations show the future back fall material in the process of ejection, and provide the first direct measurement of the acceleration of aggregates in the innermost coma (<2 km) of a comet, where gas drag is still significant.

Gas-phase binding energies for non-covalent Aβ-40 peptide/small molecule complexes from CID mass spectrometry and RRKM theory.

PubMed

Mayer, Paul M; Martineau, Eric

2011-03-21

The gas-phase binding of small molecules to the Amyloid β-40 peptide generated by electrospray ionization has been explored with collision-induced dissociation mass spectrometry and kinetic rate theory. This study discusses a simple procedure used to theoretically model the experimental breakdown diagrams for the Aβ-40 peptide complexed with a series of aminosulfonate small molecules, namely homotaurine, 3-cyclohexylamino-2-hydroxy-1-propanesulfonic acid (CAPSO), 3-(1,3,4,9-tetrahydro-2H-β-carbolin-2-yl)propane-1-sulfonic acid, 3-(1,3,4,9-tetrahydro-2H-β-carbolin-2-yl)butane-1-sulfonic acid, and 3-(cyclohexylamino)propane-1-sulfonic acid. An alternative procedure employing an extrapolation procedure for k(E) is also discussed.

A quorum-sensing molecule acts as a morphogen controlling gas vesicle organelle biogenesis and adaptive flotation in an enterobacterium

PubMed Central

Ramsay, Joshua P.; Williamson, Neil R.; Spring, David R.; Salmond, George P. C.

2011-01-01

Gas vesicles are hollow intracellular proteinaceous organelles produced by aquatic Eubacteria and Archaea, including cyanobacteria and halobacteria. Gas vesicles increase buoyancy and allow taxis toward air–liquid interfaces, enabling subsequent niche colonization. Here we report a unique example of gas vesicle-mediated flotation in an enterobacterium; Serratia sp. strain ATCC39006. This strain is a member of the Enterobacteriaceae previously studied for its production of prodigiosin and carbapenem antibiotics. Genes required for gas vesicle synthesis mapped to a 16.6-kb gene cluster encoding three distinct homologs of the main structural protein, GvpA. Heterologous expression of this locus in Escherichia coli induced copious vesicle production and efficient cell buoyancy. Gas vesicle morphogenesis in Serratia enabled formation of a pellicle-like layer of highly vacuolated cells, which was dependent on oxygen limitation and the expression of ntrB/C and cheY-like regulatory genes within the gas-vesicle gene cluster. Gas vesicle biogenesis was strictly controlled by intercellular chemical signaling, through an N-acyl homoserine lactone, indicating that in this system the quorum-sensing molecule acts as a morphogen initiating organelle development. Flagella-based motility and gas vesicle morphogenesis were also oppositely regulated by the small RNA-binding protein, RsmA, suggesting environmental adaptation through physiological control of the choice between motility and flotation as alternative taxis modes. We propose that gas vesicle biogenesis in this strain represents a distinct mechanism of mobility, regulated by oxygen availability, nutritional status, the RsmA global regulatory system, and the quorum-sensing morphogen. PMID:21873216

A quorum-sensing molecule acts as a morphogen controlling gas vesicle organelle biogenesis and adaptive flotation in an enterobacterium.

PubMed

Ramsay, Joshua P; Williamson, Neil R; Spring, David R; Salmond, George P C

2011-09-06

Gas vesicles are hollow intracellular proteinaceous organelles produced by aquatic Eubacteria and Archaea, including cyanobacteria and halobacteria. Gas vesicles increase buoyancy and allow taxis toward air-liquid interfaces, enabling subsequent niche colonization. Here we report a unique example of gas vesicle-mediated flotation in an enterobacterium; Serratia sp. strain ATCC39006. This strain is a member of the Enterobacteriaceae previously studied for its production of prodigiosin and carbapenem antibiotics. Genes required for gas vesicle synthesis mapped to a 16.6-kb gene cluster encoding three distinct homologs of the main structural protein, GvpA. Heterologous expression of this locus in Escherichia coli induced copious vesicle production and efficient cell buoyancy. Gas vesicle morphogenesis in Serratia enabled formation of a pellicle-like layer of highly vacuolated cells, which was dependent on oxygen limitation and the expression of ntrB/C and cheY-like regulatory genes within the gas-vesicle gene cluster. Gas vesicle biogenesis was strictly controlled by intercellular chemical signaling, through an N-acyl homoserine lactone, indicating that in this system the quorum-sensing molecule acts as a morphogen initiating organelle development. Flagella-based motility and gas vesicle morphogenesis were also oppositely regulated by the small RNA-binding protein, RsmA, suggesting environmental adaptation through physiological control of the choice between motility and flotation as alternative taxis modes. We propose that gas vesicle biogenesis in this strain represents a distinct mechanism of mobility, regulated by oxygen availability, nutritional status, the RsmA global regulatory system, and the quorum-sensing morphogen.

Infrared Spectroscopic and Electronic Structure Investigations of Beryllium Halide Molecules, Cations, and Anions in Noble Gas Matrices.

PubMed

Yu, Wenjie; Andrews, Lester; Wang, Xuefeng

2017-11-22

Laser-ablated Be atoms, cations, and electrons were reacted with F 2 , ClF, Cl 2 , NF 3 , CCl 4 , CF 2 Cl 2 , HCl, DCl, and SiCl 4 diluted in noble gases. The major products were the dihalides BeF 2 , BeClF, BeCl 2 , and the hydride chloride HBeCl, whose identities were confirmed by comparison with previous evaporative work, deuterium substitution, and vibrational frequency calculations. The matrix-isolated fundamental frequency of the BeF molecule is higher, and the frequency of BeCl is lower, than that determined for the gas-phase molecules. The BeF + and BeCl + cations formed strong dipole-induced dipole complexes in solid Ne, Ar, Kr, and Xe with stepwise increase in computed noble gas dissociation energies. Going down the family NgBeF + and NgBeCl + series (Ng = Ne, Ar, Kr, Xe) the Mulliken charges q(Be) decrease, while q(Ng) increases, and the dipole moments decrease, which suggests covalent bonding in the xenon species. We find that the largest intramatrix shift is Ne to Ar which follows the largest factor increase for the Ng atomic polarizabilities. Extra electrons produce Cl - , which reacts with HCl to form the stable HCl 2 - anion and possibly with BeCl 2 to give BeCl 3 - . A weak band observed in neon experiments with F 2 is probably due to BeF 3 - .

Star Polymers Reduce Islet Amyloid Polypeptide Toxicity via Accelerated Amyloid Aggregation.

PubMed

Pilkington, Emily H; Lai, May; Ge, Xinwei; Stanley, William J; Wang, Bo; Wang, Miaoyi; Kakinen, Aleksandr; Sani, Marc-Antonie; Whittaker, Michael R; Gurzov, Esteban N; Ding, Feng; Quinn, John F; Davis, Thomas P; Ke, Pu Chun

2017-12-11

Protein aggregation into amyloid fibrils is a ubiquitous phenomenon across the spectrum of neurodegenerative disorders and type 2 diabetes. A common strategy against amyloidogenesis is to minimize the populations of toxic oligomers and protofibrils by inhibiting protein aggregation with small molecules or nanoparticles. However, melanin synthesis in nature is realized by accelerated protein fibrillation to circumvent accumulation of toxic intermediates. Accordingly, we designed and demonstrated the use of star-shaped poly(2-hydroxyethyl acrylate) (PHEA) nanostructures for promoting aggregation while ameliorating the toxicity of human islet amyloid polypeptide (IAPP), the peptide involved in glycemic control and the pathology of type 2 diabetes. The binding of PHEA elevated the β-sheet content in IAPP aggregates while rendering a new morphology of "stelliform" amyloids originating from the polymers. Atomistic molecular dynamics simulations revealed that the PHEA arms served as rodlike scaffolds for IAPP binding and subsequently accelerated IAPP aggregation by increased local peptide concentration. The tertiary structure of the star nanoparticles was found to be essential for driving the specific interactions required to impel the accelerated IAPP aggregation. This study sheds new light on the structure-toxicity relationship of IAPP and points to the potential of exploiting star polymers as a new class of therapeutic agents against amyloidogenesis.

Superdiffusive gas recovery from nanopores

NASA Astrophysics Data System (ADS)

Wu, Haiyi; He, Yadong; Qiao, Rui

2016-11-01

Understanding the recovery of gas from reservoirs featuring pervasive nanopores is essential for effective shale gas extraction. Classical theories cannot accurately predict such gas recovery and many experimental observations are not well understood. Here we report molecular simulations of the recovery of gas from single nanopores, explicitly taking into account molecular gas-wall interactions. We show that, in very narrow pores, the strong gas-wall interactions are essential in determining the gas recovery behavior both quantitatively and qualitatively. These interactions cause the total diffusion coefficients of the gas molecules in nanopores to be smaller than those predicted by kinetic theories, hence slowing down the rate of gas recovery. These interactions also lead to significant adsorption of gas molecules on the pore walls. Because of the desorption of these gas molecules during gas recovery, the gas recovery from the nanopore does not exhibit the usual diffusive scaling law (i.e., the accumulative recovery scales as R ˜t1 /2 ) but follows a superdiffusive scaling law R ˜tn (n >0.5 ), which is similar to that observed in some field experiments. For the system studied here, the superdiffusive gas recovery scaling law can be captured well by continuum models in which the gas adsorption and desorption from pore walls are taken into account using the Langmuir model.

First-principles investigation on defect-induced silicene nanoribbons - A superior media for sensing NH3, NO2 and NO gas molecules

NASA Astrophysics Data System (ADS)

Walia, Gurleen Kaur; Randhawa, Deep Kamal Kaur

2018-04-01

In this paper, the electronic and transport properties of armchair silicene nanoribbons (ASiNRs) are analyzed for their application as highly selective and sensitive gas molecule sensors. The study is focused on sensing three nitrogen based gases; ammonia (NH3), nitrogen dioxide (NO2) and nitric oxide (NO), which depending upon their adsorption energy and charge transfer, form bonds of varying strength with ASiNRs. The negligible band gap of ASiNRs is tuned by adding a defect in ASiNRs. Adsorption of NH3 leads to the opening of band gap whereas on adsorption of NO2 and NO, ASiNRs exhibit metallic nature. Distinctly divergent electronic and transport properties of ASiNRs are observed and on adsorption of NH3, NO2 and NO, renders them suitable for sensing them. All gas molecules show stronger adsorption on defective ASiNRs (D-ASiNRs) as compared to pristine ASiNRs (P-ASiNRs). The work reveals that introduction of defect can drastically improve the sensitivity of ASiNRs.

A Protein Aggregation Based Test for Screening of the Agents Affecting Thermostability of Proteins

PubMed Central

Eronina, Tatyana; Borzova, Vera; Maloletkina, Olga; Kleymenov, Sergey; Asryants, Regina; Markossian, Kira; Kurganov, Boris

2011-01-01

To search for agents affecting thermal stability of proteins, a test based on the registration of protein aggregation in the regime of heating with a constant rate was used. The initial parts of the dependences of the light scattering intensity (I) on temperature (T) were analyzed using the following empiric equation: I = K agg(T−T 0)2, where K agg is the parameter characterizing the initial rate of aggregation and T 0 is a temperature at which the initial increase in the light scattering intensity is registered. The aggregation data are interpreted in the frame of the model assuming the formation of the start aggregates at the initial stages of the aggregation process. Parameter T 0 corresponds to the moment of the origination of the start aggregates. The applicability of the proposed approach was demonstrated on the examples of thermal aggregation of glycogen phosphorylase b from rabbit skeletal muscles and bovine liver glutamate dehydrogenase studied in the presence of agents of different chemical nature. The elaborated approach to the study of protein aggregation may be used for rapid identification of small molecules that interact with protein targets. PMID:21760963

Inhibition of the aggregation of lactoferrin and (-)-epigallocatechin gallate in the presence of polyphenols, oligosaccharides, and collagen peptide.

PubMed

Yang, Wei; Liu, Fuguo; Xu, Chenqi; Sun, Cuixia; Yuan, Fang; Gao, Yanxiang

2015-05-27

The aggregation of lactoferrin and (-)-epigallocatechin gallate (EGCG) was inhibited by polyphenols, oligosaccharides, and collagen peptide in this study. Polyphenols, oligosaccharides, or collagen peptide can effectively prevent the formation of lactoferrin-EGCG aggregates, respectively. The addition sequence of lactoferrin, polyphenols (oligosaccharides or collagen peptide) and EGCG can affect the turbidity and particle size of the ternary complexes in the buffer solution; however, it hardly affected the ζ-potential and fluorescence characteristics. With either positive or negative charge, polyphenols and collagen peptide disrupted the formation of lactoferrin-EGCG aggregate mainly through the mechanism of its competition with EGCG molecules which surrounded the lactoferrin molecule surface with weaker binding affinities, forming polyphenols or a collagen peptide-lactoferrin-EGCG ternary complex; for neutral oligosaccharides, the ternary complex was generated mainly through steric effects, accompanied by a change in the lactoferrin secondary structure induced by gallic acid, chlorogenic acid, and xylo-oligosaccharide. Polyphenols, oligosaccharides, or collagen peptide restraining the formation of lactoferrin-EGCG aggregate could be applied in the design of clear products in the food, pharmaceutical, and cosmetic industries.

Identification of benzothiazoles as potential polyglutamine aggregation inhibitors of Huntington's disease by using an automated filter retardation assay

PubMed Central

Heiser, Volker; Engemann, Sabine; Bröcker, Wolfgang; Dunkel, Ilona; Boeddrich, Annett; Waelter, Stephanie; Nordhoff, Eddi; Lurz, Rudi; Schugardt, Nancy; Rautenberg, Susanne; Herhaus, Christian; Barnickel, Gerhard; Böttcher, Henning; Lehrach, Hans; Wanker, Erich E.

2002-01-01

Preventing the formation of insoluble polyglutamine containing protein aggregates in neurons may represent an attractive therapeutic strategy to ameliorate Huntington's disease (HD). Therefore, the ability to screen for small molecules that suppress the self-assembly of huntingtin would have potential clinical and significant research applications. We have developed an automated filter retardation assay for the rapid identification of chemical compounds that prevent HD exon 1 protein aggregation in vitro. Using this method, a total of 25 benzothiazole derivatives that inhibit huntingtin fibrillogenesis in a dose-dependent manner were discovered from a library of ≈184,000 small molecules. The results obtained by the filter assay were confirmed by immunoblotting, electron microscopy, and mass spectrometry. Furthermore, cell culture studies revealed that 2-amino-4,7-dimethyl-benzothiazol-6-ol, a chemical compound similar to riluzole, significantly inhibits HD exon 1 aggregation in vivo. These findings may provide the basis for a new therapeutic approach to prevent the accumulation of insoluble protein aggregates in Huntington's disease and related glutamine repeat disorders. PMID:12200548

First-principles calculation of the optical properties of an amphiphilic cyanine dye aggregate.

PubMed

Haverkort, Frank; Stradomska, Anna; de Vries, Alex H; Knoester, Jasper

2014-02-13

Using a first-principles approach, we calculate electronic and optical properties of molecular aggregates of the dye amphi-pseudoisocyanine, whose structures we obtained from molecular dynamics (MD) simulations of the self-aggregation process. Using quantum chemistry methods, we translate the structural information into an effective time-dependent Frenkel exciton Hamiltonian for the dominant optical transitions in the aggregate. This Hamiltonian is used to calculate the absorption spectrum. Detailed analysis of the dynamic fluctuations in the molecular transition energies and intermolecular excitation transfer interactions in this Hamiltonian allows us to elucidate the origin of the relevant time scales; short time scales, on the order of up to a few hundreds of femtoseconds, result from internal motions of the dye molecules, while the longer (a few picosecond) time scales we ascribe to environmental motions. The absorption spectra of the aggregate structures obtained from MD feature a blue-shifted peak compared to that of the monomer; thus, our aggregates can be classified as H-aggregates, although considerable oscillator strength is carried by states along the entire exciton band. Comparison to the experimental absorption spectrum of amphi-PIC aggregates shows that the simulated line shape is too wide, pointing to too much disorder in the internal structure of the simulated aggregates.

Aggregation in particle rich environments: a textural study of examples from volcanic eruptions, meteorite impacts, and fluidized bed processing

NASA Astrophysics Data System (ADS)

Mueller, Sebastian B.; Kueppers, Ulrich; Huber, Matthew S.; Hess, Kai-Uwe; Poesges, Gisela; Ruthensteiner, Bernhard; Dingwell, Donald B.

2018-04-01

Aggregation is a common process occurring in many diverse particulate gas mixtures (e.g. those derived from explosive volcanic eruptions, meteorite impact events, and fluid bed processing). It results from the collision and sticking of particles suspended in turbulent gas/air. To date, there is no generalized model of the underlying physical processes. Here, we investigate aggregates from 18 natural deposits (16 volcanic deposits and two meteorite impact deposits) as well as aggregates produced experimentally via fluidized bed techniques. All aggregates were analyzed for their size, internal structuring, and constituent particle size distribution. Commonalities and differences between the aggregate types are then used to infer salient features of the aggregation process. Average core to rim ratios of internally structured aggregates (accretionary lapilli) is found to be similar for artificial and volcanic aggregates but up to an order of magnitude different than impact-related aggregates. Rim structures of artificial and volcanic aggregates appear to be physically similar (single, sub-spherical, regularly-shaped rims) whereas impact-related aggregates more often show multiple or irregularly shaped rims. The particle size distributions (PSDs) of all three aggregate types are similar (< 200 μm). This proves that in all three environments, aggregation occurs under broadly similar conditions despite the significant differences in source conditions (particle volume fraction, particle size distribution, particle composition, temperature), residence times, plume conditions (e.g., humidity and temperature), and dynamics of fallout and deposition. Impact-generated and volcanic aggregates share many similarities, and in some cases may be indistinguishable without their stratigraphic context.

Aggregation in particle rich environments: a textural study of examples from volcanic eruptions, meteorite impacts, and fluidized bed processing.

PubMed

Mueller, Sebastian B; Kueppers, Ulrich; Huber, Matthew S; Hess, Kai-Uwe; Poesges, Gisela; Ruthensteiner, Bernhard; Dingwell, Donald B

2018-01-01

Aggregation is a common process occurring in many diverse particulate gas mixtures (e.g. those derived from explosive volcanic eruptions, meteorite impact events, and fluid bed processing). It results from the collision and sticking of particles suspended in turbulent gas/air. To date, there is no generalized model of the underlying physical processes. Here, we investigate aggregates from 18 natural deposits (16 volcanic deposits and two meteorite impact deposits) as well as aggregates produced experimentally via fluidized bed techniques. All aggregates were analyzed for their size, internal structuring, and constituent particle size distribution. Commonalities and differences between the aggregate types are then used to infer salient features of the aggregation process. Average core to rim ratios of internally structured aggregates (accretionary lapilli) is found to be similar for artificial and volcanic aggregates but up to an order of magnitude different than impact-related aggregates. Rim structures of artificial and volcanic aggregates appear to be physically similar (single, sub-spherical, regularly-shaped rims) whereas impact-related aggregates more often show multiple or irregularly shaped rims. The particle size distributions (PSDs) of all three aggregate types are similar (< 200 μm). This proves that in all three environments, aggregation occurs under broadly similar conditions despite the significant differences in source conditions (particle volume fraction, particle size distribution, particle composition, temperature), residence times, plume conditions (e.g., humidity and temperature), and dynamics of fallout and deposition. Impact-generated and volcanic aggregates share many similarities, and in some cases may be indistinguishable without their stratigraphic context.

Process for producing an aggregate suitable for inclusion into a radiation shielding product

DOEpatents

Lessing, Paul A.; Kong, Peter C.

2000-01-01

The present invention is directed to methods for converting depleted uranium hexafluoride to a stable depleted uranium silicide in a one-step reaction. Uranium silicide provides a stable aggregate material that can be added to concrete to increase the density of the concrete and, consequently, shield gamma radiation. As used herein, the term "uranium silicide" is defined as a compound generically having the formula U.sub.x Si.sub.y, wherein the x represents the molecules of uranium and the y represent the molecules of silicon. In accordance with the present invention, uranium hexafluoride is converted to a uranium silicide by contacting the uranium hexafluoride with a silicon-containing material at a temperature in a range between about 1450.degree. C. and about 1750.degree. C. The stable depleted uranium silicide is included as an aggregate in a radiation shielding product, such as a concrete product.

Evolution of an adenine-copper cluster to a highly porous cuboidal framework: solution-phase ripening and gas-adsorption properties.

PubMed

Venkatesh, V; Pachfule, Pradip; Banerjee, Rahul; Verma, Sandeep

2014-09-15

The synthesis and directed evolution of a tetranuclear copper cluster, supported by 8-mercapto-N9-propyladenine ligand, to a highly porous three-dimensional cubic framework in the solid state is reported. The structure of this porous framework was unambiguously characterized by X-ray crystallography. The framework contains about 62 % solvent-accessible void; the presence of a free exocyclic amino group in the porous framework facilitates reversible adsorption of gas and solvent molecules. Oriented growth of framework in solution was also tracked by force and scanning electron microscopy studies, leading to identification of an intriguing ripening process, over a period of 30 days, which also revealed formation of cuboidal aggregates in solution. The elemental composition of these cuboidal aggregates was ascertained by EDAX analysis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electron impact excitation of the merocyanine molecule in the gas phase

NASA Astrophysics Data System (ADS)

Kulinich, A. V.; Ishchenko, A. A.; Kukhta, I. N.; Mitryukhin, L. K.; Kazakov, S. M.; Kukhta, A. V.

2018-03-01

Electronic transitions in a merocyanine dye were studied in the gas phase using electron energy loss spectroscopy and compared with the optical absorption spectra. It was found that the most intense band of the S1 ← S0 polymethine transition lies at 2.8 eV in vapor and 2.4 eV in n-hexane. Higher electronic transitions in the range of 3.7-7 eV were also analyzed. Besides, the singlet-triplet transition was revealed near 1.8 eV. TDDFT simulation of singlet-singlet transitions in the studied molecule was performed using B97D3, B3LYP, B3PW91 and wB97xD functionals. The calculated energy of the long-wavelength transition is closest to the experimental value with the latter. Other functionals result in the energy 0.2-0.4 eV exceeding experimental. The interpretation of higher transitions/bands is complicated due to their superposition and difference between experimental and calculated data. The excitation anisotropy spectra were measured in glycerol for more reliable determination of higher transitions and comparison with the TDDFT/PCM simulation.

Performance and durability of concrete made with demolition waste and artificial fly ash-clay aggregates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zakaria, M.; Cabrera, J.G.

1996-12-31

Demolition aggregates and artificial aggregates made with waste materials are two alternatives being studied for replacement of natural aggregates in the production of concrete. Natural aggregate sources in Europe are increasingly scarce and subject to restrictions based on environmental regulations. In many areas of the developing world sources of good quality aggregates are very limited or practically not available and therefore it has become necessary to study alternative materials. This paper presents a laboratory study on the use of demolition bricks and artificial aggregates made from fly ash-clay as coarse aggregates to make concrete. The concretes made either with demolitionmore » bricks or artificial aggregates are compared with a control mix made with natural gravel aggregates. The strength and durability characteristics of these concretes are evaluated using as a criteria compressive strength and transport properties, such as gas and water permeability. The results show clearly that concretes of good performance and durability can be produced using aggregates from demolition rubble or using artificial aggregates made with wastes such as fly ash.« less

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.

Molecular Dynamics Simulation Studies of Caffeine Aggregation in Aqueous Solution

PubMed Central

Tavagnacco, Letizia; Schnupf, Udo; Mason, Philip E.; Saboungi, Marie-Louise; Cesàro, Attilio; Brady, John W.

2011-01-01

Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly-developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molecules, which was not sensitive to the water model used. As expected, extensive aggregation of the caffeine molecules was observed, with the molecules stacking their flat faces against one another like coins, with their methylene groups staggered to avoid steric clashes. A dynamic equilibrum was observed between large n-mers, including stacks with all eight solute molecules, and smaller clusters, with the calculated osmotic coefficient being in acceptable agreement with the experimental value. The insensitivity of the results to water model and the congruence with experimental thermodynamic data suggest that the observed stacking interactions are a realistic representation of the actual association mechanism in aqueous caffeine solutions. PMID:21812485

Molecular dynamics simulation studies of caffeine aggregation in aqueous solution.

PubMed

Tavagnacco, Letizia; Schnupf, Udo; Mason, Philip E; Saboungi, Marie-Louise; Cesàro, Attilio; Brady, John W

2011-09-22

Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molecules, which was not sensitive to the water model used. As expected, extensive aggregation of the caffeine molecules was observed, with the molecules stacking their flat faces against one another like coins, with their methylene groups staggered to avoid steric clashes. A dynamic equilibrum was observed between large n-mers, including stacks with all eight solute molecules, and smaller clusters, with the calculated osmotic coefficient being in acceptable agreement with the experimental value. The insensitivity of the results to water model and the congruence with experimental thermodynamic data suggest that the observed stacking interactions are a realistic representation of the actual association mechanism in aqueous caffeine solutions.

Temperature dependence of aggregated structure of β-carotene by absorption spectral experiment and simulation

NASA Astrophysics Data System (ADS)

Lu, Liping; Wu, Jie; Wei, Liangshu; Wu, Fang

2016-12-01

β-carotene can self-assemble to form J- or H-type aggregate in hydrophilic environments, which is crucial for the proper functioning of biological system. Although several ways controlling the formation of the two types of aggregate in hydrated ethanol have been investigated in recent years, our study provided another way to control whether J- or H- β-carotene was formed and presented a method to investigate the aggregated structure. For this purpose, the aggregates of β-carotene formed at different temperatures were studied by UV-Vis spectra and a computational method based on Frenkel exciton was applied to simulate the absorption spectra to obtain the aggregated structure of the β-carotene. The analysis showed that β-carotene formed weakly coupled H-aggregate at 15 °C in 1:1 ethanol-water solvent, and with the increase of temperature it tended to form J-type of aggregate. The absorption spectral simulation based on one-dimensional Frenkel exciton model revealed that good fit with the experiment was obtained with distance between neighbor molecules r = 0.82 nm, disorder of the system D = 1500 cm- 1 for H-type and r = 1.04 nm, D = 1800 cm- 1 for J-type.

A Dynamic Study of Protein Secretion and Aggregation in the Secretory Pathway

PubMed Central

Mossuto, Maria Francesca; Sannino, Sara; Mazza, Davide; Fagioli, Claudio; Vitale, Milena; Yoboue, Edgar Djaha; Anelli, Tiziana

2014-01-01

Precise coordination of protein biogenesis, traffic and homeostasis within the early secretory compartment (ESC) is key for cell physiology. As a consequence, disturbances in these processes underlie many genetic and chronic diseases. Dynamic imaging methods are needed to follow the fate of cargo proteins and their interactions with resident enzymes and folding assistants. Here we applied the Halotag labelling system to study the behavior of proteins with different fates and roles in ESC: a chaperone, an ERAD substrate and an aggregation-prone molecule. Exploiting the Halo property of binding covalently ligands labelled with different fluorochromes, we developed and performed non-radioactive pulse and chase assays to follow sequential waves of proteins in ESC, discriminating between young and old molecules at the single cell level. In this way, we could monitor secretion and degradation of ER proteins in living cells. We can also follow the biogenesis, growth, accumulation and movements of protein aggregates in the ESC. Our data show that protein deposits within ESC grow by sequential apposition of molecules up to a given size, after which novel seeds are detected. The possibility of using ligands with distinct optical and physical properties offers a novel possibility to dynamically follow the fate of proteins in the ESC. PMID:25279560

A dynamic study of protein secretion and aggregation in the secretory pathway.

PubMed

Mossuto, Maria Francesca; Sannino, Sara; Mazza, Davide; Fagioli, Claudio; Vitale, Milena; Yoboue, Edgar Djaha; Sitia, Roberto; Anelli, Tiziana

2014-01-01

Precise coordination of protein biogenesis, traffic and homeostasis within the early secretory compartment (ESC) is key for cell physiology. As a consequence, disturbances in these processes underlie many genetic and chronic diseases. Dynamic imaging methods are needed to follow the fate of cargo proteins and their interactions with resident enzymes and folding assistants. Here we applied the Halotag labelling system to study the behavior of proteins with different fates and roles in ESC: a chaperone, an ERAD substrate and an aggregation-prone molecule. Exploiting the Halo property of binding covalently ligands labelled with different fluorochromes, we developed and performed non-radioactive pulse and chase assays to follow sequential waves of proteins in ESC, discriminating between young and old molecules at the single cell level. In this way, we could monitor secretion and degradation of ER proteins in living cells. We can also follow the biogenesis, growth, accumulation and movements of protein aggregates in the ESC. Our data show that protein deposits within ESC grow by sequential apposition of molecules up to a given size, after which novel seeds are detected. The possibility of using ligands with distinct optical and physical properties offers a novel possibility to dynamically follow the fate of proteins in the ESC.

Intra-aggregate CO2 enrichment: a modelling approach for aerobic soils

NASA Astrophysics Data System (ADS)

Schlotter, D.; Schack-Kirchner, H.

2013-02-01

CO2 concentration gradients inside soil aggregates, caused by the respiration of soil microorganisms and fungal hyphae, might lead to variations in the soil solution chemistry on a mm-scale, and to an underestimation of the CO2 storage. But, up to now, there seems to be no feasible method for measuring CO2 inside natural aggregates with sufficient spatial resolution. We combined a one-dimensional model for gas diffusion in the inter-aggregate pore space with a cylinder diffusion model, simulating the consumption/production and diffusion of O2 and CO2 inside soil aggregates with air- and water-filled pores. Our model predicts that for aerobic respiration (respiratory quotient = 1) the intra-aggregate increase in the CO2 partial pressure can never be higher than 0.9 kPa for siliceous, and 0.1 kPa for calcaric aggregates, independent of the level of water-saturation. This suggests that only for siliceous aggregates CO2 produced by aerobic respiration might cause a high small-scale spatial variability in the soil solution chemistry. In calcaric aggregates, however, the contribution of carbonate species to the CO2 transport should lead to secondary carbonates on the aggregate surfaces. As regards the total CO2 storage in aerobic soils, both siliceous and calcaric, the effect of intra-aggregate CO2 gradients seems to be negligible. To assess the effect of anaerobic respiration on the intra-aggregate CO2 gradients, the development of a device for measuring CO2 on a mm-scale in soils is indispensable.

Self-assembled nanoparticle aggregates: Organizing disorder for high performance surface-enhanced spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fasolato, C.; Center for Life Nanoscience@Sapienza, Istituto Italiano di Tecnologia, Rome; Domenici, F., E-mail: fabiodomenici@gmail.com

2015-06-23

The coherent oscillations of the surface electron gas, known as surface plasmons, in metal nanostructures can give rise to the localization of intense electromagnetic fields at the metal-dielectric interface. These strong fields are exploited in surface enhanced spectroscopies, such as Surface Enhanced Raman Scattering (SERS), for the detection and characterization of molecules at very low concentration. Still, the implementation of SERS-based biosensors requires a high level of reproducibility, combined with cheap and simple fabrication methods. For this purpose, SERS substrates based on self-assembled aggregates of commercial metallic nanoparticles (Nps) can meet all the above requests. Following this line, we reportmore » on a combined micro-Raman and Atomic Force Microscopy (AFM) analysis of the SERS efficiency of micrometric silver Np aggregates (enhancement factors up to 10{sup 9}) obtained by self-assembly. Despite the intrinsic disordered nature of these Np clusters, we were able to sort out some general rules relating the specific aggregate morphology to its plasmonic response. We found strong evidences of cooperative effects among the NPs within the cluster and namely a clear dependence of the SERS-efficiency on both the cluster area (basically linear) and the number of stacked NPs layers. A cooperative action among the superimposed layers has been proved also by electromagnetic simulations performed on simplified nanostructures consisting of stacking planes of ordered Nps. Being clear the potentialities of these disordered self-assembled clusters, in terms of both easy fabrication and signal enhancement, we developed a specific nanofabrication protocol, based on electron beam lithography and molecular functionalization, that allowed for a fine control of the Np assemblies into designed shapes fixing their area and height. In particular, we fabricated 2D ordered arrays of disordered clusters choosing gold Nps owing to their high stability. AFM

Fe-doped graphene nanosheet as an adsorption platform of harmful gas molecules (CO, CO2, SO2 and H2S), and the co-adsorption in O2 environments

NASA Astrophysics Data System (ADS)

Cortés-Arriagada, Diego; Villegas-Escobar, Nery; Ortega, Daniela E.

2018-01-01

The adsorption of pollutant gases (CO, CO2, SO2 and H2S) onto Fe-doped graphene nanosheets (FeG) is studied on the basis of density functional theory calculations at the PBE/Def2-SVP level of theory. The most stable adsorption configurations, binding characteristics, electronic properties and stability at room temperature of the FeG-Gas interactions is fully analyzed. The gas molecules are chemisorbed onto FeG with adsorption energies in the range of 0.54-1.8 eV, with an enhanced adsorption strength compared to intrinsic graphene. The stability of the FeG-Gas interactions is dominated by Lewis-acid-base interactions, and its strength is sorted as SO2 > CO > H2S > CO2. The adsorption stability is also retained at room temperature (300 K). Due to the strong interaction of SO2, CO, and H2S, FeG could catalyze or activate these gas molecules, suggesting the possibility of FeG as a catalyst substrate. The electron acceptor/donor character of CO, CO2, SO2 and H2S molecules when adsorbed onto FeG causes charge transfer processes that are responsible for the change in conductance of FeG; thus, the response of the HOMO-LUMO gap of FeG under gas adsorption could be useful for sensing applications. Furthermore, the analysis of the co-adsorption in O2 environments shows that the CO2 interaction turns unstable onto FeG, while the sensing response towards H2S is suppressed. Finally, these results give new insights into the emerging applications of Fe-doped graphene in gas capture/filtration devices, solid-state gas sensors or as a catalyst substrate.

Using bacterial inclusion bodies to screen for amyloid aggregation inhibitors.

PubMed

Villar-Piqué, Anna; Espargaró, Alba; Sabaté, Raimon; de Groot, Natalia S; Ventura, Salvador

2012-05-03

The amyloid-β peptide (Aβ42) is the main component of the inter-neuronal amyloid plaques characteristic of Alzheimer's disease (AD). The mechanism by which Aβ42 and other amyloid peptides assemble into insoluble neurotoxic deposits is still not completely understood and multiple factors have been reported to trigger their formation. In particular, the presence of endogenous metal ions has been linked to the pathogenesis of AD and other neurodegenerative disorders. Here we describe a rapid and high-throughput screening method to identify molecules able to modulate amyloid aggregation. The approach exploits the inclusion bodies (IBs) formed by Aβ42 when expressed in bacteria. We have shown previously that these aggregates retain amyloid structural and functional properties. In the present work, we demonstrate that their in vitro refolding is selectively sensitive to the presence of aggregation-promoting metal ions, allowing the detection of inhibitors of metal-promoted amyloid aggregation with potential therapeutic interest. Because IBs can be produced at high levels and easily purified, the method overcomes one of the main limitations in screens to detect amyloid modulators: the use of expensive and usually highly insoluble synthetic peptides.

Identifying Mechanisms of Interfacial Dynamics Using Single-Molecule Tracking

PubMed Central

Kastantin, Mark; Walder, Robert; Schwartz, Daniel K.

2012-01-01

The “soft” (i.e. non-covalent) interactions between molecules and surfaces are complex and highly-varied (e.g. hydrophobic, hydrogen bonding, ionic) often leading to heterogeneous interfacial behavior. Heterogeneity can arise either from spatial variation of the surface/interface itself or from molecular configurations (i.e. conformation, orientation, aggregation state, etc.). By observing adsorption, diffusion, and desorption of individual fluorescent molecules, single-molecule tracking can characterize these types of heterogeneous interfacial behavior in ways that are inaccessible to traditional ensemble-averaged methods. Moreover, the fluorescence intensity or emission wavelength (in resonance energy transfer experiments) can be used to simultaneously track molecular configuration and directly relate this to the resulting interfacial mobility or affinity. In this feature article, we review recent advances involving the use of single-molecule tracking to characterize heterogeneous molecule-surface interactions including: multiple modes of diffusion and desorption associated with both internal and external molecular configuration, Arrhenius activated interfacial transport, spatially dependent interactions, and many more. PMID:22716995

Mixing Behavior in Small Molecule: Fullerene Organic Photovoltaics [On the Mixing Behavior in Small Molecule: Fullerene Organic Photovoltaics

DOE PAGES

Oosterhout, Stefan D.; Savikhin, Victoria; Zhang, Junxiang; ...

2017-02-22

Here, we report a novel method to determine the amount of pure, aggregated phase of donor and acceptor in organic photovoltaic (OPV) bulk heterojunctions. By determination of the diffraction intensity per unit volume for both donor and acceptor, the volume content of pure, aggregated donor and acceptor in the blend can be determined. We find that for the small molecule X2:[6,6]-phenyl-C61-butyric acid methyl ester (PCBM) system, in contrast to most polymer systems, all the PCBM is aggregated, indicating there is negligible miscibility of PCBM with X2. This provides an explanation why the performance of OPV devices of X2:PCBM are highmore » over a large range of PCBM concentrations. This is in contrast to many other OPV blends, where PCBM forms a mixed phase with the donor and does not provide sufficient transport for electrons when the PCBM concentration is low. This study demonstrates that a mixed phase is not necessarily a requirement for good OPV device performance.« less

Molecular insights into early stage aggregation of di-Fmoc-L-lysine in binary mixture of organic solvent and water

NASA Astrophysics Data System (ADS)

Huda, Md Masrul; Rai, Neeraj

Molecular gels are relatively new class of soft materials, which are formed by the supramolecular aggregation of low molecular weight gelators (LMWGs) in organic solvents and/or water. Hierarchical self-assembly of small gelator molecules lead to three-dimensional complex fibrillar networks, which restricts the flow of solvents and results in viscous solid like materials or gels. These gels have drawn significant attentions for their potential applications for drug delivery, tissue engineering, materials for sensors etc. As of now, self-assembly of gelator molecules into one-dimensional fibers is not well understood, although that is very important to design new gelators for desired applications. Here, we present molecular dynamics study that provides molecular level insight into early stage aggregation of selected gelator, di-Fmoc-L-lysine in binary mixture of organic solvent and water. We will present the role of different functional groups of gelator molecule such as aromatic ring, amide, and carboxylic group on aggregation. We will also present the effect of concentrations of gelator and solvent on self-assembly of gelators. This study has captured helical fiber growth and branching of fiber, which is in good agreement with experimental observations.

Controlled Aggregation of Ferritin to Modulate MRI Relaxivity

PubMed Central

Bennett, Kevin M.; Shapiro, Erik M.; Sotak, Christopher H.; Koretsky, Alan P.

2008-01-01

Ferritin is an iron storage protein expressed in varying concentrations in mammalian cells. The deposition of ferric iron in the core of ferritin makes it a magnetic resonance imaging contrast agent, and ferritin has recently been proposed as a gene expression reporter protein for magnetic resonance imaging. To date, ferritin has been overexpressed in vivo and has been coexpressed with transferrin receptor to increase iron loading in cells. However, ferritin has a relatively low T2 relaxivity (R2 ≈ 1 mM−1s−1) at typical magnetic field strengths and so requires high levels of expression to be detected. One way to modulate the transverse relaxivity of a superparamagnetic agent is to cause it to aggregate, thereby manipulating the magnetic field gradients through which water diffuses. In this work, it is demonstrated by computer simulation and in vitro that aggregation of ferritin can alter relaxivity. The effects of aggregate size and intraaggregate perturber spacing on R2 are studied. Computer modeling indicates that the optimal spacing of the ferritin molecules in aggregate for increasing R2 is 100–200 nm for a typical range of water diffusion rates. Chemical cross-linking of ferritin at 12 Å spacing led to a 70% increase in R2 compared to uncross-linked ferritin controls. To modulate ferritin aggregation in a potentially biologically relevant manner, ferritin was attached to actin and polymerized in vitro. The polymerization of ferritin-F-actin caused a 20% increase in R2 compared to unpolymerized ferritin-G-actin. The R2-value was increased by another 10% by spacing the ferritin farther apart on the actin filaments. The modulation of ferritin aggregation by binding to cytoskeletal elements may be a useful strategy to make a functional reporter gene for magnetic resonance imaging. PMID:18326661

Dimension dependence of clustering dynamics in models of ballistic aggregation and freely cooling granular gas

NASA Astrophysics Data System (ADS)

Paul, Subhajit; Das, Subir K.

2018-03-01

Via event-driven molecular dynamics simulations we study kinetics of clustering in assemblies of inelastic particles in various space dimensions. We consider two models, viz., the ballistic aggregation model (BAM) and the freely cooling granular gas model (GGM), for each of which we quantify the time dependence of kinetic energy and average mass of clusters (that form due to inelastic collisions). These quantities, for both the models, exhibit power-law behavior, at least in the long time limit. For the BAM, corresponding exponents exhibit strong dimension dependence and follow a hyperscaling relation. In addition, in the high packing fraction limit the behavior of these quantities become consistent with a scaling theory that predicts an inverse relation between energy and mass. On the other hand, in the case of the GGM we do not find any evidence for such a picture. In this case, even though the energy decay, irrespective of packing fraction, matches quantitatively with that for the high packing fraction picture of the BAM, it is inversely proportional to the growth of mass only in one dimension, and the growth appears to be rather insensitive to the choice of the dimension, unlike the BAM.

α-Synuclein aggregation, seeding and inhibition by scyllo-inositol

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ibrahim, Tarek; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M4N 3M5, ON; McLaurin, JoAnne, E-mail: jmclaurin@sri.utoronto.ca

2016-01-15

Recent literature demonstrates the accelerated aggregation of α-synuclein, a protein implicated in the pathogenesis of Parkinson's disease (PD), by the presence of preformed fibrillar conformers in vitro. Furthermore, these preformed fibrillar seeds are suggested to accelerate pathological induction in vivo when injected into the brains of mice. Variation in the results of in vivo studies is proposed to be caused by α-synuclein conformational variants. To investigate the impact of amino acid sequence on seeding efficiency, human and mouse α-synuclein seeds, which vary at 7 amino acid residues, were generated and cross-seeding kinetics studied. Using transmission electron microscopy (TEM), we confirmed that mouse α-synucleinmore » aggregated more rapidly than human α-synuclein. Subsequently, we determined that seeding of human and mouse α-synuclein was more rapid in the presence of seeds generated from the same species. In addition, an established amyloid inhibitor, scyllo-inositol, was examined for potential inhibitory effects on α-synuclein aggregation. TEM analysis of protein:inhibitor assays demonstrated that scyllo-inositol inhibits the aggregation of α-synuclein, suggesting the therapeutic potential of the small molecule in PD. - Highlights: • Mouse α-syn fibrillizes in a significantly shorter timeframe than human α-syn. • Seeding of monomers is more efficient when seeds originate from the same species. • scyllo-Inositol has anti-aggregation effects on mouse and human α-syn.« less

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).

Sorption of small molecules in polymeric media

NASA Astrophysics Data System (ADS)

Camboni, Federico; Sokolov, Igor M.

2016-12-01

We discuss the sorption of penetrant molecules from the gas phase by a polymeric medium within a model which is very close in spirit to the dual sorption mode model: the penetrant molecules are partly dissolved within the polymeric matrix, partly fill the preexisting voids. The only difference with the initial dual sorption mode situation is the assumption that the two populations of molecules are in equilibrium with each other. Applying basic thermodynamics principles we obtain the dependence of the penetrant concentration on the pressure in the gas phase and find that this is expressed via the Lambert W-function, a different functional form than the one proposed by dual sorption mode model. The Lambert-like isotherms appear universally at low and moderate pressures and originate from the assumption that the internal energy in a polymer-penetrant-void ternary mixture is (in the lowest order) a bilinear form in the concentrations of the three components. Fitting the existing data shows that in the domain of parameters where the dual sorption mode model is typically applied, the Lambert function, which describes the same behavior as the one proposed by the gas-polymer matrix model, fits the data equally well.

The efficiency of photodissociation for molecules in interstellar ices

NASA Astrophysics Data System (ADS)

Kalvāns, J.

2018-05-01

Processing by interstellar photons affects the composition of the icy mantles on interstellar grains. The rate of photodissociation in solids differs from that of molecules in the gas phase. The aim of this work was to determine an average, general ratio between photodissociation coefficients for molecules in ice and gas. A 1D astrochemical model was utilized to simulate the chemical composition for a line of sight through a collapsing interstellar cloud core, whose interstellar extinction changes with time. At different extinctions, the calculated column densities of icy carbon oxides and ammonia (relative to water ice) were compared to observations. The latter were taken from literature data of background stars sampling ices in molecular clouds. The best-fit value for the solid/gas photodissociation coefficient ratio was found to be ≈0.3. In other words, gas-phase photodissociation rate coefficients have to be reduced by a factor of 0.3 before applying them to icy species. A crucial part of the model is a proper inclusion of cosmic-ray induced desorption. Observations sampling gas with total extinctions in excess of ≈22 mag were found to be uncorrelated to modelling results, possibly because of grains being covered with non-polar molecules.

Detection of ionized gas molecules in air by graphene and carbon nanotube networks

NASA Astrophysics Data System (ADS)

Hao, Ji; Li, Bo; Yung, Hyun Young; Liu, Fangze; Hong, Sanghyung; Jung, Yung Joon; Kar, Swastik

The liquid phase ions sensing by graphene and carbon nanotube has been demonstrated in many publications due to the minimum gate voltage easily shift induced by ionic gating effect, but it is still unclear for vapor phase ions sensing. Here we want to report that the ionized gas molecules in air can be also very sensitively detected by graphene and carbon nanotube networks under very low applied voltage, which shows the very high charge to current amplification factor, the value can be up to 108 A/C, and the direction of current-change can be used to differentiate the positive and negative ions. In further, the field effect of graphene device induced by vapor phase ions was discussed. NSF ECCS 1202376, NSF ECCS CAREER 1351424 and NSF DMREF 1434824, a Northeastern University Provost's Tier-1 seed Grant for interdisciplinary research, Technology Innovation Program (10050481) from Ministry of Trade, Industry & Energy of Republic of Korea.

Aggregate-based sub-CMC Solubilization of n-Alkanes by Monorhamnolipid Biosurfactant.

PubMed

Zhong, Hua; Yang, Xin; Tan, Fei; Brusseau, Mark L; Yang, Lei; Liu, Zhifeng; Zeng, Guangming; Yuan, Xingzhong

2016-03-01

Solubilization of n -decane, dodecane, tetradecane and hexadecane by monorhamnolipid biosurfactant (monoRL) at concentrations near the critical micelle concentration (CMC) was investigated. The apparent solubility of all the four alkanes increases linearly with increasing monoRL concentration either below or above CMC. The capacity of solubilization presented by the molar solubilization ratio (MSR), however, is stronger at monoRL concentrations below CMC than above CMC. The MSR decreases following the order dodecane > decane > tetradecane > hexadecane at monoRL concentration below CMC. Formation of aggregates at sub-CMC monoRL concentrations was demonstrated by dynamic light scattering (DLS) and cryo-transmission electron microscopy examination. DLS-based size ( d ) and zeta potential of the aggregates decrease with increasing monoRL concentration. The surface excess ( Γ ) of monoRL calculated based on alkane solubility and aggregate size data increases rapidly with increasing bulk monoRL concentration, and then asymptotically approaches the maximum surface excess ( Γ max ). Relation between Γ and d indicates that the excess of monoRL molecules at the aggregate surface greatly impacts the surface curvature. The results demonstrate formation of aggregates for alkane solubilization at monoRL concentrations below CMC, indicating the potential of employing low-concentration rhamnolipid for enhanced solubilization of hydrophobic organic compounds.

Biotin-streptavidin-induced aggregation of gold nanorods: tuning rod-rod orientation.

PubMed

Gole, Anand; Murphy, Catherine J

2005-11-08

We report herein biotin-streptavidin-mediated aggregation studies of long gold nanorods. We have previously demonstrated end-to-end linkages of gold nanorods driven by the biotin-streptavidin interaction (Caswell et al. J. Am. Chem. Soc. 2003, 125, 13914). In that report, the specific binding of biotin disulfide to the gold nanorod edges was achieved due to the preferred binding of thiol molecules to the Au[111] surface (gold nanorod ends) as opposed to the gold nanorod side faces. This led to the end-end linkage of gold nanorods upon subsequent addition of streptavidin. In this report we demonstrate a simple procedure to biotinylate the entire gold nanorod surface and subsequently form a 3-D assembly by addition of streptavidin. Gold nanorods were synthesized by the three-step seeding protocol documented in our previous articles. The surface of gold nanorods was further modified by a layer of a weak polyelectrolyte, poly(acrylic acid), PAA. A biotin molecule which has an amine group at one end (biotin-PEO-amine) was anchored to the carboxylic acid group of the polyelectrolyte using the well-known carbodiimide chemistry. This process biotinylates the entire gold nanorod surface. Addition of streptavidin further leads to aggregation of gold nanorods. A closer look at the aggregates reveals a preferential side-to-side assembly of gold nanorods. The gold nanorods were characterized at each stage by UV-vis spectroscopy, light scattering, and transmission electron microscopy (TEM) measurements.

Cellular Inclusion Bodies of Mutant Huntingtin Exon 1 Obscure Small Fibrillar Aggregate Species

PubMed Central

Sahl, Steffen J.; Weiss, Lucien E.; Duim, Whitney C.; Frydman, Judith; Moerner, W. E.

2012-01-01

The identities of toxic aggregate species in Huntington's disease pathogenesis remain ambiguous. While polyQ-expanded huntingtin (Htt) is known to accumulate in compact inclusion bodies inside neurons, this is widely thought to be a protective coping response that sequesters misfolded conformations or aggregated states of the mutated protein. To define the spatial distributions of fluorescently-labeled Htt-exon1 species in the cell model PC12m, we employed highly sensitive single-molecule super-resolution fluorescence imaging. In addition to inclusion bodies and the diffuse pool of monomers and oligomers, fibrillar aggregates ~100 nm in diameter and up to ~1–2 µm in length were observed for pathogenic polyQ tracts (46 and 97 repeats) after targeted photo-bleaching of the inclusion bodies. These short structures bear a striking resemblance to fibers described in vitro. Definition of the diverse Htt structures in cells will provide an avenue to link the impact of therapeutic agents to aggregate populations and morphologies. PMID:23193437

Aggregation Behavior and a Putative Aggregation Pheromone in Sugar Beet Root Maggot Flies (Diptera: Ulidiidae)

PubMed Central

Emmert, Susan Y.; Tindall, Kelly; Ding, Hongjian; Boetel, Mark A.; Rajabaskar, D.; Eigenbrode, Sanford D.

2017-01-01

Male-biased aggregations of sugar beet root maggot, Tetanops myopaeformis (Röder) (Diptera: Ulidiidae), flies were observed on utility poles near sugar beet (Beta vulgaris L. [Chenopodiaceae]) fields in southern Idaho; this contrasts with the approximately equal sex ratio typically observed within fields. Peak observation of mating pairs coincided with peak diurnal abundance of flies. Volatiles released by individual male and female flies were sampled from 08:00 to 24:00 hours in the laboratory using solid-phase microextraction and analyzed using gas chromatography/mass spectrometry (GC/MS). Eleven compounds were uniquely detected from males. Three of these compounds (2-undecanol, 2-decanol, and sec-nonyl acetate) were detected in greater quantities during 12:00–24:00 hours than during 08:00–12:00 hours. The remaining eight compounds uniquely detected from males did not exhibit temporal trends in release. Both sexes produced 2-nonanol, but males produced substantially higher (ca. 80-fold) concentrations of this compound than females, again peaking after 12:00 hours. The temporal synchrony among male aggregation behavior, peak mating rates, and release of certain volatile compounds by males suggest that T. myopaeformis flies exhibit lekking behavior and produce an associated pheromone. Field assays using synthetic blends of the putative aggregation pheromone showed evidence of attraction in both females and males. PMID:28423428

High-Throughput Multiplexed Quantitation of Protein Aggregation and Cytotoxicity in a Huntington’s Disease Model

PubMed Central

Titus, Steven A; Southall, Noel; Marugan, Juan; Austin, Christopher P; Zheng, Wei

2012-01-01

A hallmark of Huntington’s disease is the presence of a large polyglutamine expansion in the first exon of the Huntingtin protein and the propensity of protein aggregation by the mutant proteins. Aberrant protein aggregation also occurs in other polyglutamine expansion disorders, as well as in other neurodegenerative diseases including Parkinson’s, Alzheimer’s, and prion diseases. However, the pathophysiological role of these aggregates in the cell death that characterizes the diseases remains unclear. Identification of small molecule probes that modulate protein aggregation and cytotoxicity caused by aggregated proteins may greatly facilitate the studies on pathogenesis of these diseases and potentially lead to development of new therapies. Based on a detergent insoluble property of the Huntingtin protein aggregates, we have developed a homogenous assay to rapidly quantitate the levels of protein aggregates in a cellular model of Huntington’s disease. The protein aggregation assay has also been multiplexed with a protease release assay for the measurement of cytotoxicity resulting from aggregated proteins in the same cells. Through a testing screen of a compound library, we have demonstrated that this multiplexed cytotoxicity and protein aggregation assay has ability to identify active compounds that prevent cell death and/or modulate protein aggregation in cells of the Huntington’s disease model. Therefore, this multiplexed screening approach is also useful for development of high-throughput screening assays for other neurodegenerative diseases involving protein aggregation. PMID:23346268

Experimental volcanic ash aggregation: Internal structuring of accretionary lapilli and the role of liquid bonding

NASA Astrophysics Data System (ADS)

Mueller, Sebastian B.; Kueppers, Ulrich; Ayris, Paul M.; Jacob, Michael; Dingwell, Donald B.

2016-01-01

Explosive volcanic eruptions can release vast quantities of pyroclastic material into Earth's atmosphere, including volcanic ash, particles with diameters less than two millimeters. Ash particles can cluster together to form aggregates, in some cases reaching up to several centimeters in size. Aggregation alters ash transport and settling behavior compared to un-aggregated particles, influencing ash distribution and deposit stratigraphy. Accretionary lapilli, the most commonly preserved type of aggregates within the geologic record, can exhibit complex internal stratigraphy. The processes involved in the formation and preservation of these aggregates remain poorly constrained quantitatively. In this study, we simulate the variable gas-particle flow conditions which may be encountered within eruption plumes and pyroclastic density currents via laboratory experiments using the ProCell Lab System® of Glatt Ingenieurtechnik GmbH. In this apparatus, solid particles are set into motion in a fluidized bed over a range of well-controlled boundary conditions (particle concentration, air flow rate, gas temperature, humidity, liquid composition). Experiments were conducted with soda-lime glass beads and natural volcanic ash particles under a range of experimental conditions. Both glass beads and volcanic ash exhibited the capacity for aggregation, but stable aggregates could only be produced when materials were coated with high but volcanically-relevant concentrations of NaCl. The growth and structure of aggregates was dependent on the initial granulometry, while the rate of aggregate formation increased exponentially with increasing relative humidity (12-45% RH), before overwetting promoted mud droplet formation. Notably, by use of a broad granulometry, we generated spherical, internally structured aggregates similar to some accretionary pellets found in volcanic deposits. Adaptation of a powder-technology model offers an explanation for the origin of natural accretionary

Polyvinylpyrrolidone- (PVP-) coated silver aggregates for high performance surface-enhanced Raman scattering in living cells.

PubMed

Tan, Xuebin; Wang, Zhuyuan; Yang, Jing; Song, Chunyuan; Zhang, Ruohu; Cui, Yiping

2009-11-04

A biocompatible and stable surface-enhanced Raman scattering (SERS) probe has been successfully synthesized through a simple route with silver aggregates. Polyvinylpyrrolidone (PVP), a biocompatible polymer, was utilized to control the aggregation process and improve the chemical stability of the aggregates. Extinction spectroscopy and TEM results show the aggregation degree and core-shell structure of the probe. It is found that when we employ 4-mercaptobenzoic acid (4MBA), crystal violet (CV), Rhodamine 6G (R6G) or 4,4'-bipyridine molecules as Raman reporters, the SERS signal from the proposed probe can remain at a high level under aggressive chemical environments, even after being incorporated into living cells. In comparison with the traditional probes without the PVP shell, the new ones exhibit strong surface-enhanced effects and low toxicity towards living cells. We demonstrate that the PVP-coated silver aggregates are highly SERS effective, for which the fabrication protocol is advantageous in its simplicity and reproducibility.

Selective Encaging of N2O in N2O-N2 Binary Gas Hydrates via Hydrate-Based Gas Separation.

PubMed

Yang, Youjeong; Shin, Donghoon; Choi, Seunghyun; Woo, Yesol; Lee, Jong-Won; Kim, Dongseon; Shin, Hee-Young; Cha, Minjun; Yoon, Ji-Ho

2017-03-21

The crystal structure and guest inclusion behaviors of nitrous oxide-nitrogen (N 2 O-N 2 ) binary gas hydrates formed from N 2 O/N 2 gas mixtures are determined through spectroscopic analysis. Powder X-ray diffraction results indicate that the crystal structure of all the N 2 O-N 2 binary gas hydrates is identified as the structure I (sI) hydrate. Raman spectra for the N 2 O-N 2 binary gas hydrate formed from N 2 O/N 2 (80/20, 60/40, 40/60 mol %) gas mixtures reveal that N 2 O molecules occupy both large and small cages of the sI hydrate. In contrast, there is a single Raman band of N 2 O molecules for the N 2 O-N 2 binary gas hydrate formed from the N 2 O/N 2 (20/80 mol %) gas mixture, indicating that N 2 O molecules are trapped in only large cages of the sI hydrate. From temperature-dependent Raman spectra and the Predictive Soave-Redlich-Kwong (PSRK) model calculation, we confirm the self-preservation of N 2 O-N 2 binary gas hydrates in the temperature range of 210-270 K. Both the experimental measurements and the PSRK model calculations demonstrate the preferential occupation of N 2 O molecules rather than N 2 molecules in the hydrate cages, leading to a possible process for separating N 2 O from gas mixtures via hydrate formation. The phase equilibrium conditions, pseudo-pressure-composition (P-x) diagram, and gas storage capacity of N 2 O-N 2 binary gas hydrates are discussed in detail.

Singlet fission in linear chains of molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ambrosio, Francesco, E-mail: F.Ambrosio@warwick.ac.uk, E-mail: A.Troisi@warwick.ac.uk; Troisi, Alessandro, E-mail: F.Ambrosio@warwick.ac.uk, E-mail: A.Troisi@warwick.ac.uk

2014-11-28

We develop a model configuration interaction Hamiltonian to study the electronic structure of a chain of molecules undergoing singlet fission. We first consider models for dimer and trimer and then we use a matrix partitioning technique to build models of arbitrary size able to describe the relevant electronic structure for singlet fission in linear aggregates. We find that the multi-excitonic state (ME) is stabilized at short inter-monomer distance and the extent of this stabilization depends upon the size of orbital coupling between neighboring monomers. We also find that the coupling between ME states located on different molecules is extremely smallmore » leading to bandwidths in the order of ∼10 meV. This observation suggests that multi-exciton states are extremely localized by electron-phonon coupling and that singlet fission involves the transition between a relatively delocalized Frenkel exciton and a strongly localized multi-exciton state. We adopt the methodology commonly used to study non-radiative transitions to describe the singlet fission dynamics in these aggregates and we discuss the limit of validity of the approach. The results indicate that the phenomenology of singlet fission in molecular crystals is different in many important ways from what is observed in isolated dimers.« less

Properties of cold-bonded lightweight artificial aggregate containing bottom ash with different curing regime

NASA Astrophysics Data System (ADS)

Mohamad Ibrahim, Norlia; Nizar Ismail, Khairul; Che Amat, Roshazita; Mohamad Ghazali, Mohamad Iqbal

2018-03-01

Cold-bonded pelletizing technique is frequently used in aggregate manufacturing process as it can minimise the energy consumption. It has contributed to both economical and environmental advantages because it helps to reduce the gas emissions problems. Bottom ash collected from municipal solid waste incineration (MSWI) plant was selected as raw material in this study and was utilised as a partial replacement for cement for artificial aggregate production. Several percentage of ash replacement was selected ranged from 10 to 50%. Aggregate pellets were subjected to different types of curing condition which is room-water (RW), room-room (RR), oven-room (OR) and oven-water (OW) condition. Properties of aggregate pellets were examined to obtain its density, water absorption, aggregate impact value (AIV) and specific gravity (SG). The results indicated that the most efficient curing regime is by exposing the aggregate in RW condition. The optimum aggregate was selected at 20% where it has satisfied the required density of 739.5kg/m3, and classified as strong aggregate with AIV 14. However, the water absorption of aggregate increased proportionately with the increment of ash content.

Polymerization in the gas phase, in clusters, and on nanoparticle surfaces.

PubMed

El-Shall, M Samy

2008-07-01

Gas phase and cluster experiments provide unique opportunities to quantitatively study the effects of initiators, solvents, chain transfer agents, and inhibitors on the mechanisms of polymerization. Furthermore, a number of important phenomena, unique structures, and novel properties may exist during gas-phase and cluster polymerization. In this regime, the structure of the growing polymer may change dramatically and the rate coefficient may vary significantly upon the addition of a single molecule of the monomer. These changes would be reflected in the properties of the oligomers deposited from the gas phase. At low pressures, cationic and radical cationic polymerizations may proceed in the gas phase through elimination reactions. In the same systems at high pressure, however, the ionic intermediates may be stabilized, and addition without elimination may occur. In isolated van der Waals clusters of monomer molecules, sequential polymerization with several condensation steps can occur on a time scale of a few microseconds following the ionization of the gas-phase cluster. The cluster reactions, which bridge gas-phase and condensed-phase chemistry, allow examination of the effects of controlled states of aggregation. This Account describes several examples of gas-phase and cluster polymerization studies where the most significant results can be summarized as follows: (1) The carbocation polymerization of isobutene shows slower rates with increasing polymerization steps resulting from entropy barriers, which could explain the need for low temperatures for the efficient propagation of high molecular weight polymers. (2) Radical cation polymerization of propene can be initiated by partial charge transfer from an ionized aromatic molecule such as benzene coupled with covalent condensation of the associated propene molecules. This novel mechanism leads exclusively to the formation of propene oligomer ions and avoids other competitive products. (3) Structural information

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

Low-refractive-index dye-aggregate films with small absorption based on anomalous dispersion.

PubMed

Wakamatsu, Takashi; Watanabe, Keita; Saito, Kazuhiro

2005-02-20

Complex-refractive-index spectra of Squarylium (SQ) dye-aggregate films deposited upon metal films have been investigated by measurements of properties of the films including absorption spectra (AS) and attenuated total reflection. Complex refractive indices are estimated by Kramers-Kronig analysis for the AS and by a theoretical curve-fitting analysis for attenuated total reflection. The dye-aggregate films exhibited an absorption that was blueshifted from that of a monomer, as a result of the H-aggregate formation of SQ molecules, and had a changing refractive index with anomalous dispersion about the H-absorption band. From both measurements of the SQ films it was found that there is a region of low absorption in the short-wavelength side of the absorption band and that the refractive index there is lower than that of glass.

Low-refractive-index dye-aggregate films with small absorption based on anomalous dispersion

NASA Astrophysics Data System (ADS)

Wakamatsu, Takashi; Watanabe, Keita; Saito, Kazuhiro

2005-02-01

Complex-refractive-index spectra of Squarylium (SQ) dye-aggregate films deposited upon metal films have been investigated by measurements of properties of the films including absorption spectra (AS) and attenuated total reflection. Complex refractive indices are estimated by Kramers-Kronig analysis for the AS and by a theoretical curve-fitting analysis for attenuated total reflection. The dye-aggregate films exhibited an absorption that was blueshifted from that of a monomer, as a result of the H-aggregate formation of SQ molecules, and had a changing refractive index with anomalous dispersion about the H-absorption band. From both measurements of the SQ films it was found that there is a region of low absorption in the short-wavelength side of the absorption band and that the refractive index there is lower than that of glass.

Gas-controlled dynamic vacuum insulation with gas gate

DOEpatents

Benson, David K.; Potter, Thomas F.

1994-06-07

Disclosed is a dynamic vacuum insulation comprising sidewalls enclosing an evacuated chamber and gas control means for releasing hydrogen gas into a chamber to increase gas molecule conduction of heat across the chamber and retrieving hydrogen gas from the chamber. The gas control means includes a metal hydride that absorbs and retains hydrogen gas at cooler temperatures and releases hydrogen gas at hotter temperatures; a hydride heating means for selectively heating the metal hydride to temperatures high enough to release hydrogen gas from the metal hydride; and gate means positioned between the metal hydride and the chamber for selectively allowing hydrogen to flow or not to flow between said metal hydride and said chamber.

Gas-controlled dynamic vacuum insulation with gas gate

DOEpatents

Benson, D.K.; Potter, T.F.

1994-06-07

Disclosed is a dynamic vacuum insulation comprising sidewalls enclosing an evacuated chamber and gas control means for releasing hydrogen gas into a chamber to increase gas molecule conduction of heat across the chamber and retrieving hydrogen gas from the chamber. The gas control means includes a metal hydride that absorbs and retains hydrogen gas at cooler temperatures and releases hydrogen gas at hotter temperatures; a hydride heating means for selectively heating the metal hydride to temperatures high enough to release hydrogen gas from the metal hydride; and gate means positioned between the metal hydride and the chamber for selectively allowing hydrogen to flow or not to flow between said metal hydride and said chamber. 25 figs.

Inhibition of p53 Mutant Peptide Aggregation In Vitro by Cationic Osmolyte Acetylcholine Chloride.

PubMed

Chen, Zhaolin; Kanapathipillai, Mathumai

2017-01-01

Mutations of tumor suppressor protein p53 are present in almost about 50% of all cancers. It has been reported that the p53 mutations cause aggregation and subsequent loss of p53 function, leading to cancer progression. Here in this study we focus on the inhibitory effects of cationic osmolyte molecules acetylcholine chloride, and choline on an aggregation prone 10 amino acid p53 mutant peptide WRPILTIITL, and the corresponding wildtype peptide RRPILTIITL in vitro. The characterization tools used for this study include Thioflavin- T (ThT) induced fluorescence, transmission electron microscopy (TEM), congo red binding, turbidity, dynamic light scattering (DLS), and cell viability assays. The results show that acetylcholine chloride in micromolar concentrations significantly inhibit p53 mutant peptide aggregation in vitro, and could be promising candidate for p53 mutant/ misfolded protein aggregation inhibition. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Dynamics of soil biogeochemical gas emissions shaped by remolded aggregate sizes and carbon configurations under hydration cycles.

PubMed

Ebrahimi, Ali; Or, Dani

2018-01-01

Changes in soil hydration status affect microbial community dynamics and shape key biogeochemical processes. Evidence suggests that local anoxic conditions may persist and support anaerobic microbial activity in soil aggregates (or in similar hot spots) long after the bulk soil becomes aerated. To facilitate systematic studies of interactions among environmental factors with biogeochemical emissions of CO 2 , N 2 O and CH 4 from soil aggregates, we remolded silt soil aggregates to different sizes and incorporated carbon at different configurations (core, mixed, no addition). Assemblies of remolded soil aggregates of three sizes (18, 12, and 6 mm) and equal volumetric proportions were embedded in sand columns at four distinct layers. The water table level in each column varied periodically while obtaining measurements of soil GHG emissions for the different aggregate carbon configurations. Experimental results illustrate that methane production required prolonged inundation and highly anoxic conditions for inducing measurable fluxes. The onset of unsaturated conditions (lowering water table) resulted in a decrease in CH 4 emissions while temporarily increasing N 2 O fluxes. Interestingly, N 2 O fluxes were about 80% higher form aggregates with carbon placement in center (anoxic) core compared to mixed carbon within aggregates. The fluxes of CO 2 were comparable for both scenarios of carbon sources. These experimental results highlight the importance of hydration dynamics in activating different GHG production and affecting various transport mechanisms about 80% of total methane emissions during lowering water table level are attributed to physical storage (rather than production), whereas CO 2 emissions (~80%) are attributed to biological activity. A biophysical model for microbial activity within soil aggregates and profiles provides a means for results interpretation and prediction of trends within natural soils under a wide range of conditions. © 2017 John

The physical basis for absorption of light. [effects on wave functions of gas molecules and atoms

NASA Technical Reports Server (NTRS)

Pickett, H. M.

1979-01-01

The effects of light absorption on the wave functions of gas-phase molecules and atoms are investigated by high resolution spectral measurements of radiation emerging from a sample. A Stark-modulated sample of methyl fluoride was irradiated at the 102 GHz rotational transition and the emergent radiation was resolved by means of a spectrum analyzer. For signal oscillator frequencies below or above the molecular resonance by one modulation frequency, the amplitudes of the upper and lower modulation sidebands are found to be of nonuniform intensity, which is inconsistent with amplitude modulation. Emission due to polarization is, however, calculated to be consistent with the results observed, indicating that light absorption should be considered as a subtractive stimulated emission.

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.

Detection of IgG aggregation by a high throughput method based on extrinsic fluorescence.

PubMed

He, Feng; Phan, Duke H; Hogan, Sabine; Bailey, Robert; Becker, Gerald W; Narhi, Linda O; Razinkov, Vladimir I

2010-06-01

The utility of extrinsic fluorescence as a tool for high throughput detection of monoclonal antibody aggregates was explored. Several IgG molecules were thermally stressed and the high molecular weight species were fractionated using size-exclusion chromatography (SEC). The isolated aggregates and monomers were studied by following the fluorescence of an extrinsic probe, SYPRO Orange. The dye displayed high sensitivity to structurally altered, aggregated IgG structures compared to the native form, which resulted in very low fluorescence in the presence of the dye. An example of the application is presented here to demonstrate the properties of this detection method. The fluorescence assay was shown to correlate with the SEC method in quantifying IgG aggregates. The fluorescent probe method appears to have potential to detect protein particles that could not be analyzed by SEC. This method may become a powerful high throughput tool to detect IgG aggregates in pharmaceutical solutions and to study other protein properties involving aggregation. It can also be used to study the kinetics of antibody particle formation, and perhaps allow identification of the species, which are the early building blocks of protein particles. (c) 2009 Wiley-Liss, Inc. and the American Pharmacists Association

Polarized hydrogen/deuterium molecules

NASA Astrophysics Data System (ADS)

Shestakov, Yu V.; Nikolenko, D. M.; Rachek, I. A.; Sadykov, R. Sh; Toporkov, D. K.; Yurchenko, A. V.; Zevakov, S. A.

2017-12-01

The prototype of a polarized molecular hydrogen/deuterium source which is based on the classical Stern-Gerlach separation scheme has been tested at the Budker Institute of Nuclear Physics (BINP), Novosibirsk. It consists of the circular slit nozzle cooled down to 6.5 K and the two superconducting sextupole magnets. The flux of polarized hydrogen molecules of 3·1012 mol/s was measured for a total gas flow through the nozzle of 5·10-2 Torr·l/s. The obtained results will be used to develop a much more intense source of polarized molecules.

The role of healed N-vacancy defective BC2N sheet and nanotube by NO molecule in oxidation of NO and CO gas molecules

NASA Astrophysics Data System (ADS)

Nematollahi, Parisa; Esrafili, Mehdi D.; Neyts, Erik C.

2018-06-01

In this study, the healing of N-vacancy boron carbonitride nanosheet (NV-BC2NNS) and nanotube (NV-BC2NNT) by NO molecule is studied by means of density functional theory calculations. Two different N-vacancies are considered in each of these structures in which the vacancy site is surrounded by either three B-atoms (NB) or by two B- and one C-atom (NBC). By means of the healed BC2NNS and BC2NNT as a support, the removal of two toxic gas molecules (NO and CO) are applicable. It should be noted that the obtained energy barriers of both healing and oxidizing processes are significantly lower than those of graphene, carbon nanotubes or boron nitride nanostructures. Also, at the end of the oxidation process, the pure BC2NNS or BC2NNT is obtained without any additional defects. Therefore, by using this method, we can considerably purify the defective BC2NNS/BC2NNT. Moreover, according to the thermochemistry calculations we can further confirm that the healing process of the NV-BC2NNS and NV-BC2NNT by NO are feasible at room temperature. So, we can claim that this study could be very helpful in both purifying the defective BC2NNS/BC2NNT while in the same effort removing toxic NO and CO gases.

Aggregate development in C 60/N-methyl-2-pyrrolidone solution and its mixture with water as revealed by extraction and mass spectroscopy

NASA Astrophysics Data System (ADS)

Kyzyma, O. A.; Korobov, M. V.; Avdeev, M. V.; Garamus, V. M.; Snegir, S. V.; Petrenko, V. I.; Aksenov, V. L.; Bulavin, L. A.

2010-06-01

The aggregate development in C 60/N-methyl-2-pyrrolidone (C 60/NMP) solution with time is studied by the extraction (hexane) and mass spectroscopy. It is shown that only molecular C 60 in NMP is extracted in hexane, which makes it possible to follow a change in the concentration of non-aggregated fullerene in C 60/NMP during the aggregate growth. It is concluded that almost all fullerene dissolved in NMP is in the aggregates after one month. The reorganization of the aggregates is detected when water is added to the aggregated solution C 60/NMP. Both methods prove that in this case individual fullerene molecules are detached from the aggregates, which contradicts somewhat to complete insolubility of C 60 in water.

Laser desorption vs. electrospray of polyyne-threaded rotaxanes: Preventing covalent cross-linking and promoting noncovalent aggregation

NASA Astrophysics Data System (ADS)

Neugebauer, Thomas S.; Franz, Michael; Frankenberger, Stephanie; Tykwinski, Rik R.; Drewello, Thomas

2018-02-01

Laser-induced cross-linking of polyynes is successfully hindered when the polyyne is encapsulated as part of a rotaxane and therefore protected by a surrounding macrocycle. When the rotaxane is electrosprayed, however, noncovalent aggregate ions are efficiently formed. Aggregates of considerable size (including more than 50 rotaxane molecules with masses beyond 100k Da) and charge states (up to 13 charges and beyond) have been observed. Either protons or sodium cations act as the charge carriers. These aggregates are not formed when the individual components of the rotaxane, i.e., the macrocycle or the polyyne, are separately electrosprayed. This underlines the structural importance of the rotaxane for the aggregate formation. Straightforward force field calculations indicate that the polyyne thread hinders the folding of the macrocycles, which facilitates the bonding interaction between the two components.

Exploring the structural diversity in inhibitors of α-synuclein amyloidogenic folding, aggregation and neurotoxicity

NASA Astrophysics Data System (ADS)

Das, Sukanya; Pukala, Tara L.; Smid, Scott D.

2018-05-01

Aggregation of α-Synuclein (αS) protein to amyloid fibrils is a neuropathological hallmark of Parkinson’s disease (PD). Growing evidence suggests that extracellular αS aggregation plays a pivotal role in neurodegeneration found in PD in addition to the intracellular αS aggregates in Lewy bodies (LB). Here, we identified and compared a diverse set of molecules capable of mitigating protein aggregation and exogenous toxicity of αSA53T, a more aggregation-prone αS mutant found in familial PD. For the first time, we investigated the αS anti-amyloid activity of semi-synthetic flavonoid 2', 3', 4' trihydroxyflavone or 2-D08, which was compared with natural flavones myricetin and transilitin, as well as such structurally diverse polyphenols as honokiol and punicalagin. Additionally, two novel synthetic compounds with a dibenzyl imidazolidine scaffold, Compound 1 and Compound 2, were also investigated as they exhibited favourable binding with αSA53T. All seven compounds inhibited αSA53T aggregation as demonstrated by Thioflavin T fluorescence assays, with modified fibril morphology observed by transmission electron microscopy. Ion mobility-mass spectrometry (IM-MS) was used to monitor the structural conversion of native αSA53T into amyloidogenic conformations and all seven compounds preserved the native unfolded conformations of αSA53T following 48 hrs incubation. The presence of each test compound in a 1:2 molar ratio was also shown to inhibit the neurotoxicity of preincubated αSA53T using phaeochromocytoma (PC12) cell viability assays. Among the seven tested compounds 2-D08, honokiol and the synthetic Compound 2 demonstrated the highest inhibition of aggregation, coupled with neuroprotection from preincubated αSA53T in vitro. Molecular docking predicted that all compounds bound near the lysine-rich region of the N-terminus of αSA53T, where the flavonoids and honokiol predominantly interacted with Lys 23. Overall, these findings highlight that i

Controlling Plasmon-Enhanced Fluorescence via Intersystem Crossing in Photoswitchable Molecules.

PubMed

Wang, Mingsong; Hartmann, Gregory; Wu, Zilong; Scarabelli, Leonardo; Rajeeva, Bharath Bangalore; Jarrett, Jeremy W; Perillo, Evan P; Dunn, Andrew K; Liz-Marzán, Luis M; Hwang, Gyeong S; Zheng, Yuebing

2017-10-01

By harnessing photoswitchable intersystem crossing (ISC) in spiropyran (SP) molecules, active control of plasmon-enhanced fluorescence in the hybrid systems of SP molecules and plasmonic nanostructures is achieved. Specifically, SP-derived merocyanine (MC) molecules formed by photochemical ring-opening reaction display efficient ISC due to their zwitterionic character. In contrast, ISC in quinoidal MC molecules formed by thermal ring-opening reaction is negligible. The high ISC rate can improve fluorescence quantum yield of the plasmon-modified spontaneous emission, only when the plasmonic electromagnetic field enhancement is sufficiently high. Along this line, extensive photomodulation of fluorescence is demonstrated by switching the ISC in MC molecules at Au nanoparticle aggregates, where strongly enhanced plasmonic hot spots exist. The ISC-mediated plasmon-enhanced fluorescence represents a new approach toward controlling the spontaneous emission of fluorophores near plasmonic nanostructures, which expands the applications of active molecular plasmonics in information processing, biosensing, and bioimaging. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Protein aggregation and particle formation in prefilled glass syringes.

PubMed

Gerhardt, Alana; Mcgraw, Nicole R; Schwartz, Daniel K; Bee, Jared S; Carpenter, John F; Randolph, Theodore W

2014-06-01

The stability of therapeutic proteins formulated in prefilled syringes (PFS) may be negatively impacted by the exposure of protein molecules to silicone oil-water interfaces and air-water interfaces. In addition, agitation, such as that experienced during transportation, may increase the detrimental effects (i.e., protein aggregation and particle formation) of protein interactions with interfaces. In this study, surfactant-free formulations containing either a monoclonal antibody or lysozyme were incubated in PFS, where they were exposed to silicone oil-water interfaces (siliconized syringe walls), air-water interfaces (air bubbles), and agitation stress (occurring during end-over-end rotation). Using flow microscopy, particles (≥2 μm diameter) were detected under all conditions. The highest particle concentrations were found in agitated, siliconized syringes containing an air bubble. The particles formed in this condition consisted of silicone oil droplets and aggregated protein, as well as agglomerates of protein aggregates and silicone oil. We propose an interfacial mechanism of particle generation in PFS in which capillary forces at the three-phase (silicone oil-water-air) contact line remove silicone oil and gelled protein aggregates from the interface and transport them into the bulk. This mechanism explains the synergistic effects of silicone oil-water interfaces, air-water interfaces, and agitation in the generation of particles in protein formulations. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Vitamin k3 inhibits protein aggregation: Implication in the treatment of amyloid diseases

PubMed Central

Alam, Parvez; Chaturvedi, Sumit Kumar; Siddiqi, Mohammad Khursheed; Rajpoot, Ravi Kant; Ajmal, Mohd Rehan; Zaman, Masihuz; Khan, Rizwan Hasan

2016-01-01

Protein misfolding and aggregation have been associated with several human diseases such as Alzheimer’s, Parkinson’s and familial amyloid polyneuropathy etc. In this study, anti-fibrillation activity of vitamin k3 and its effect on the kinetics of amyloid formation of hen egg white lysozyme (HEWL) and Aβ-42 peptide were investigated. Here, in combination with Thioflavin T (ThT) fluorescence assay, circular dichroism (CD), transmission electron microscopy and cell cytotoxicity assay, we demonstrated that vitamin k3 significantly inhibits fibril formation as well as the inhibitory effect is dose dependent manner. Our experimental studies inferred that vitamin k3 exert its neuro protective effect against amyloid induced cytotoxicity through concerted pathway, modifying the aggregation formation towards formation of nontoxic aggregates. Molecular docking demonstrated that vitamin k3 mediated inhibition of HEWL and Aβ-42 fibrillogenesis may be initiated by interacting with proteolytic resistant and aggregation prone regions respectively. This work would provide an insight into the mechanism of protein aggregation inhibition by vitamin k3; pave the way for discovery of other small molecules that may exert similar effect against amyloid formation and its associated neurodegenerative diseases. PMID:27230476

Vitamin k3 inhibits protein aggregation: Implication in the treatment of amyloid diseases.

PubMed

Alam, Parvez; Chaturvedi, Sumit Kumar; Siddiqi, Mohammad Khursheed; Rajpoot, Ravi Kant; Ajmal, Mohd Rehan; Zaman, Masihuz; Khan, Rizwan Hasan

2016-05-27

Protein misfolding and aggregation have been associated with several human diseases such as Alzheimer's, Parkinson's and familial amyloid polyneuropathy etc. In this study, anti-fibrillation activity of vitamin k3 and its effect on the kinetics of amyloid formation of hen egg white lysozyme (HEWL) and Aβ-42 peptide were investigated. Here, in combination with Thioflavin T (ThT) fluorescence assay, circular dichroism (CD), transmission electron microscopy and cell cytotoxicity assay, we demonstrated that vitamin k3 significantly inhibits fibril formation as well as the inhibitory effect is dose dependent manner. Our experimental studies inferred that vitamin k3 exert its neuro protective effect against amyloid induced cytotoxicity through concerted pathway, modifying the aggregation formation towards formation of nontoxic aggregates. Molecular docking demonstrated that vitamin k3 mediated inhibition of HEWL and Aβ-42 fibrillogenesis may be initiated by interacting with proteolytic resistant and aggregation prone regions respectively. This work would provide an insight into the mechanism of protein aggregation inhibition by vitamin k3; pave the way for discovery of other small molecules that may exert similar effect against amyloid formation and its associated neurodegenerative diseases.

Aggregation Properties and Liquid Crystal Phase of a Dye Based on Naphthalenetetracarboxylic Acid

NASA Astrophysics Data System (ADS)

Tomasik, Michelle; Collings, Peter

2007-03-01

R003 is a dye produced for thin film optical components by Optiva, Inc.^1 made from the sulfonation of the dibenzimidazole derivative of naphthalenetetracarboxylic acid. Its molecular structure is very different from the aggregating food dye previously investigated in our laboratory^2 and R003 forms a liquid crystal phase at significantly lower concentrations. We have performed polarizing microscopy, absorption spectroscopy, and x-ray diffraction experiments in order to determine the phase diagram and aggregate structure. In addition, we have included both translational and orientational entropy in the theoretical analysis of the aggregation process, and have used a more realistic lineshape in analyzing the absorption data. Our results indicate that the ``bond energy'' for molecules in an aggregate is even larger than for the previously studied dye and that the aggregate structure has a cross-sectional area equal to two or three molecular areas rather than one.^1Lazarev, P., N. Ovchinnikova, M. Paukshto, SID Int. Symp. Digest of Tech. Papers, San Jose, California, June XXXII, 571 (2001).^2V. R. Horowitz, L. A. Janowitz, A. L. Modic, P. A. Heiney, and P. J. Collings, Phys. Rev. E 72, 041710 (2005).

Aggregation Number in Water/n-Hexanol Molecular Clusters Formed in Cyclohexane at Different Water/n-Hexanol/Cyclohexane Compositions Calculated by Titration 1H NMR.

PubMed

Flores, Mario E; Shibue, Toshimichi; Sugimura, Natsuhiko; Nishide, Hiroyuki; Moreno-Villoslada, Ignacio

2017-11-09

Upon titration of n-hexanol/cyclohexane mixtures of different molar compositions with water, water/n-hexanol clusters are formed in cyclohexane. Here, we develop a new method to estimate the water and n-hexanol aggregation numbers in the clusters that combines integration analysis in one-dimensional 1 H NMR spectra, diffusion coefficients calculated by diffusion-ordered NMR spectroscopy, and further application of the Stokes-Einstein equation to calculate the hydrodynamic volume of the clusters. Aggregation numbers of 5-15 molecules of n-hexanol per cluster in the absence of water were observed in the whole range of n-hexanol/cyclohexane molar fractions studied. After saturation with water, aggregation numbers of 6-13 n-hexanol and 0.5-5 water molecules per cluster were found. O-H and O-O atom distances related to hydrogen bonds between donor/acceptor molecules were theoretically calculated using density functional theory. The results show that at low n-hexanol molar fractions, where a robust hydrogen-bond network is held between n-hexanol molecules, addition of water makes the intermolecular O-O atom distance shorter, reinforcing molecular association in the clusters, whereas at high n-hexanol molar fractions, where dipole-dipole interactions dominate, addition of water makes the intermolecular O-O atom distance longer, weakening the cluster structure. This correlates with experimental NMR results, which show an increase in the size and aggregation number in the clusters upon addition of water at low n-hexanol molar fractions, and a decrease of these magnitudes at high n-hexanol molar fractions. In addition, water produces an increase in the proton exchange rate between donor/acceptor molecules at all n-hexanol molar fractions.

Calcium oxalate monohydrate aggregation induced by aggregation of desialylated Tamm-Horsfall protein

PubMed Central

Viswanathan, Pragasam; Rimer, Jeffrey D.; Kolbach, Ann M.; Kleinman, Jack G.

2011-01-01

Tamm-Horsfall protein (THP) is thought to protect against calcium oxalate monohydrate (COM) stone formation by inhibiting COM aggregation. Several studies reported that stone formers produce THP with reduced levels of glycosylation, particularly sialic acid levels, which leads to reduced negative charge. In this study, normal THP was treated with neuraminidase to remove sialic acid residues, confirmed by an isoelectric point shift to higher pH. COM aggregation assays revealed that desialylated THP (ds-THP) promoted COM aggregation, while normal THP inhibited aggregation. The appearance of protein aggregates in solutions at ds-THP concentrations ≥1 µg/mL in 150 mM NaCl correlated with COM aggregation promotion, implying that ds-THP aggregation induced COM aggregation. The aggregation-promoting effect of the ds-THP was independent of pH above its isoelectric point, but was substantially reduced at low ionic strength, where protein aggregation was much reduced. COM aggregation promotion was maximized at a ds-THP to COM mass ratio of ~0.025, which can be explained by a model wherein partial COM surface coverage by ds-THP aggregates promotes crystal aggregation by bridging opposing COM surfaces, whereas higher surface coverage leads to repulsion between adsorbed ds-THP aggregates. Thus, desialylation of THP apparently abrogates a normal defensive action of THP by inducing protein aggregation, and subsequently COM aggregation, a condition that favors kidney stone formation. PMID:21229239

New Occurrence of Shocked Graphite Aggregates at Barringer Crater

NASA Astrophysics Data System (ADS)

Miura, Y.; Noma, Y.; Iancu, O. G.

1993-07-01

High-pressure carbon minera]s are considered to be formed by solid-solid transformation under static or impact high-pressure condition, but shocked quartz aggregates of impact craters are considered to be formed by quenched accretion of various aggregates by dynamic impact process [1-3]. The main purpose of this study is to elucidate new findings and occurrences of shocked graphite (SG) aggregates [2,3] at the Barringer meteorite crater. The graphite nodule block of Barringer Crater used in this study is collected near the rim. The sample is compared with standard graphite samples of Korea, Madagascar, and artificial impact graphites. There are four different mineral aggregates of the Barringer graphite nodule sample: (1) shocked graphite-1, (2) shocked graphite-2 and hexagonal diamond in the vein, (3) shocked quartz-1 (with kamacite) in the rim, and (4) calcite in the rim (Table 1). X-ray diffraction peaks of shocked graphite reveal low X-ray intensity, high Bragg-angle shift of X-ray diffraction peak, and multiple splitting of X-ray diffraction peaks. X-ray calculated density (rho) has been determined by X-ray diffractometer by the equation of density deviation Delta rho (%) = 100 x {(rho-rho(sub)0)/rho(sub)0}, where standard density rho(sub)0 is 2.255 g/cm^3 in Korean graphite [2,3]. The high-density value of shocked graphite grain obtained in Barringer is Delta rho = +0.6 +/- 0.1%. Shocked hexagonal diamonds (chaoite) show a high value of Delta rho = +0.6 +/- 0.9%. Analytical electron microscopy data reveal three different aggregates in the graphite nodule samples (Table 1): (1) shocked graphite-1 in the matrix, which contains uniformly Fe and Ca elements formed under gas state; (2) shocked graphite-2 in the vein, where crystallized shocked graphites and hexagonal diamonds are surrounded by kamacite-rich metals formed under gas-melt states of mixed compositions from iron meteorite and target rocks; and (3) shocked quartz-1 and kamacite in the rim, where

Determination of external and internal mass transfer limitation in nitrifying microbial aggregates.

PubMed

Wilén, Britt-Marie; Gapes, Daniel; Keller, Jürg

2004-05-20

In this article we present a study of the effects of external and internal mass transfer limitation of oxygen in a nitrifying system. The oxygen uptake rates (OUR) were measured on both a macro-scale with a respirometric reactor using off-gas analysis (Titrimetric and Off-Gas Analysis (TOGA) sensor) and on a micro-scale with microsensors. These two methods provide independent, accurate measurements of the reaction rates and concentration profiles around and in the granules. The TOGA sensor and microsensor measurements showed a significant external mass transfer effect at low dissolved oxygen (DO) concentrations in the bulk liquid while it was insignificant at higher DO concentrations. The oxygen distribution with anaerobic or anoxic conditions in the center clearly shows major mass transfer limitation in the aggregate interior. The large drop in DO concentration of 22-80% between the bulk liquid and aggregate surface demonstrates that the external mass transfer resistance is also highly important. The maximum OUR even for floccular biomass was only attained at much higher DO concentrations (approximately 8 mg/L) than typically used in such systems. For granules, the DO required for maximal activity was estimated to be >20 mg/L, clearly indicating the effects of the major external and internal mass transfer limitations on the overall biomass activity. Smaller aggregates had a larger volumetric OUR indicating that the granules may have a lower activity in the interior part of the aggregate. Copyright 2004 Wiley Periodicals, Inc.

Protein Folding and Aggregation into Amyloid: The Interference by Natural Phenolic Compounds

PubMed Central

Stefani, Massimo; Rigacci, Stefania

2013-01-01

Amyloid aggregation is a hallmark of several degenerative diseases affecting the brain or peripheral tissues, whose intermediates (oligomers, protofibrils) and final mature fibrils display different toxicity. Consequently, compounds counteracting amyloid aggregation have been investigated for their ability (i) to stabilize toxic amyloid precursors; (ii) to prevent the growth of toxic oligomers or speed that of fibrils; (iii) to inhibit fibril growth and deposition; (iv) to disassemble preformed fibrils; and (v) to favor amyloid clearance. Natural phenols, a wide panel of plant molecules, are one of the most actively investigated categories of potential amyloid inhibitors. They are considered responsible for the beneficial effects of several traditional diets being present in green tea, extra virgin olive oil, red wine, spices, berries and aromatic herbs. Accordingly, it has been proposed that some natural phenols could be exploited to prevent and to treat amyloid diseases, and recent studies have provided significant information on their ability to inhibit peptide/protein aggregation in various ways and to stimulate cell defenses, leading to identify shared or specific mechanisms. In the first part of this review, we will overview the significance and mechanisms of amyloid aggregation and aggregate toxicity; then, we will summarize the recent achievements on protection against amyloid diseases by many natural phenols. PMID:23765219

Multicomponent Gas Diffusion and an Appropriate Momentum Boundary Condition

NASA Technical Reports Server (NTRS)

Noever, David A.

1994-01-01

Multicomponent gas diffusion is reviewed with particular emphasis on gas flows near solid boundaries-the so-called Kramers-Kistemaker effect. The aim is to derive an appropriate momentum boundary condition which governs many gaseous species diffusing together. The many species' generalization of the traditional single gas condition, either as slip or stick (no-slip), is not obvious, particularly for technologically important cases of lower gas pressures and very dissimilar molecular weight gases. No convincing theoretical case exists for why two gases should interact with solid boundaries equally but in opposite flow directions, such that the total gas flow exactly vanishes. ln this way, the multicomponent no-slip boundary requires careful treatment The approaches discussed here generally adopt a microscopic model for gas-solid contact. The method has the advantage that the mathematics remain tractable and hence experimentally testable. Two new proposals are put forward, the first building in some molecular collision physics, the second drawing on a detailed view of surface diffusion which does not unphysically extrapolate bulk gas properties to govern the adsorbed molecules. The outcome is a better accounting of previously anomalous experiments. Models predict novel slip conditions appearing even for the case of equal molecular weight components. These approaches become particularly significant in view of a conceptual contradiction found to arise in previous derivations of the appropriate boundary conditions. The analogous case of three gases, one of which is uniformly distributed and hence non-diffusing, presents a further refinement which gives unexpected flow reversals near solid boundaries. This case is investigated alone and for aggregating gas species near their condensation point. In addition to predicting new physics, this investigation carries practical implications for controlling vapor diffusion in the growth of crystals used in medical diagnosis (e

Electric motor-transformer aggregate in hermetic objects of transport vehicles

NASA Astrophysics Data System (ADS)

Zabora, Igor

2017-10-01

The construction and features of operation for new electrical unit - electric motor-transformer aggregate (DTA) are considered. Induction motors are intended for operation in hermetic plants with extreme conditions surrounding gas, steam-to-gas and liquid environment at a high temperature (to several hundred of degrees). Main objective of spent researches is the substantiation of possibility reliable and effective electric power transform with electric machine means directly in hermetic objects with extreme conditions environment by means of new DTA. The principle and job analysis of new disk induction motors of block-module type are observed.

Anle138b and related compounds are aggregation specific fluorescence markers and reveal high affinity binding to α-synuclein aggregates.

PubMed

Deeg, Andreas A; Reiner, Anne M; Schmidt, Felix; Schueder, Florian; Ryazanov, Sergey; Ruf, Viktoria C; Giller, Karin; Becker, Stefan; Leonov, Andrei; Griesinger, Christian; Giese, Armin; Zinth, Wolfgang

2015-09-01

Special diphenyl-pyrazole compounds and in particular anle138b were found to reduce the progression of prion and Parkinson's disease in animal models. The therapeutic impact of these compounds was attributed to the modulation of α-synuclein and prion-protein aggregation related to these diseases. Photophysical and photochemical properties of the diphenyl-pyrazole compounds anle138b, anle186b and sery313b and their interaction with monomeric and aggregated α-synuclein were studied by fluorescence techniques. The fluorescence emission of diphenyl-pyrazole is strongly increased upon incubation with α-synuclein fibrils, while no change in fluorescence emission is found when brought in contact with monomeric α-synuclein. This points to a distinct interaction between diphenyl-pyrazole and the fibrillar structure with a high binding affinity (Kd=190±120nM) for anle138b. Several α-synuclein proteins form a hydrophobic binding pocket for the diphenyl-pyrazole compound. A UV-induced dehalogenation reaction was observed for anle138b which is modulated by the hydrophobic environment of the fibrils. Fluorescence of the investigated diphenyl-pyrazole compounds strongly increases upon binding to fibrillar α-synuclein structures. Binding at high affinity occurs to hydrophobic pockets in the fibrils. The observed particular fluorescence properties of the diphenyl-pyrazole molecules open new possibilities for the investigation of the mode of action of these compounds in neurodegenerative diseases. The high binding affinity to aggregates and the strong increase in fluorescence upon binding make the compounds promising fluorescence markers for the analysis of aggregation-dependent epitopes. Copyright © 2015 Elsevier B.V. All rights reserved.

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

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.

Porphyrin Cyclodextrin Conjugates Modulate Amyloid Beta Peptide Aggregation and Cytotoxicity.

PubMed

Oliveri, Valentina; Zimbone, Stefania; Giuffrida, Maria Laura; Bellia, Francesco; Tomasello, Marianna Flora; Vecchio, Graziella

2018-04-25

Although fibrillar amyloid beta peptide (Aβ) aggregates are one of the major hallmarks of Alzheimer's disease, increasing evidence suggests that soluble Aβ oligomers are the primary toxic species. Targeting the oligomeric species could represent an effective strategy to interfere with Aβ toxicity. In this work, the biological properties of 5[4-(6-O-β-cyclodextrin)-phenyl],10,15,20-tri(4-hydroxyphenyl)-porphyrin and its zinc complex were tested, as new molecules that interact with Aβ and effectively prevent its cytotoxicity. We found that these systems can cross the cell membrane to deliver Aβ intracellularly and promote its clearance. Our results provide evidence for the use of cyclodextrin-porphyrin derivatives as a promising strategy to target amyloid aggregation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Exploring the Structural Diversity in Inhibitors of α-Synuclein Amyloidogenic Folding, Aggregation, and Neurotoxicity

PubMed Central

Das, Sukanya; Pukala, Tara L.; Smid, Scott D.

2018-01-01

Aggregation of α-Synuclein (αS) protein to amyloid fibrils is a neuropathological hallmark of Parkinson's disease (PD). Growing evidence suggests that extracellular αS aggregation plays a pivotal role in neurodegeneration found in PD in addition to the intracellular αS aggregates in Lewy bodies (LB). Here, we identified and compared a diverse set of molecules capable of mitigating protein aggregation and exogenous toxicity of αSA53T, a more aggregation-prone αS mutant found in familial PD. For the first time, we investigated the αS anti-amyloid activity of semi-synthetic flavonoid 2′, 3′, 4′ trihydroxyflavone or 2-D08, which was compared with natural flavones myricetin and transilitin, as well as such structurally diverse polyphenols as honokiol and punicalagin. Additionally, two novel synthetic compounds with a dibenzyl imidazolidine scaffold, Compound 1 and Compound 2, were also investigated as they exhibited favorable binding with αSA53T. All seven compounds inhibited αSA53T aggregation as demonstrated by Thioflavin T fluorescence assays, with modified fibril morphology observed by transmission electron microscopy. Ion mobility-mass spectrometry (IM-MS) was used to monitor the structural conversion of native αSA53T into amyloidogenic conformations and all seven compounds preserved the native unfolded conformations of αSA53T following 48 h incubation. The presence of each test compound in a 1:2 molar ratio was also shown to inhibit the neurotoxicity of preincubated αSA53T using phaeochromocytoma (PC12) cell viability assays. Among the seven tested compounds 2-D08, honokiol, and the synthetic Compound 2 demonstrated the highest inhibition of aggregation, coupled with neuroprotection from preincubated αSA53T in vitro. Molecular docking predicted that all compounds bound near the lysine-rich region of the N-terminus of αSA53T, where the flavonoids and honokiol predominantly interacted with Lys 23. Overall, these findings highlight that (i

EDITORIAL: Focus on Cold and Ultracold Molecules FOCUS ON COLD AND ULTRACOLD MOLECULES

NASA Astrophysics Data System (ADS)

Carr, Lincoln D.; Ye, Jun

2009-05-01

Cold and ultracold molecules are the next wave of ultracold physics, giving rise to an exciting array of scientific opportunities, including many body physics for novel quantum phase transitions, new states of matter, and quantum information processing. Precision tests of fundamental physical laws benefit from the existence of molecular internal structure with exquisite control. The study of novel collision and reaction dynamics will open a new chapter of quantum chemistry. Cold molecules bring together researchers from a variety of fields, including atomic, molecular, and optical physics, chemistry and chemical physics, quantum information science and quantum simulations, condensed matter physics, nuclear physics, and astrophysics, a truly remarkable synergy of scientific explorations. For the past decade there have been steady advances in direct cooling techniques, from buffer-gas cooling to cold molecular beams to electro- and magneto-molecular decelerators. These techniques have allowed a large variety of molecules to be cooled for pioneering studies. Recent amazing advances in experimental techniques combining the ultracold and the ultraprecise have furthermore brought molecules to the point of quantum degeneracy. These latter indirect cooling techniques magnetically associate atoms from a Bose-Einstein condensate and/or a quantum degenerate Fermi gas, transferring at 90% efficiency highly excited Fano-Feshbach molecules, which are on the order of 10 000 Bohr radii in size, to absolute ground state molecules just a few Bohr across. It was this latter advance, together with significant breakthroughs in internal state manipulations, which inspired us to coordinate this focus issue now, and is the reason why we say the next wave of ultracold physics has now arrived. Whether directly or indirectly cooled, heteronuclear polar molecules offer distinct new features in comparison to cold atoms, while sharing all of their advantages (purity, high coherence

Edge strand engineering prevents native-like aggregation in Sulfolobus solfataricus acylphosphatase.

PubMed

de Rosa, Matteo; Bemporad, Francesco; Pellegrino, Sara; Chiti, Fabrizio; Bolognesi, Martino; Ricagno, Stefano

2014-09-01

β-proteins are constantly threatened by the risk of aggregation because β-sheets are inherently structured for edge-to-edge interactions. To avoid native-like aggregation, evolution has resulted in a set of strategies that prevent intermolecular β-interactions. Acylphosphatase from Sulfolobus solfataricus (Sso AcP) represents a suitable model for the study of such a process. Under conditions promoting aggregation, Sso AcP acquires a native-like conformational state whereby an unstructured N-terminal segment interacts with the edge β-strand B4 of an adjacent Sso AcP molecule. Because B4 is poorly protected against aggregation, this interaction triggers the aggregation cascade without the need for unfolding. Recently, three single Sso AcP mutants (V84D, Y86E and V84P) were designed to engineer additional protection against aggregation in B4 and were observed to successfully impair native-like aggregation in all three variants at the expense of a lower stability. To understand the structural basis of the reduced aggregation propensity and lower stability, the crystal structures of the Sso AcP variants were determined in the present study. Structural analysis reveals that the V84D and Y86E mutations exert protection by the insertion of an edge negative charge. A conformationally less regular B4 underlies protection against aggregation in the V84P mutant. The thermodynamic basis of instability is discussed. Moreover, kinetic experiments indicate that aggregation of the three mutants is not native-like and is independent of the interaction between B4 and the unstructured N-terminal segment. The reported data rationalize previous evidence regarding Sso AcP native-like aggregation and provide a basis for the design of aggregation-free proteins. The atomic coordinates and related experimental data for the Sso AcP mutants V84P, V84D, ΔN11 Y86E have been deposited in the Protein Data Bank under accession numbers 4OJ3, 4OJG and 4OJH, respectively. • Sso AcP and Sso Ac

Natural gas hydrates; vast resource, uncertain future

USGS Publications Warehouse

Collett, T.S.

2001-01-01

Gas hydrates are naturally occurring icelike solids in which water molecules trap gas molecules in a cagelike structure known as a clathrate. Although many gases form hydrates in nature, methane hydrate is by far the most common; methane is the most abundant natural gas. The volume of carbon contained in methane hydrates worldwide is estimated to be twice the amount contained in all fossil fuels on Earth, including coal.

Complex molecules in the W51 North region

NASA Astrophysics Data System (ADS)

Rong, Jialei; Qin, Sheng-Li; Zapata, Luis A.; Wu, Yuefang; Liu, Tie; Zhang, Chengpeng; Peng, Yaping; Zhang, Li; Liu, Ying

2016-01-01

We present Submillimeter Array (SMA) molecular-line observations in two 2-GHz wide bands centred at 217.5 and 227.5 GHz, towards the massive star-forming region W51 North. We identified 84 molecular-line transitions from 17 species and their isotopologues. The molecular gas distribution of these lines mainly peaks in the continuum position of W51 North, and has a small tail extending to the west, probably associated with W51 d2. In addition to the commonly detected nitrogen- and oxygen-bearing species, we detected a large number of transitions of acetone (CH3COCH3) and methyl formate (CH3OCHO), which might suggest that these molecules are present in an early evolutionary stage of massive stars. We have also found that W51 North is an ethanol-rich source. There is no obvious difference in the molecular gas distributions between the oxygen-bearing and nitrogen-bearing molecules. Under the assumption of local thermodynamic equilibrium, with the XCLASS tool, the molecular column densities and rotation temperatures are estimated. We have found that the oxygen-bearing molecules have considerably higher column densities and fractional abundances than the nitrogen-bearing molecules. The rotation temperatures range from 100 to 200 K, suggesting that the molecular emission could originate from a warm environment. Finally, based on the gas distributions, fractional abundances and the rotation temperatures, we conclude that CH3OH, C2H5OH, CH3COCH3 and CH3CH2CN might be synthesized on the grain surface, while gas phase chemistry is responsible for the production of CH3OCH3, CH3OCHO and CH2CHCN.

Electrostatic Effects in Filamentous Protein Aggregation

PubMed Central

Buell, Alexander K.; Hung, Peter; Salvatella, Xavier; Welland, Mark E.; Dobson, Christopher M.; Knowles, Tuomas P.J.

2013-01-01

Electrostatic forces play a key role in mediating interactions between proteins. However, gaining quantitative insights into the complex effects of electrostatics on protein behavior has proved challenging, due to the wide palette of scenarios through which both cations and anions can interact with polypeptide molecules in a specific manner or can result in screening in solution. In this article, we have used a variety of biophysical methods to probe the steady-state kinetics of fibrillar protein self-assembly in a highly quantitative manner to detect how it is modulated by changes in solution ionic strength. Due to the exponential modulation of the reaction rate by electrostatic forces, this reaction represents an exquisitely sensitive probe of these effects in protein-protein interactions. Our approach, which involves a combination of experimental kinetic measurements and theoretical analysis, reveals a hierarchy of electrostatic effects that control protein aggregation. Furthermore, our results provide a highly sensitive method for the estimation of the magnitude of binding of a variety of ions to protein molecules. PMID:23473495

Strong Aggregation-Induced CPL Response Promoted by Chiral Emissive Nematic Liquid Crystals (N*-LCs).

PubMed

Li, Xiaojing; Li, Qian; Wang, Yuxiang; Quan, Yiwu; Chen, Dongzhong; Cheng, Yixiang

2018-05-29

In this paper we designed a kind of aggregation-induced emission (AIE) chiral fluorescence emitters (R/S-BINOL-CN enantiomers) in the aggregate state. Chiral emissive nematic liquid crystals (N*-LCs) prepared by doping this kind of AIE-active R/S-BINOL-CN enantiomers into a common achiral nematic liquid crystal (N-LC, E7) can self-assemble as the regularly planar Grandjean texture leading to high luminescence dissymmetry factor (glum) of aggregation-induced circularly polarized luminescence (AI-CPL) signal up to 0.41, which can be attributed to dipolar interactions from polar cyano groups and π-π interactions between binaphthyl moiety of the dopant R/S-BINOL-CN and biphenyl group of the host molecules (E7). © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Detection and characterization of the tin dihydride (SnH2 and SnD2) molecule in the gas phase

NASA Astrophysics Data System (ADS)

Smith, Tony C.; Clouthier, Dennis J.

2018-01-01

The SnH2 and SnD2 molecules have been detected for the first time in the gas phase by laser-induced fluorescence (LIF) and emission spectroscopic techniques through the à 1B1-X ˜ 1A1 electronic transition. These reactive species were prepared in a pulsed electric discharge jet using (CH3)4Sn or SnH4/SnD4 precursors diluted in high pressure argon. Transitions to the electronic excited state of the jet-cooled molecules were probed with LIF, and the ground state energy levels were measured from single rovibronic level emission spectra. The LIF spectrum of SnD2 afforded sufficient rotational structure to determine the ground and excited state geometries: r0″ = 1.768 Å, θ0″ = 91.0°, r0' = 1.729 Å, θ0' = 122.9°. All of the observed LIF bands show evidence of a rotational-level-dependent predissociation process which rapidly decreases the fluorescence yield and lifetime with increasing rotational angular momentum in each excited vibronic level. This behavior is analogous to that observed in SiH2 and GeH2 and is suggested to lead to the formation of ground state tin atoms and hydrogen molecules.

Cholinesterases and cell proliferation in "nonstratified" and "stratified" cell aggregates from chicken retina and tectum.

PubMed

Vollmer, G; Layer, P G

1987-12-01

Dissociated single cells from chicken retina or tectum kept in rotation-mediated cell culture aggregate, proliferate and establish a certain degree of histotypical cell-to-cell relationships ("sorting out"), but these systems never form highly laminated aggregates ("nonstratified" R- and T-aggregates). In contrast, a mixture of retinal plus pigment epithelial cells forms highly "stratified" aggregates ("RPE-aggregates", see Vollmer et al. 1984). The present comparative study of "stratified" and "nonstratified" aggregates enables us to investigate the process of cell proliferation uncoupled from that of tissue stratification. Here we try to relate these two basic neurogenetic processes with patterns of expression of cholinesterases (AChE, BChE) during formation of both types of aggregates. During early aggregate formation, in both "stratified" and "nonstratified" aggregates an increased butyrylcholinesterase activity is observed close to mitotically active cells. Quantitatively both phenomena show their maxima after 2-3 days in culture. In contrast, AChE-expression in all systems increases with incubation time. In nonproliferative areas, in the center of RPE-aggregates, the formation of plexiform layers is characterized initially by weak BChE- and then strong AChE-activity. These areas correspond with the inner (IPL) and outer (OPL) plexiform layers of the retina in vivo. Although by sucrose gradient centrifugation we find that the 6S- and the fiber-associated 11S-molecules of AChE are present in all types of aggregates, during the culture period the ratio of 11S/6S-forms increases only in RPE-aggregates, which again indicates the advanced degree of differentiation within these aggregates.(ABSTRACT TRUNCATED AT 250 WORDS)

Large χ(3) of squarylium dye J aggregates measured using the Z-scan technique

NASA Astrophysics Data System (ADS)

Tatsuura, Satoshi; Wada, Osamu; Tian, Minquan; Furuki, Makoto; Sato, Yasuhiro; Iwasa, Izumi; Pu, Lyong Sun; Kawashima, Hitoshi

2001-10-01

Third-order nonlinear optical coefficients χ(3) were measured for the J aggregates of two types of squarylium dye derivatives at resonant and near-resonant wavelengths by using the Z-scan technique. The maximum χ(3) value evaluated at one-photon resonance was 2.9×10-6 e.s.u., which was greater than that of phthalocyanines by 4 orders of magnitude. χ(3) for one squarylium derivative was approximately two times as large as that of the other. This can be attributed to the difference of the number of molecules contributing to a coherent state in each J aggregate.

Regulation of aggregate size and pattern by adenosine and caffeine in cellular slime molds

PubMed Central

2012-01-01

that cytosolic glucose and extracellular cAMP levels are the other major determinants regulating aggregate size and pattern. Importantly, the aggregation process is conserved among different lineages of cellular slime molds despite using unrelated signalling molecules for aggregation. PMID:22269093

Regulation of aggregate size and pattern by adenosine and caffeine in cellular slime molds.

PubMed

Jaiswal, Pundrik; Soldati, Thierry; Thewes, Sascha; Baskar, Ramamurthy

2012-01-23

extracellular cAMP levels are the other major determinants regulating aggregate size and pattern. Importantly, the aggregation process is conserved among different lineages of cellular slime molds despite using unrelated signalling molecules for aggregation.

The influence of the dispersion corrections on the performance of DFT method in modeling HNgY noble gas molecules and their complexes

NASA Astrophysics Data System (ADS)

Cukras, Janusz; Sadlej, Joanna

2018-01-01

The letter reports a comparative assessment of the usefulness of the two different Grimme's corrections for evaluating dispersion interaction (DFT-D3 and DFT-D3BJ) for the representative molecules of the family of noble-gas hydrides HXeY and their complexes with the HZ molecules, where Y and Z are F/Cl/OH/SH. with special regard to the dispersion term calculated by means of the symmetry-adapted perturbation theory (at the SAPT0 level). The results indicate that despite differences in the total interactions energy (DFT + corrections) versus SAPT0 results, the sequence of contributions of the individual dispersion terms is still maintained. Both dispersion corrections perform similarly and they improve the results suggesting that it is worthwhile to include them in calculations.

Aggregation of carbon dioxide sequestration storage assessment units

USGS Publications Warehouse

Blondes, Madalyn S.; Schuenemeyer, John H.; Olea, Ricardo A.; Drew, Lawrence J.

2013-01-01

The U.S. Geological Survey is currently conducting a national assessment of carbon dioxide (CO2) storage resources, mandated by the Energy Independence and Security Act of 2007. Pre-emission capture and storage of CO2 in subsurface saline formations is one potential method to reduce greenhouse gas emissions and the negative impact of global climate change. Like many large-scale resource assessments, the area under investigation is split into smaller, more manageable storage assessment units (SAUs), which must be aggregated with correctly propagated uncertainty to the basin, regional, and national scales. The aggregation methodology requires two types of data: marginal probability distributions of storage resource for each SAU, and a correlation matrix obtained by expert elicitation describing interdependencies between pairs of SAUs. Dependencies arise because geologic analogs, assessment methods, and assessors often overlap. The correlation matrix is used to induce rank correlation, using a Cholesky decomposition, among the empirical marginal distributions representing individually assessed SAUs. This manuscript presents a probabilistic aggregation method tailored to the correlations and dependencies inherent to a CO2 storage assessment. Aggregation results must be presented at the basin, regional, and national scales. A single stage approach, in which one large correlation matrix is defined and subsets are used for different scales, is compared to a multiple stage approach, in which new correlation matrices are created to aggregate intermediate results. Although the single-stage approach requires determination of significantly more correlation coefficients, it captures geologic dependencies among similar units in different basins and it is less sensitive to fluctuations in low correlation coefficients than the multiple stage approach. Thus, subsets of one single-stage correlation matrix are used to aggregate to basin, regional, and national scales.

Mechanisms of Soil Aggregation: a biophysical modeling framework

NASA Astrophysics Data System (ADS)

Ghezzehei, T. A.; Or, D.

2016-12-01

Soil aggregation is one of the main crosscutting concepts in all sub-disciplines and applications of soil science from agriculture to climate regulation. The concept generally refers to adhesion of primary soil particles into distinct units that remain stable when subjected to disruptive forces. It is one of the most sensitive soil qualities that readily respond to disturbances such as cultivation, fire, drought, flooding, and changes in vegetation. These changes are commonly quantified and incorporated in soil models indirectly as alterations in carbon content and type, bulk density, aeration, permeability, as well as water retention characteristics. Soil aggregation that is primarily controlled by organic matter generally exhibits hierarchical organization of soil constituents into stable units that range in size from a few microns to centimeters. However, this conceptual model of soil aggregation as the key unifying mechanism remains poorly quantified and is rarely included in predictive soil models. Here we provide a biophysical framework for quantitative and predictive modeling of soil aggregation and its attendant soil characteristics. The framework treats aggregates as hotspots of biological, chemical and physical processes centered around roots and root residue. We keep track of the life cycle of an individual aggregate from it genesis in the rhizosphere, fueled by rhizodeposition and mediated by vigorous microbial activity, until its disappearance when the root-derived resources are depleted. The framework synthesizes current understanding of microbial life in porous media; water holding and soil binding capacity of biopolymers; and environmental controls on soil organic matter dynamics. The framework paves a way for integration of processes that are presently modeled as disparate or poorly coupled processes, including storage and protection of carbon, microbial activity, greenhouse gas fluxes, movement and storage of water, resistance of soils against

Kinetics of Inclusion Body Formation and Its Correlation with the Characteristics of Protein Aggregates in Escherichia coli

PubMed Central

Upadhyay, Arun K.; Murmu, Aruna; Singh, Anupam; Panda, Amulya K.

2012-01-01

The objective of the research was to understand the structural determinants governing protein aggregation into inclusion bodies during expression of recombinant proteins in Escherichia coli. Recombinant human growth hormone (hGH) and asparaginase were expressed as inclusion bodies in E.coli and the kinetics of aggregate formation was analyzed in details. Asparaginase inclusion bodies were of smaller size (200 nm) and the size of the aggregates did not increase with induction time. In contrast, the seeding and growth behavior of hGH inclusion bodies were found to be sequential, kinetically stable and the aggregate size increased from 200 to 800 nm with induction time. Human growth hormone inclusion bodies showed higher resistance to denaturants and proteinase K degradation in comparison to those of asparaginase inclusion bodies. Asparaginase inclusion bodies were completely solubilized at 2–3 M urea concentration and could be refolded into active protein, whereas 7 M urea was required for complete solubilization of hGH inclusion bodies. Both hGH and asparaginase inclusion bodies showed binding with amyloid specific dyes. In spite of its low β-sheet content, binding with dyes was more prominent in case of hGH inclusion bodies than that of asparaginase. Arrangements of protein molecules present in the surface as well as in the core of inclusion bodies were similar. Hydrophobic interactions between partially folded amphiphillic and hydrophobic alpha-helices were found to be one of the main determinants of hGH inclusion body formation. Aggregation behavior of the protein molecules decides the nature and properties of inclusion bodies. PMID:22479486

Spectroscopic study of non-amphiphilic 2-(4-biphenylyl)-5-(4- tert-butylphenyl)-l,3,4-oxadiazole aggregates at air-water interface and in Langmuir-Blodgett films

NASA Astrophysics Data System (ADS)

Acharya, Somobrata; Bhattacharjee, D.; Sarkar, Jyotirmoy; Talapatra, G. B.

2004-07-01

This Letter reports the spectroscopic characteristics of a non-amphiphilic 2-(4-biphenylyl)-5-(4- tert-butylphenyl)-1,3,4-oxadiazole (buPBD) molecule, in Langmuir and Langmuir-Blodgett (LB) films mixed with polymethyl methacrylate (PMMA) as well as with arachidic acid (AA). The π- A isotherms of buPBD mixed with PMMA/AA at different molefractions show that at very low surface pressure, a phase transition corresponding to a reorientation of the buPBD molecules occur, whereas at high surface pressure, buPBD molecules form aggregates among the hydrophobic tail part of PMMA/AA. Absorption and fluorescence spectroscopic study of the mixed LB films reveal formation of different types of aggregates.

Natural Gas Evolution in a Gas Hydrate Melt: Effect of Thermodynamic Hydrate Inhibitors.

PubMed

Sujith, K S; Ramachandran, C N

2017-01-12

Natural gas extraction from gas hydrate sediments by injection of hydrate inhibitors involves the decomposition of hydrates. The evolution of dissolved gas from the hydrate melt is an important step in the extraction process. Using classical molecular dynamics simulations, we study the evolution of dissolved methane from its hydrate melt in the presence of two thermodynamic hydrate inhibitors, NaCl and CH 3 OH. An increase in the concentration of hydrate inhibitors is found to promote the nucleation of methane nanobubbles in the hydrate melt. Whereas NaCl promotes bubble formation by enhancing the hydrophobic interaction between aqueous CH 4 molecules, CH 3 OH molecules assist bubble formation by stabilizing CH 4 bubble nuclei formed in the solution. The CH 3 OH molecules accumulate around the nuclei leading to a decrease in the surface tension at their interface with water. The nanobubbles formed are found to be highly dynamic with frequent exchange of CH 4 molecules between the bubble and the surrounding liquid. A quantitative analysis of the dynamic behavior of the bubble is performed by introducing a unit step function whose value depends on the location of CH 4 molecules with respect to the bubble. It is observed that an increase in the concentration of thermodynamic hydrate inhibitors reduces the exchange process, making the bubble less dynamic. It is also found that for a given concentration of the inhibitor, larger bubbles are less dynamic compared to smaller ones. The dependence of the dynamic nature of nanobubbles on bubble size and inhibitor concentration is correlated with the solubility of CH 4 and the Laplace pressure within the bubble. The effect of CO 2 on the formation of nanobubble in the CH 4 -CO 2 mixed gas hydrate melt in the presence of inhibitors is also examined. The simulations show that the presence of CO 2 molecules significantly reduces the induction time for methane nanobubble nucleation. The role of CO 2 in the early nucleation of

Nanoprobing of the effect of Cu2+ cations on misfolding, interaction and aggregation of amyloid β peptide

PubMed Central

Lv, Zhengjian; Condron, Margaret M.; Teplow, David B.; Lyubchenko, Yuri L.

2012-01-01

Misfolding and aggregation of the amyloid β-protein (Aβ) are hallmarks of Alzheimer’s disease. Both processes are dependent on the environmental conditions, including the presence of divalent cations, such as Cu2+. Cu2+ cations regulate early stages of Aβ aggregation, but the molecular mechanism of Cu2+ regulation is unknown. In this study we applied single molecule AFM force spectroscopy to elucidate the role of Cu2+ cations on interpeptide interactions. By immobilizing one of two interacting Aβ42 molecules on a mica surface and tethering the counterpart molecule onto the tip, we were able to probe the interpeptide interactions in the presence and absence of Cu2+ cations at pH 7.4, 6.8, 6.0, 5.0, and 4.0. The results show that the presence of Cu2+ cations change the pattern of Aβ interactions for pH values between pH 7.4 and pH 5.0. Under these conditions, Cu2+ cations induce Aβ42 peptide structural changes resulting in N–termini interactions within the dimers. Cu2+ cations also stabilize the dimers. No effects of Cu2+ cations on Aβ–Aβ interactions were observed at pH 4.0, suggesting that peptide protonation changes the peptide-cation interaction. The effect of Cu2+ cations on later stages of Aβ aggregation was studied by AFM topographic images. The results demonstrate that substoichiometric Cu2+ cations accelerate the formation of fibrils at pH 7.4 and 5.0, whereas no effect of Cu2+ cations was observed at pH 4.0. Taken together, the combined AFM force spectroscopy and imaging analyses demonstrate that Cu2+ cations promote both the initial and the elongation stages of Aβ aggregation, but protein protonation diminishes the effect of Cu2+. PMID:23143330

Enantiomer analysis of chiral carboxylic acids by AIE molecules bearing optically pure aminol groups.

PubMed

Zheng, Yan-Song; Hu, Yu-Jian; Li, Dong-Mi; Chen, Yi-Chang

2010-01-15

Pure enantiomers of carboxylic acids are a class of important biomolecules, chiral drugs, chiral reagents, etc. Analysis of the enantiomers usually needs expensive instrument or complex chiral receptors. However, to develop simple and reliable methods for the enantiomer analysis of acids is difficult. In this paper, chiral recognition of 2,3-dibenzoyltartaric acid and mandelic acid was first carried out by aggregation-induced emission molecules bearing optically pure aminol group, which was easily synthesized. The chiral recognition is not only seen by naked eyes but also measured by fluorophotometer. The difference of fluorescence intensity between the two enantiomers of the acids aroused by the aggregation-induced emission molecules was up to 598. The chiral recognition could be applied to quantitative analysis of enantiomer content of chiral acids. More chiral AIE amines need to be developed for enantiomer analysis of more carboxylic acids.

COMMERCIAL DEMONSTRATION OF THE MANUFACTURED AGGREGATE PROCESSING TECHNOLOGY UTILIZING SPRAY DRYER ASH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roy Scandrol

2003-04-01

Universal Aggregates, LLC proposes to design, construct and operate a lightweight aggregate manufacturing plant at the Birchwood Power Facility in King George, Virginia. The installation and start-up expenses for the Birchwood Aggregate Facility are $19.5 million. The DOE share is $7.2 million (37%) and the Universal Aggregates share is $12.3 (63%). The project team consists of CONSOL Energy Inc., P.J. Dick, Inc., SynAggs, LLC, and Universal Aggregates, LLC. The Birchwood Facility will transform 115,000 tons per year of spray dryer by-products that are currently being disposed of in an offsite landfill into 167,000 tons of a useful product, lightweight aggregatesmore » that can be used to manufacture lightweight aggregates that can be used to manufacture lightweight and medium weight masonry blocks. In addition to the environmental benefits, the Birchwood Facility will create eight (8) manufacturing jobs plus additional employment in the local trucking industry to deliver the aggregate to customers or reagents to the facility. A successful demonstration would lead to additional lightweight aggregate manufacturing facilities in the United States. There are currently twenty-one (21) spray dryer facilities operating in the United States that produce an adequate amount of spray dryer by-product to economically justify the installation of a lightweight aggregate manufacturing facility. Industry sources believe that as additional scrubbing is required, dry flue gas desulfurization (FGD) technologies will be the technology of choice. Letters from potential lightweight aggregate customers indicate that there is a market for the product once the commercialization barriers are eliminated by this demonstration project.« less

Exciton Level Structure and Dynamics in Tubular Porphyrin Aggregates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wan, Yan; Stradomska, Anna; Fong, Sarah

2014-10-30

We present an account of the optical properties of the Frenkel excitons in self-assembled porphyrin tubular aggregates that represent an analog to natural photosynthetic antennae. Using a combination of ultrafast optical spectroscopy and stochastic exciton modeling, we address both linear and nonlinear exciton absorption, relaxation pathways, and the role of disorder. The static disorder-dominated absorption and fluorescence line widths show little temperature dependence for the lowest excitons (Q band), which we successfully simulate using a model of exciton scattering on acoustic phonons in the host matrix. Temperature-dependent transient absorption of and fluorescence from the excitons in the tubular aggregates aremore » marked by nonexponential decays with time scales ranging from a few picoseconds to a few nanoseconds, reflecting complex relaxation mechanisms. Combined experimental and theoretical investigations indicate that nonradiative pathways induced by traps and defects dominate the relaxation of excitons in the tubular aggregates. We model the pumpprobe spectra and ascribe the excited-state absorption to transitions from one-exciton states to a manifold of mixed one- and two-exciton states. Our results demonstrate that while the delocalized Frenkel excitons (over 208 (1036) molecules for the optically dominant excitons in the Q (B) band) resulting from strong intermolecular coupling in these aggregates could potentially facilitate efficient energy transfer, fast relaxation due to defects and disorder probably present a major limitation for exciton transport over large distances.« less

Mechanism by which DHA inhibits the aggregation of KLVFFA peptides: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Zhou, Hong; Liu, Shengtang; Shao, Qiwen; Ma, Dongfang; Yang, Zaixing; Zhou, Ruhong

2018-03-01

Docosahexaenoic acid (DHA) is one of the omega-3 polyunsaturated fatty acids, which has shown promising applications in lowering Aβ peptide neurotoxicity in vitro by preventing aggregation of Aβ peptides and relieving accumulation of Aβ fibrils. Unfortunately, the underlying molecular mechanisms of how DHA interferes with the aggregation of Aβ peptides remain largely enigmatic. Herein, aggregation behaviors of amyloid-β(Aβ)16-21 peptides (KLVFFA) with or without the presence of a DHA molecule were comparatively studied using extensive all-atom molecular dynamics simulations. We found that DHA could effectively suppress the aggregation of KLVFFA peptides by redirecting peptides to unstructured oligomers. The highly hydrophobic and flexible nature of DHA made it randomly but tightly entangled with Leu-17, Phe-19, and Phe-20 residues to form unstructured but stable complexes. These lower-ordered unstructured oligomers could eventually pass through energy barriers to form ordered β-sheet structures through large conformational fluctuations. This study depicts a microscopic picture for understanding the role and mechanism of DHA in inhibition of aggregation of Aβ peptides, which is generally believed as one of the important pathogenic mechanisms of Alzheimer's disease.

Differences in the Pathways of Proteins Unfolding Induced by Urea and Guanidine Hydrochloride: Molten Globule State and Aggregates

PubMed Central

Povarova, Olga I.; Kuznetsova, Irina M.; Turoverov, Konstantin K.

2010-01-01

It was shown that at low concentrations guanidine hydrochloride (GdnHCl) can cause aggregation of proteins in partially folded state and that fluorescent dye 1-anilinonaphthalene-8-sulfonic acid (ANS) binds with these aggregates rather than with hydrophobic clusters on the surface of protein in molten globule state. That is why the increase in ANS fluorescence intensity is often recorded in the pathway of protein denaturation by GdnHCl, but not by urea. So what was previously believed to be the molten globule state in the pathway of protein denaturation by GdnHCl, in reality, for some proteins represents the aggregates of partially folded molecules. PMID:21152408

Radiationless Electronic Excitation Energy Transfer Between Monolayers of J-Aggregates

NASA Astrophysics Data System (ADS)

Chmereva, T. M.; Kucherenko, M. G.

2018-06-01

Radiationless electronic excitation energy transfer between monolayers of cyanine dye molecules forming J-aggregates by means of surface plasmons of the metal film of nanometer thickness inserted between the monolayers is theoretically investigated. A dependence of the rate of energy transfer on the geometrical and electrodynamic parameters of the system is established. It is demonstrated that the energy transfer between the monolayers is more effective in the presence of the metal film than in a nonconductive medium.

ELECTRIC CHARGING OF DUST AGGREGATES AND ITS EFFECT ON DUST COAGULATION IN PROTOPLANETARY DISKS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okuzumi, Satoshi

2009-06-20

Mutual sticking of dust aggregates is the first step toward planetesimal formation in protoplanetary disks. In spite that the electric charging of dust particles is well recognized in some contexts, it has been largely ignored in the current modeling of dust coagulation. In this study, we present a general analysis of the dust charge state in protoplanetary disks, and then demonstrate how the electric charging could dramatically change the currently accepted scenario of dust coagulation. First, we describe a new semianalytical method to calculate the dust charge state and gas ionization state self-consistently. This method is far more efficient thanmore » previous numerical methods, and provides a general and clear description of the charge state of a gas-dust mixture. Second, we apply this analysis to compute the collisional cross section of growing aggregates taking their charging into account. As an illustrative example, we focus on early evolutionary stages where the dust has been thought to grow into fractal (D {approx} 2) aggregates with a quasi-monodisperse (i.e., narrow) size distribution. We find that, for a wide range of model parameters, the fractal growth is strongly inhibited by the electric repulsion between colliding aggregates and eventually 'freezes out' on its way to the subsequent growth stage involving collisional compression. Strong disk turbulence would help the aggregates to overcome this growth barrier, but then it would cause catastrophic collisional fragmentation in later growth stages. These facts suggest that the combination of electric repulsion and collisional fragmentation would impose a serious limitation on dust growth in protoplanetary disks. We propose a possible scenario of dust evolution after the freezeout. Finally, we point out that the fractal growth of dust aggregates tends to maintain a low ionization degree and, as a result, a large magnetorotationally stable region in the disk.« less

Influence of the aggregate state on band structure and optical properties of C60 computed with different methods

NASA Astrophysics Data System (ADS)

Pal, Amrita; Arabnejad, Saeid; Yamashita, Koichi; Manzhos, Sergei

2018-05-01

C60 and C60 based molecules are efficient acceptors and electron transport layers for planar perovskite solar cells. While properties of these molecules are well studied by ab initio methods, those of solid C60, specifically its optical absorption properties, are not. We present a combined density functional theory-Density Functional Tight Binding (DFTB) study of the effect of solid state packing on the band structure and optical absorption of C60. The valence and conduction band edge energies of solid C60 differ on the order of 0.1 eV from single molecule frontier orbital energies. We show that calculations of optical properties using linear response time dependent-DFT(B) or the imaginary part of the dielectric constant (dipole approximation) can result in unrealistically large redshifts in the presence of intermolecular interactions compared to available experimental data. We show that optical spectra computed from the frequency-dependent real polarizability can better reproduce the effect of C60 aggregation on optical absorption, specifically with a generalized gradient approximation functional, and may be more suited to study effects of molecular aggregation.

Tailoring the antibody response to aggregated Aß using novel Alzheimer-vaccines.

PubMed

Mandler, Markus; Santic, Radmila; Gruber, Petra; Cinar, Yeliz; Pichler, Dagmar; Funke, Susanne Aileen; Willbold, Dieter; Schneeberger, Achim; Schmidt, Walter; Mattner, Frank

2015-01-01

Recent evidence suggests Alzheimer-Disease (AD) to be driven by aggregated Aß. Capitalizing on the mechanism of molecular mimicry and applying several selection layers, we screened peptide libraries for moieties inducing antibodies selectively reacting with Aß-aggregates. The technology identified a pool of peptide candidates; two, AFFITOPES AD01 and AD02, were assessed as vaccination antigens and compared to Aβ1-6, the targeted epitope. When conjugated to Keyhole Limpet Hemocyanin (KLH) and adjuvanted with aluminum, all three peptides induced Aß-targeting antibodies (Abs). In contrast to Aß1-6, AD01- or AD02-induced Abs were characterized by selectivity for aggregated forms of Aß and absence of reactivity with related molecules such as Amyloid Precursor Protein (APP)/ secreted APP-alpha (sAPPa). Administration of AFFITOPE-vaccines to APP-transgenic mice was found to reduce their cerebral amyloid burden, the associated neuropathological alterations and to improve their cognitive functions. Thus, the AFFITOME-technology delivers vaccines capable of inducing a distinct Ab response. Their features may be beneficial to AD-patients, a hypothesis currently tested within a phase-II-study.

Tailoring the Antibody Response to Aggregated Aß Using Novel Alzheimer-Vaccines

PubMed Central

Gruber, Petra; Cinar, Yeliz; Pichler, Dagmar; Funke, Susanne Aileen; Willbold, Dieter; Schneeberger, Achim; Schmidt, Walter; Mattner, Frank

2015-01-01

Recent evidence suggests Alzheimer-Disease (AD) to be driven by aggregated Aß. Capitalizing on the mechanism of molecular mimicry and applying several selection layers, we screened peptide libraries for moieties inducing antibodies selectively reacting with Aß-aggregates. The technology identified a pool of peptide candidates; two, AFFITOPES AD01 and AD02, were assessed as vaccination antigens and compared to Aβ1-6, the targeted epitope. When conjugated to Keyhole Limpet Hemocyanin (KLH) and adjuvanted with aluminum, all three peptides induced Aß-targeting antibodies (Abs). In contrast to Aß1-6, AD01- or AD02-induced Abs were characterized by selectivity for aggregated forms of Aß and absence of reactivity with related molecules such as Amyloid Precursor Protein (APP)/ secreted APP-alpha (sAPPa). Administration of AFFITOPE-vaccines to APP-transgenic mice was found to reduce their cerebral amyloid burden, the associated neuropathological alterations and to improve their cognitive functions. Thus, the AFFITOME-technology delivers vaccines capable of inducing a distinct Ab response. Their features may be beneficial to AD-patients, a hypothesis currently tested within a phase-II-study. PMID:25611858

J-aggregation of a water-soluble tetracationic porphyrin in mixed LB films with a calix[8]arene carboxylic acid derivative.

PubMed

Miguel, Gustavo de; Pérez-Morales, Marta; Martín-Romero, María T; Muñoz, Eulogia; Richardson, Tim H; Camacho, Luis

2007-03-27

The molecular organization of a mixed film, containing a water-soluble tetracationic porphyrin (TMPyP) and a p-tert-butyl calix[8]arene octacarboxylic acid derivative (C8A), at the air-water interface and on a solid support (LB film), has been investigated. Although the TMPyP aggregation was not detected at the air-water interface, TMPyP J-aggregates have been found in the LB films (Y-type). Unlike tetraanionic porphyrins, for example TSPP, the TMPyP J-aggregates are not induced by a zwitterion formation. The TMPyP J-aggregation is a result of a "double comb" configuration, where porphyrins from opposite layers are interwoven in a linear infinite J-aggregate. Our results confirm that TMPyP molecules tend to self-aggregate strongly, provided the electrostatic repulsions of their peripheral groups are cancelled by the anionic groups of the C8A matrix.

GAS6/TAM Pathway Signaling in Hemostasis and Thrombosis.

PubMed

Law, Luke A; Graham, Douglas K; Di Paola, Jorge; Branchford, Brian R

2018-01-01

The GAS6/TYRO3-AXL-MERTK (TAM) signaling pathway is essential for full and sustained platelet activation, as well as thrombus stabilization. Inhibition of this pathway decreases platelet aggregation, shape change, clot retraction, aggregate formation under flow conditions, and surface expression of activation markers. Transgenic mice deficient in GAS6, or any of the TAM family of receptors that engage this ligand, exhibit in vivo protection against arterial and venous thrombosis but do not demonstrate either spontaneous or prolonged bleeding compared to their wild-type counterparts. Comparable results are observed in wild-type mice treated with pharmacological inhibitors of the GAS6-TAM pathway. Thus, GAS6/TAM inhibition offers an attractive novel therapeutic option that may allow for a moderate reduction in platelet activation and decreased thrombosis while still permitting the primary hemostatic function of platelet plug formation.

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.

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

Modulation of partition and localization of perfume molecules in sodium dodecyl sulfate micelles.

PubMed

Fan, Yaxun; Tang, Haiqiu; Strand, Ross; Wang, Yilin

2016-01-07

The influence of perfume molecules on the self-assembly of the anionic surfactant sodium dodecyl sulfate (SDS) and their localization in SDS micelles have been investigated by ζ potential, small angle X-ray scattering (SAXS), one- and two-dimensional NMR and isothermal titration microcalorimetry (ITC). A broad range of perfume molecules varying in octanol/water partition coefficients P are employed. The results indicate that the surface charge, size and aggregation number of the SDS micelles strongly depend on the hydrophobicity/hydrophilicity degree of perfume molecules. Three distinct regions along the log P values are identified. Hydrophilic perfumes (log P < 2.0) partially incorporate into the SDS micelles and do not lead to micelle swelling, whereas hydrophobic perfumes (log P > 3.5) are solubilized close to the end of the hydrophobic chains in the SDS micelles and enlarge the micelles with higher ζ potential and a larger aggregation number. The incorporated fraction and micelle properties show increasing tendency for the perfumes in the intermediate log P region (2.0 < log P < 3.5). Besides, the molecular conformation of perfume molecules also affects these properties. The perfumes with a linear chain structure or an aromatic group can penetrate into the palisade layer and closely pack with the SDS molecules. Furthermore, the thermodynamic parameters obtained from ITC show that the binding of the perfumes in the intermediate log P region is more spontaneous than those in the other two log P regions, and the micellization of SDS with the perfumes is driven by entropy.

Azaphilones inhibit tau aggregation and dissolve tau aggregates in vitro.

PubMed

Paranjape, Smita R; Riley, Andrew P; Somoza, Amber D; Oakley, C Elizabeth; Wang, Clay C C; Prisinzano, Thomas E; Oakley, Berl R; Gamblin, T Chris

2015-05-20

The aggregation of the microtubule-associated protein tau is a seminal event in many neurodegenerative diseases, including Alzheimer's disease. The inhibition or reversal of tau aggregation is therefore a potential therapeutic strategy for these diseases. Fungal natural products have proven to be a rich source of useful compounds having wide varieties of biological activities. We have previously screened Aspergillus nidulans secondary metabolites for their ability to inhibit tau aggregation in vitro using an arachidonic acid polymerization protocol. One aggregation inhibitor identified was asperbenzaldehyde, an intermediate in azaphilone biosynthesis. We therefore tested 11 azaphilone derivatives to determine their tau assembly inhibition properties in vitro. All compounds tested inhibited tau filament assembly to some extent, and four of the 11 compounds had the advantageous property of disassembling preformed tau aggregates in a dose-dependent fashion. The addition of these compounds to the tau aggregates reduced both the total length and number of tau polymers. The most potent compounds were tested in in vitro reactions to determine whether they interfere with tau's normal function of stabilizing microtubules (MTs). We found that they did not completely inhibit MT assembly in the presence of tau. These derivatives are very promising lead compounds for tau aggregation inhibitors and, more excitingly, for compounds that can disassemble pre-existing tau filaments. They also represent a new class of anti-tau aggregation compounds with a novel structural scaffold.

Novel β-amyloid aggregation inhibitors possessing a turn mimic.

PubMed

Hamada, Yoshio; Miyamoto, Naoko; Kiso, Yoshiaki

2015-04-01

Amyloid β peptide, the main component of senile plaques found in the brain of Alzheimer disease (AD) patients, is a molecular target for AD therapeutic intervention. A number of potential AD therapeutics have been reported, including inhibitors of β-secretase, γ-secretase, and Aβ aggregation, and anti-amyloid agents, such as neprilysin, insulin degrading enzyme (IDE), and Aβ antibodies. Recently, we reported potent small-sized β-secretase (BACE1) inhibitors, which could serve as anti-AD drugs. However AD is a progressive disorder, where dementia symptoms gradually worsen over several decades, and therefore may require many years to get cured. One possible way to achieve a greater therapeutic effect is through simultaneous administration of multiple drugs, similar to those used in Highly Active Anti-Retroviral Therapy (HAART) used to treat AIDS. In order to overcome AD, we took a drug discovery approach to evaluate, novel β-amyloid aggregation inhibitors. Previously, we reported that a tong-type compound possessing a turn mimic as the inhibitor of HIV-1 protease dimerization. Oligomerized amyloid β peptides contain a turn structure within the molecule. Here, we designed and synthesized novel β-amyloid aggregation inhibitors with a turn-mimic template, based on the turn conformer of the oligomerized amyloid β peptides. Copyright © 2015 Elsevier Ltd. All rights reserved.

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%.

Protein Aggregation and Molecular Crowding: Perspectives From Multiscale Simulations.

PubMed

Musiani, F; Giorgetti, A

2017-01-01

Cells are extremely crowded environments, thus the use of diluted salted aqueous solutions containing a single protein is too simplistic to mimic the real situation. Macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, interactions with cognate biomolecules, and pathological aggregation. The latter phenomenon typically leads to the formation of amyloid fibrils that are linked to several lethal neurodegenerative diseases, but that can also play a functional role in certain organisms. The majority of molecular simulations performed before the last few years were conducted in diluted solutions and were restricted both in the timescales and in the system dimensions by the available computational resources. In recent years, several computational solutions were developed to get close to physiological conditions. In this review we summarize the main computational techniques used to tackle the issue of protein aggregation both in a diluted and in a crowded environment. © 2017 Elsevier Inc. All rights reserved.

Understanding and modulating the high-energy properties of noble-gas hydrides from their long-bonding: an NBO/NRT investigation on HNgCO+/CS+/OSi+ and HNgCN/NC (Ng = He, Ar, Kr, Xe, Rn) molecules.

PubMed

Zhang, Guiqiu; Song, Junjie; Fu, Lei; Tang, Kongshuang; Su, Yue; Chen, Dezhan

2018-04-18

The noble-gas hydrides, HNgX (X is an electronegative atom or fragment), represent potential high-energy materials because their two-body decomposition process, HNgX → Ng + HX, is strongly exoergic. Our previous studies have shown that each member of the HNgX (X = halogen atom or CN/NC fragment) molecules is composed of three leading resonance structures: two ω-bonding structures (H-Ng+ :X- and H:- Ng+-X) and one long-bonding structure (H∧X). The last one paints a novel [small sigma, Greek, circumflex]-type long-bonding picture. The present study focuses on the relationship between this novel bonding motif and the unusual energetic properties. We chose HNgCO+/CS+/OSi+/CN/NC, with the formula HNgAB (Ng = He, Ar, Kr, Xe, Rn; AB = CO+/CS+/OSi+/CN/NC) as the research system. We first investigated the bonding of HNgCO+ and its analogous HNgCS+/OSi+ species using NBO/NRT methods, and quantitatively compared the bonding with that in HNgCN/NC molecules. NBO/NRT results showed that each of the HNgCO+/CS+/OSi+ molecules could be better represented as a resonance hybrid of ω-bonding and long-bonding structures, but the long-bonding is much weaker than that in HNgCN/NC molecules. Furthermore, we introduced the long-bonding concept into the rationalization of the high-energy properties, and found a good correlation between the highly exothermic two-body dissociation channel and the long-bond order, bH-A. We also found that the long-bond order is highly tunable for these noble-gas hydrides due to its dependence on the nature of the electronegative AB fragments or the central noble-gas atoms, Ng. On the basis of these results, we could optimize the energetic properties by changing the long-bonding motif of our studied molecules. Overall, this study shows that the long-bonding model provides an easy way to rationalize and modulate the unusual energy properties of noble-gas hydrides, and that it is helpful to predict some noble-gas hydrides as potential energetic materials.

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...

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.

Ionic liquid-induced aggregate formation and their applications.

PubMed

Dutta, Rupam; Kundu, Sangita; Sarkar, Nilmoni

2018-06-01

In the last two decades, researchers have extensively studied highly stable and ordered supramolecular assembly formation using oppositely charged surfactants. Thereafter, surface-active ionic liquids (SAILs), a special class of room temperature ionic liquids (RTILs), replace the surfactants to form various supramolecular aggregates. Therefore, in the last decade, the building blocks of the supramolecular aggregates (micelle, mixed micelle, and vesicular assemblies) have changed from oppositely charged surfactant/surfactant pair to surfactant/SAIL and SAIL/SAIL pair. It is also found that various biomolecules can also interact with SAILs to construct biologically important supramolecular assemblies. The very latest addition to this combination of ion pairs is the dye molecules having a long hydrophobic chain part along with a hydrophilic ionic head group. Thus, dye/surfactant or dye/SAIL pair also produces different assemblies through electrostatic, hydrophobic, and π-π stacking interactions. Vesicles are one of the important self-assemblies which mimic cellular membranes, and thus have biological application as a drug carrier. Moreover, vesicles can act as a suitable microreactor for nanoparticle synthesis.

Valorization of lignite combustion residues and ferroalumina in the production of aggregates.

PubMed

Anagnostopoulos, I M; Stivanakis, V E; Angelopoulos, G N; Papamantellos, D C

2010-02-15

The present research study investigates the synergy of industrial solid by-products from lignite combustion (fly ash and bottom ash) and aluminum production (ferroalumina) in the production of lightweight aggregates (LWA). The process consists of two stages, pelletization and sintering. Bottom ash (BA) is used as the principal raw material in mixtures while ferroalumina (FAL) is added in lower percentages (5-30 wt%). BA carbon content is used as the fuel of sintering process in high temperatures, around 1250 degrees C, and gas generation is responsible for porous structure formation. Physical properties such as porosity, water absorption and bulk density, of sintering products are measured. Increase of FAL percentage in sintering mixtures results in decrease of porosity from 61% to 35% and of water absorption from 61% to 21% and in increase of bulk density from 1.02 g/cm(3) to 1.80 g/cm(3) of the produced aggregates. Aggregates produced by FAL addition up to 20 wt% are characterized as LWA. Aggregates formed are used in the production of concrete specimens. Compressive strength of concrete increases by increasing FAL addition in aggregates from 5 wt% to 15 wt% (highest strength value), while decrease by increasing FAL addition from 20 wt% to 30 wt%. FAL addition in lignite ashes sintering mixtures (up to 15 wt%) is considered as an important parameter for enhancing aggregates strength.

Analysis of the vibronic fine structure in circularly polarized emission spectra from chiral molecular aggregates.

PubMed

Spano, Frank C; Zhao, Zhen; Meskers, Stefan C J

2004-06-08

Using a Frenkel-exciton model, the degree of circular polarization of the luminescence (g(lum)) from one-dimensional, helical aggregates of chromophoric molecules is investigated theoretically. The coupling between the electronic excitation and a local, intramolecular vibrational mode is taken into account. Analytical expressions for the fluorescence band shape and g(lum) are presented for the case of strong and weak electronic coupling between the chromophoric units. Results are compared to those from numerical calculations obtained using the three particle approximation. g(lum) for the 0-0 vibronic band is found to be independent of the relative strength of electronic coupling between chromophores and excitation-vibration coupling. It depends solely on the number of coherently coupled molecules. In contrast, for the higher vibronic transitions[g(lum)] decreases with decreasing strength of the electronic coupling. In the limit of strong electronic coupling, [g(lum)] is almost constant throughout the series of vibronic transitions but for weak coupling [g(lum)] becomes vanishingly small for all vibronic transitions except for the 0-0 transition. The results are interpreted in terms of dynamic localization of the excitation during the zero point vibrational motion in the excited state of the aggregate. It is concluded that circular polarization measurements provide an independent way to determine the coherence size and bandwidth of the lowest exciton state for chiral aggregates. (c) 2004 American Institute of Physics.

A nanoscale bio-inspired light-harvesting system developed from self-assembled alkyl-functionalized metallochlorin nano-aggregates

NASA Astrophysics Data System (ADS)

Ocakoglu, Kasim; Joya, Khurram S.; Harputlu, Ersan; Tarnowska, Anna; Gryko, Daniel T.

2014-07-01

Self-assembled supramolecular organization of nano-structured biomimetic light-harvesting modules inside solid-state nano-templates can be exploited to develop excellent light-harvesting materials for artificial photosynthetic devices. We present here a hybrid light-harvesting system mimicking the chlorosomal structures of the natural photosynthetic system using synthetic zinc chlorin units (ZnChl-C6, ZnChl-C12 and ZnChl-C18) that are self-aggregated inside the anodic aluminum oxide (AAO) nano-channel membranes. AAO nano-templates were modified with a TiO2 matrix and functionalized with long hydrophobic chains to facilitate the formation of supramolecular Zn-chlorin aggregates. The transparent Zn-chlorin nano-aggregates inside the alkyl-TiO2 modified AAO nano-channels have a diameter of ~120 nm in a 60 μm length channel. UV-Vis studies and fluorescence emission spectra further confirm the formation of the supramolecular ZnChl aggregates from monomer molecules inside the alkyl-functionalized nano-channels. Our results prove that the novel and unique method can be used to produce efficient and stable light-harvesting assemblies for effective solar energy capture through transparent and stable nano-channel ceramic materials modified with bio-mimetic molecular self-assembled nano-aggregates.Self-assembled supramolecular organization of nano-structured biomimetic light-harvesting modules inside solid-state nano-templates can be exploited to develop excellent light-harvesting materials for artificial photosynthetic devices. We present here a hybrid light-harvesting system mimicking the chlorosomal structures of the natural photosynthetic system using synthetic zinc chlorin units (ZnChl-C6, ZnChl-C12 and ZnChl-C18) that are self-aggregated inside the anodic aluminum oxide (AAO) nano-channel membranes. AAO nano-templates were modified with a TiO2 matrix and functionalized with long hydrophobic chains to facilitate the formation of supramolecular Zn-chlorin aggregates. The

Our Galactic Neighbor Hosts Complex Organic Molecules

NASA Astrophysics Data System (ADS)

Hensley, Kerry

2018-03-01

For the first time, data from the Atacama Large Millimeter/submillimeter Array (ALMA) reveal the presence of methyl formate and dimethyl ether in a star-forming region outside our galaxy. This discovery has important implications for the formation and survival of complex organic compounds importantfor the formation of life in low-metallicity galaxies bothyoung and old.No Simple Picture of Complex Molecule FormationALMA, pictured here with the Magellanic Clouds above, has observed organic molecules in our Milky Way Galaxy and beyond. [ESO/C. Malin]Complex organic molecules (those with at least six atoms, one or more of which must be carbon) are the precursors to the building blocks of life. Knowing how and where complex organic molecules can form is a key part of understanding how life came to be on Earth and how it might arise elsewhere in the universe. From exoplanet atmospheres to interstellar space, complex organic molecules are ubiquitous in the Milky Way.In our galaxy, complex organic molecules are often found in the intense environments of hot cores clumps of dense molecular gas surrounding the sites of star formation. However, its not yet fully understood how the complex organic molecules found in hot cores come to be. One possibility is that the compounds condense onto cold dust grains long before the young stars begin heating their natal shrouds. Alternatively, they might assemble themselves from the hot, dense gas surrounding the blazing protostars.Composite infrared and optical image of the N 113 star-forming region in the LMC. The ALMA coverage is indicated by the gray line. Click to enlarge. [Sewio et al. 2018]Detecting Complexity, a Galaxy AwayUsing ALMA, a team of researchers led by Marta Sewio (NASA Goddard Space Flight Center) recently detected two complex organic molecules methyl formate and dimethyl ether for the first time in our neighboring galaxy, the Large Magellanic Cloud (LMC). Previous searches for organic molecules in the LMC detected

Theoretical insights into aggregation-induced helicity modulation of a perylene bisimide derivative.

PubMed

Liang, Lijun; Li, Xin

2018-02-12

Formation of helical chiroptical self-assemblies via noncovalent interaction is a widely observed phenomenon in nature, the mechanism of which remains insufficiently understood. Employing an amphiphilic perylene-sugar dyad molecule (PBI-HAG) as an example, we report that the modulatable supramolecular helicity may emerge from an aggregating process that is dominated by competition between two types of noncovalent interaction: hydrogen bonding and π-π stacking. The interplay between these two driving forces, which is greatly affected by the solvent environment, determines the morphology the supramolecular assembly of PBI-HAGs. In particular, a non-layered supramolecular structure was formed in octane owing to stabilization effects of intermolecular hydrogen bonds, whereas a layered supramolecular structure was formed in water because of energetically favorable π-π stacking of aromatic rings. The formation of distinct supramolecular architectures in different solvents was reinforced by simulated circular dichroism spectra, which show opposite signals consistent with experimental observations. The results of this study could help us understand aggregation-induced supramolecular chirality of noncovalent self-assemblies. Graphical abstract Left Typical structures of amphiphilic perylene-sugar dyad (PBI-HAG) aggregates in different octane and water. Right Simulated CD and UV-Vis spectra of core PBIs aggregates in octane and water.

SPECIAL ISSUE DEVOTED TO THE 80TH BIRTHDAY OF S.A. AKHMANOV: Transient coherent anti-Stokes Raman scattering spectroscopy as a tool for measuring the diffusion coefficient and size of gas molecules

NASA Astrophysics Data System (ADS)

Nikitin, Sergei Yu

2009-07-01

Formulas are derived for evaluating the diffusion coefficient and size of gas molecules from transient coherent anti-Stokes Raman scattering measurements. Numerical estimates are presented for hydrogen.

Composition, buoyancy regulation and fate of ice algal aggregates in the Central Arctic Ocean.

PubMed

Fernández-Méndez, Mar; Wenzhöfer, Frank; Peeken, Ilka; Sørensen, Heidi L; Glud, Ronnie N; Boetius, Antje

2014-01-01

Sea-ice diatoms are known to accumulate in large aggregates in and under sea ice and in melt ponds. There is recent evidence from the Arctic that such aggregates can contribute substantially to particle export when sinking from the ice. The role and regulation of microbial aggregation in the highly seasonal, nutrient- and light-limited Arctic sea-ice ecosystem is not well understood. To elucidate the mechanisms controlling the formation and export of algal aggregates from sea ice, we investigated samples taken in late summer 2011 and 2012, during two cruises to the Eurasian Basin of the Central Arctic Ocean. Spherical aggregates densely packed with pennate diatoms, as well as filamentous aggregates formed by Melosira arctica showed sign of different stages of degradation and physiological stoichiometries, with carbon to chlorophyll a ratios ranging from 110 to 66700, and carbon to nitrogen molar ratios of 8-35 and 9-40, respectively. Sub-ice algal aggregate densities ranged between 1 and 17 aggregates m(-2), maintaining an estimated net primary production of 0.4-40 mg C m(-2) d(-1), and accounted for 3-80% of total phototrophic biomass and up to 94% of local net primary production. A potential factor controlling the buoyancy of the aggregates was light intensity, regulating photosynthetic oxygen production and the amount of gas bubbles trapped within the mucous matrix, even at low ambient nutrient concentrations. Our data-set was used to evaluate the distribution and importance of Arctic algal aggregates as carbon source for pelagic and benthic communities.

Composition, Buoyancy Regulation and Fate of Ice Algal Aggregates in the Central Arctic Ocean

PubMed Central

Fernández-Méndez, Mar; Wenzhöfer, Frank; Peeken, Ilka; Sørensen, Heidi L.; Glud, Ronnie N.; Boetius, Antje

2014-01-01

Sea-ice diatoms are known to accumulate in large aggregates in and under sea ice and in melt ponds. There is recent evidence from the Arctic that such aggregates can contribute substantially to particle export when sinking from the ice. The role and regulation of microbial aggregation in the highly seasonal, nutrient- and light-limited Arctic sea-ice ecosystem is not well understood. To elucidate the mechanisms controlling the formation and export of algal aggregates from sea ice, we investigated samples taken in late summer 2011 and 2012, during two cruises to the Eurasian Basin of the Central Arctic Ocean. Spherical aggregates densely packed with pennate diatoms, as well as filamentous aggregates formed by Melosira arctica showed sign of different stages of degradation and physiological stoichiometries, with carbon to chlorophyll a ratios ranging from 110 to 66700, and carbon to nitrogen molar ratios of 8–35 and 9–40, respectively. Sub-ice algal aggregate densities ranged between 1 and 17 aggregates m−2, maintaining an estimated net primary production of 0.4–40 mg C m−2 d−1, and accounted for 3–80% of total phototrophic biomass and up to 94% of local net primary production. A potential factor controlling the buoyancy of the aggregates was light intensity, regulating photosynthetic oxygen production and the amount of gas bubbles trapped within the mucous matrix, even at low ambient nutrient concentrations. Our data-set was used to evaluate the distribution and importance of Arctic algal aggregates as carbon source for pelagic and benthic communities. PMID:25208058

Difficulties in Laboratory Studies and Astronomical Observations of Organic Molecules: Hydroxyacetone and Lactic Acid

NASA Technical Reports Server (NTRS)

Apponi, A. J.; Brewster, M. A.; Hoy, J.; Ziurys, L. M.

2006-01-01

For the past 35 years, radio astronomy has revealed a rich organic chemistry in the interstellar gas, which is exceptionally complex towards active star-forming regions. New solar systems condense out of this gas and may influence the evolution of life on newly formed planets. Much of the biologically important functionality is present among the some 130 gas-phase molecules found to date, including alcohols, aldehydes, ketones, acids, amines, amides and even the simplest sugar - glycolaldehyde. Still, many unidentified interstellar radio signals remain, and their identification relies on further laboratory study. The molecules hydroxyacetone and lactic acid are relatively small organic molecules, but possess rather complex rotational spectra owing to their high asymmetry. Hydroxyacetone is particularly problematic because it possess a very low barrier to internal rotation, and exhibits strong coupling of the free-rotor states with the overall rotation of the molecule. As in the case of acetamide, a full decomposition method was employed to order the resultant eigenstates onto normal asymmetric top eigenvectors.

Propionibacterium-Produced Coproporphyrin III Induces Staphylococcus aureus Aggregation and Biofilm Formation

PubMed Central

Wollenberg, Michael S.; Claesen, Jan; Escapa, Isabel F.; Aldridge, Kelly L.; Fischbach, Michael A.

2014-01-01

ABSTRACT The majority of bacteria detected in the nostril microbiota of most healthy adults belong to three genera: Propionibacterium, Corynebacterium, and Staphylococcus. Among these staphylococci is the medically important bacterium Staphylococcus aureus. Almost nothing is known about interspecies interactions among bacteria in the nostrils. We observed that crude extracts of cell-free conditioned medium from Propionibacterium spp. induce S. aureus aggregation in culture. Bioassay-guided fractionation implicated coproporphyrin III (CIII), the most abundant extracellular porphyrin produced by human-associated Propionibacterium spp., as a cause of S. aureus aggregation. This aggregation response depended on the CIII dose and occurred during early stationary-phase growth, and a low pH (~4 to 6) was necessary but was not sufficient for its induction. Additionally, CIII induced plasma-independent S. aureus biofilm development on an abiotic surface in multiple S. aureus strains. In strain UAMS-1, CIII stimulation of biofilm depended on sarA, a key biofilm regulator. This study is one of the first demonstrations of a small-molecule-mediated interaction among medically relevant members of the nostril microbiota and the first description of a role for CIII in bacterial interspecies interactions. Our results indicate that CIII may be an important mediator of S. aureus aggregation and/or biofilm formation in the nostril or other sites inhabited by Propionibacterium spp. and S. aureus. PMID:25053784

Incorporation of Biomaterials in Multicellular Aggregates Modulates Pluripotent Stem Cell Differentiation

PubMed Central

Bratt-Leal, Andrés M.; Carpenedo, Richard L.; Ungrin, Mark; Zandstra, Peter W.; McDevitt, Todd C.

2010-01-01

Biomaterials are increasingly being used to engineer the biochemical and biophysical properties of the extracellular stem cell microenvironment in order to tailor niche characteristics and direct cell phenotype. To date, stem cell-biomaterial interactions have largely been studied by introducing stem cells into artificial environments, such as 2D cell culture on biomaterial surfaces, encapsulation of cell suspensions within hydrogel materials, or cell seeding on 3D polymeric scaffolds. In this study, microparticles fabricated from different materials, such as agarose, PLGA and gelatin, were stably integrated, in a dose-dependent manner, within aggregates of pluripotent stem cells (PSCs) prior to differentiation as a means to directly examine stem cell-biomaterial interactions in 3D. Interestingly, the presence of the materials within the stem cell aggregates differentially modulated the gene and protein expression patterns of several differentiation markers without adversely affecting cell viability. Microparticle incorporation within 3D stem cell aggregates can control the spatial presentation of extracellular environmental cues (i.e. soluble factors, extracellular matrix and intercellular adhesion molecules) as a means to direct the differentiation of stem cells for tissue engineering and regenerative medicine applications. In addition, these results suggest that the physical presence of microparticles within stem cell aggregates does not compromise PSC differentiation, but in fact the choice of biomaterials can impact the propensity of stem cells to adopt particular differentiated cell phenotypes. PMID:20864164

Direct Imaging of Exciton Transport in Tubular Porphyrin Aggregates by Ultrafast Microscopy.

PubMed

Wan, Yan; Stradomska, Anna; Knoester, Jasper; Huang, Libai

2017-05-31

Long-range exciton transport is a key challenge in achieving efficient solar energy harvesting in both organic solar cells and photosynthetic systems. Self-assembled molecular aggregates provide the potential for attaining long-range exciton transport through strong intermolecular coupling. However, there currently lacks an experimental tool to directly characterize exciton transport in space and in time to elucidate mechanisms. Here we report a direct visualization of exciton diffusion in tubular molecular aggregates by transient absorption microscopy with ∼200 fs time resolution and ∼50 nm spatial precision. These direct measurements provide exciton diffusion constants of 3-6 cm 2 s -1 for the tubular molecular aggregates, which are 3-5 times higher than a theoretical lower bound obtained by assuming incoherent hopping. These results suggest that coherent effects play a role, despite the fact that exciton states near the band bottom crucial for transport are only weakly delocalized (over <10 molecules). The methods presented here establish a direct approach for unraveling the mechanisms and main parameters underlying exciton transport in large molecular assemblies.

Understanding amyloid aggregation by statistical analysis of atomic force microscopy images

NASA Astrophysics Data System (ADS)

Adamcik, Jozef; Jung, Jin-Mi; Flakowski, Jérôme; de Los Rios, Paolo; Dietler, Giovanni; Mezzenga, Raffaele

2010-06-01

The aggregation of proteins is central to many aspects of daily life, including food processing, blood coagulation, eye cataract formation disease and prion-related neurodegenerative infections. However, the physical mechanisms responsible for amyloidosis-the irreversible fibril formation of various proteins that is linked to disorders such as Alzheimer's, Creutzfeldt-Jakob and Huntington's diseases-have not yet been fully elucidated. Here, we show that different stages of amyloid aggregation can be examined by performing a statistical polymer physics analysis of single-molecule atomic force microscopy images of heat-denatured β-lactoglobulin fibrils. The atomic force microscopy analysis, supported by theoretical arguments, reveals that the fibrils have a multistranded helical shape with twisted ribbon-like structures. Our results also indicate a possible general model for amyloid fibril assembly and illustrate the potential of this approach for investigating fibrillar systems.

Rational Topological Design for Fluorescence Enhancement upon Aggregation of Distyrylfuran Derivatives.

PubMed

Mallet, Charlotte; Moussallem, Chady; Faurie, Alexandre; Allain, Magali; Gohier, Frédéric; Skene, William G; Frère, Pierre

2015-05-18

A series of 2,5-distyrylfuran derivatives bearing pentafluorophenyl- and cyanovinyl units have been synthesized for aggregation-induced emission (AIE). The effect of the type and extent of the supramolecular connections on the AIE of the furan derivatives were examined and correlated with their X-ray crystal structures. It was found that the simultaneous presence of cyano and perfluorophenyl units strongly enhances the fluorescence upon aggregation. Single-crystal X-ray diffraction analysis confirmed that CH⋅⋅⋅F, F⋅⋅⋅F, CH⋅⋅⋅nitrile, Ar⋅⋅⋅ArF (Ar=aryl, ArF =fluoroaryl), and nitrile⋅⋅⋅ArF intra- and intermolecular interactions drive the topology of the molecule and that solid-state supramolecular contacts favor AIE of the furan derivatives. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effects of the surroundings and conformerisation of n-dodecane molecules on evaporation/condensation processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gun’ko, Vladimir M.; Sir Harry Ricardo Laboratories, School of Computing, Engineering and Mathematics, University of Brighton, Cockcroft Building, Lewes Road, Brighton BN2 4GJ; Nasiri, Rasoul

2015-01-21

The evaporation/condensation coefficient (β) and the evaporation rate (γ) for n-dodecane vs. temperature, gas pressure, gas and liquid density, and solvation effects at a droplet surface are analysed using quantum chemical density functional theory calculations of several ensembles of conformers of n-dodecane molecules in the gas phase (hybrid functional ωB97X-D with the cc-pVTZ and cc-pVDZ basis sets) and in liquid phase (solvation method: SMD/ωB97X-D). It is shown that β depends more strongly on a number of neighbouring molecules interacting with an evaporating molecule at a droplet surface (this number is estimated through changes in the surface Gibbs free energy ofmore » solvation) than on pressure in the gas phase or conformerisation and cross-conformerisation of molecules in both phases. Thus, temperature and the surrounding effects at droplet surfaces are the dominant factors affecting the values of β for n-dodecane molecules. These values are shown to be similar (at reduced temperatures T/T{sub c} < 0.8) or slightly larger (at T/T{sub c} > 0.8) than the values of β calculated by the molecular dynamics force fields (MD FF) methods. This endorses the reliability of the previously developed classical approach to estimation of β by the MD FF methods, except at temperatures close to the critical temperature.« less

Defining and systematic analyses of aggregation indices to evaluate degree of calcium oxalate crystal aggregation

NASA Astrophysics Data System (ADS)

Chaiyarit, Sakdithep; Thongboonkerd, Visith

2017-12-01

Crystal aggregation is one of the most crucial steps in kidney stone pathogenesis. However, previous studies of crystal aggregation were rarely done and quantitative analysis of aggregation degree was handicapped by a lack of the standard measurement. We thus performed an in vitro assay to generate aggregation of calcium oxalate monohydrate (COM) crystals with various concentrations (25-800 µg/ml) in saturated aggregation buffer. The crystal aggregates were analyzed by microscopic examination, UV-visible spectrophotometry, and GraphPad Prism6 software to define a total of 12 aggregation indices (including number of aggregates, aggregated mass index, optical density, aggregation coefficient, span, number of aggregates at plateau time-point, aggregated area index, aggregated diameter index, aggregated symmetry index, time constant, half-life, and rate constant). The data showed linear correlation between crystal concentration and almost all of these indices, except only for rate constant. Among these, number of aggregates provided the greatest regression coefficient (r=0.997; p<0.001), whereas the equally second rank included aggregated mass index and optical density (r=0.993; p<0.001 and r=‑0.993; p<0.001, respectively) and the equally forth were aggregation coefficient and span (r=0.991; p<0.001 for both). These five indices are thus recommended as the most appropriate indices for quantitative analysis of COM crystal aggregation in vitro.

Exploration of sensing of nitrogen dioxide and ozone molecules using novel TiO2/Stanene heterostructures employing DFT calculations

NASA Astrophysics Data System (ADS)

Abbasi, Amirali; Sardroodi, Jaber Jahanbin

2018-06-01

Based on the density functional theory (DFT) calculations, we explored the sensing capabilities and electronic structures of TiO2/Stanene heterostructures as novel and highly efficient materials for detection of toxic NO2 and O3 molecules in the environment. Studied gas molecules were positioned at different sites and orientations towards the nanocomposite, and the adsorption process was examined based on the most stable structures. We found that both of these molecules are chemically adsorbed on the TiO2/Stanene heterostructures. The calculations of the adsorption energy indicate that the fivefold coordinated titanium sites of the TiO2/Stanene are the most stable sites for the adsorption of NO2 and O3 molecules. The side oxygen atoms of the gas molecules were found to be chemically bonded to these titanium atoms. The adsorption of gas molecules is an exothermic process, and the adsorption on the pristine nanocomposite is more favorable in energy than that on the nitrogen-doped nanocomposite. The effects of van der Waals interactions were taken into account, which indicate the adsorption energies were increased for the most sable configurations. The gas sensing response and charge transfers were analyzed in detail. The pristine nanocomposites have better sensing response than the doped ones. The spin density distribution plots indicate that the magnetization was mainly located over the adsorbed gas molecules. Mulliken charge analysis reveals that both NO2 and O3 molecules behave as charge acceptors, as evidenced by the accumulation of electronic charges on the adsorbed molecules predicted by charge density difference calculations. Our DFT results provide a theoretical basis for an innovative gas sensor system designed from a sensitive TiO2/Stanene heterostructures for efficient detection of harmful air pollutants such as NO2 and O3.

Coordination-Directed Stacking and Aggregation-Induced Emission Enhancement of the Zn(II) Schiff Base Complex.

PubMed

Wang, Dan; Li, Shu-Mu; Zheng, Jian-Quan; Kong, Duan-Yang; Zheng, Xiang-Jun; Fang, De-Cai; Jin, Lin-Pei

2017-01-17

2-(Trityliminomethyl)-quinolin-8-ol (HL) and its Zn(II) complex were synthesized and characterized by single-crystal X-ray diffraction. HL is an unsymmetrical molecule and coordinated with Zn(II) ion to form ZnL 2 in the antiparallel-mode arrangement via Zn-O (hydroxyl group) and Zn-N (quinoline ring) of HL. A high degree of ZnL 2 molecules ordering stacking is formed by the coordination bonds and intermolecular π-π interactions, in which head-to-tail arrangement (J-mode stacking) for L - is found. HL is nonfluorescent and ZnL 2 is weakly fluorescent in THF. The fluorescence emission of ZnL 2 enhances in THF/H 2 O as H 2 O% (volume %) is above 60% and aggregates particles with several hundred nanometers are formed, which is confirmed by DLS data and TEM images. The J-aggregates stacking for L - in ZnL 2 results in aggregation-induced emission enhancement (AIEE) for ZnL 2 in THF/H 2 O. Theoretical computations based on B3LYP/6-31G(d, p) and TD-B3LYP/6-31G(d, p) methods were carried out. ESIPT is the supposed mechanism for fluorescent silence of HL, and fluorescence emission of ZnL 2 is attributed to the restriction of ESIPT process. The oscillator strength of ZnL 2 increases from 0.017 for monomer to 0.032 for trimer. It indicates that a high degree of ZnL 2 molecules ordering stacking in THF/H 2 O is of benefit to fluorescence enhancement. HL is an ESIPT-coupled AIEE chemosensor for Zn(II) with high selectivity and sensitivity in aqueous medium. HL can efficiently detect intracellular Zn(II) ions because of ESIPT-coupled AIEE property of ZnL 2 in mixed solvent.

AFM-Based Single Molecule Techniques: Unraveling the Amyloid Pathogenic Species

PubMed Central

Ruggeri, Francesco Simone; Habchi, Johnny; Cerreta, Andrea; Dietler, Giovanni

2016-01-01

Background A wide class of human diseases and neurodegenerative disorders, such as Alzheimer’s disease, is due to the failure of a specific peptide or protein to keep its native functional conformational state and to undergo a conformational change into a misfolded state, triggering the formation of fibrillar cross-β sheet amyloid aggregates. During the fibrillization, several coexisting species are formed, giving rise to a highly heterogeneous mixture. Despite its fundamental role in biological function and malfunction, the mechanism of protein self-assembly and the fundamental origins of the connection between aggregation, cellular toxicity and the biochemistry of neurodegeneration remains challenging to elucidate in molecular detail. In particular, the nature of the specific state of proteins that is most prone to cause cytotoxicity is not established. Methods: In the present review, we present the latest advances obtained by Atomic Force Microscopy (AFM) based techniques to unravel the biophysical properties of amyloid aggregates at the nanoscale. Unraveling amyloid single species biophysical properties still represents a formidable experimental challenge, mainly because of their nanoscale dimensions and heterogeneous nature. Bulk techniques, such as circular dichroism or infrared spectroscopy, are not able to characterize the heterogeneity and inner properties of amyloid aggregates at the single species level, preventing a profound investigation of the correlation between the biophysical properties and toxicity of the individual species. Conclusion: The information delivered by AFM based techniques could be central to study the aggregation pathway of proteins and to design molecules that could interfere with amyloid aggregation delaying the onset of misfolding diseases. PMID:27189600

Angular motion of a PAH molecule in interstellar environment

NASA Technical Reports Server (NTRS)

Rouan, D.; Leger, Alain; Omont, A.; Giard, Martin

1989-01-01

Polycyclic aromatic hydrocarbon (PAH) molecules have recently been proposed as an important and hitherto undetected component of the Interstellar Medium (ISM). The theory was based on an explanation of the Unidentified IR Emission Bands by Leger et al. It has already led to a verified prediction on extended galactic and extragalactic emissions measured by IRAS, or by a recent balloon borne experiment. The physics that rules the motion of such molecules in the ISM was studied, taking into account their coupling with the ambient gas, the radiation field (absorption and emission) and the static magnetic field. This is important for many implications of the PAH theory such as the radio emission by these molecules or the expected polarization of their IR emission. A reflection nebulae is considered where the situation is rather well known. Every day life of a mean PAH molecule in such a region is as follows: every 3 hrs a UV photon is absorbed heating the molecule to a thousand degs; the temperature decay due to cooling by IR emission follows then within a few seconds. A collision with a molecule of gas occurs typically once a week, while an H atom is ejected or captured at the same rate. A typical cooling cycle after a heat impulse is given. The PAH molecules studied as representative of the family has typically 50 atoms, a radius of 4.5 A, is circular and has a molecular mass of M = 300; its permanent dipole moment is 3 Debye.

Sustainable aggregates production : green applications for aggregate by-products.

DOT National Transportation Integrated Search

2015-06-01

Increased emphasis in the construction industry on sustainability and recycling requires production of : aggregate gradations with lower dust (cleaner aggregates) and smaller maximum sizeshence, increased : amount of quarry by-products (QBs). QBs ...

Pyromellitamide gelators: exponential rate of aggregation, hierarchical assembly, and their viscoelastic response to anions.

PubMed

Tong, Katie W K; Dehn, Sabrina; Webb, James E A; Nakamura, Kio; Braet, Filip; Thordarson, Pall

2009-08-04

The gelation and aggregation properties of a newly synthesized structurally simplified tetrahexyl pyromellitamide 2 have been studied and compared to the previously reported tetra(ethylhexanoate) pyromellitide 1, indicating that the ester groups in the latter significantly impede its aggregation. Morphology studies (AFM and TEM) on the aggregates formed by tetrahexyl pyromellitamide 2 in cyclohexane revealed highly uniform aggregates with different dimensions at different starting concentrations, suggesting that this molecule aggregates in a hierarchical fashion from a one-dimensional supramolecular polymer through hollow tubes or compressed helices to a network structure and then to a gel. This hypothesis is further supported by viscosity measurements that indicate a crossover point where individual supramolecular fibers get entangled at concentrations above ca. 3 mM in cyclohexane. Addition of 1 equiv of tetraalkylammonium salts of chloride or bromide, however, caused the viscosities of these pyromellitamide solutions to drop by a factor of 2-3 orders of magnitude, demonstrating the sensitivity of these aggregates to the presence of small anions. The sensitivity to anions does depend on the solubility of the salts used as small anion salts with little solubility in cyclohexane did not show this effect. Time-dependent viscosity studies showed that the aggregation of pyromellitamide 2 follows an exponential rate law, possibly related to the columnar rearrangements that are associated with the observed 6 angstroms contraction in d spacing in the XRD pattern of these gels. These results, particularly on the importance of kinetics of aggregation of self-assembled pyromellitamide gels, will be useful for future development of related materials for a number of applications, including tissue engineering and drug delivery.

The effect of pH and concentration upon aggregation transitions in aqueous solutions of poloxamine T701.

PubMed

Armstrong, J K; Chowdhry, B Z; Snowden, M J; Dong, J; Leharne, S A

2001-10-23

Thermally induced aggregation transitions have been investigated for aqueous solutions of the poloxamine block copolymer T701-(OE(4)OP(13))(2)NCH(2)CH(2)N(OP(13)OE(4))(2)-using differential scanning calorimetry. The calorimetric signals obtained were fitted to a mass action model description of aggregation using a previously reported analytical procedure (Patterson et al., Langmuir 13 (1997) 2219). The presence of a central ethylene diamine moiety in the molecular structure renders the T701 molecule basic; this was confirmed and measured by acid/base titration. Basicity is shown to have an important impact upon aggregation. At low pH (2.5), the poloxamine exists in its protonated form and the bulk solution proton concentration is sufficient to suppress de-protonation, aggregation-as a consequence-is shifted to a higher temperature range. Any increase in pH reduces the temperature range over which aggregation occurs. The derived experimental calorimetric parameters, obtained from model fitting procedures, can be used to compute the fraction of poloxamine existing in an aggregated form, at any particular temperature. The data sets obtained were interpolated to show that at human body temperature (310.6 K) the fraction of poloxamine found in its aggregated form is zero at a pH of 2.5. However at a pH of 6.8, the percentage aggregation increases to about 85%. These aggregation characteristics of T701 have important implications for the design of drug delivery systems, which incorporate poloxamines.

Target molecules detection by waveguiding in a photonic silicon membrane

DOEpatents

Letant, Sonia E [Livermore, CA; Van Buuren, Anthony [Livermore, CA; Terminello, Louis [Danville, CA; Hart, Bradley R [Brentwood, CA

2006-12-26

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

Target molecules detection by waveguiding in a photonic silicon membrane

DOEpatents

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

2004-08-31

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

Key role of the N-terminus of chicken annexin A5 in vesicle aggregation.

PubMed

Turnay, Javier; Guzmán-Aránguez, Ana; Lecona, Emilio; Barrasa, Juan I; Olmo, Nieves; Lizarbe, Ma Antonia

2009-05-01

Annexins are calcium-dependent phospholipid-binding proteins involved in calcium signaling and intracellular membrane trafficking among other functions. Vesicle aggregation is a crucial event to make possible the membrane remodeling but this process is energetically unfavorable, and phospholipid membranes do not aggregate and fuse spontaneously. This issue can be circumvented by the presence of different agents such as divalent cations and/or proteins, among them some annexins. Although human annexin A5 lacks the ability to aggregate vesicles, here we demonstrate that its highly similar chicken ortholog induces aggregation of vesicles containing acidic phospholipids even at low protein and/or calcium concentration by establishment of protein dimers. Our experiments show that the ability to aggregate vesicles mainly resides in the N-terminus as truncation of the N-terminus of chicken annexin A5 significantly decreases this process and replacement of the N-terminus of human annexin A5 by that of chicken switches on aggregation; in both cases, there are no changes in the overall protein structure and only minor changes in phospholipid binding. Electrostatic repulsions between negatively charged residues in the concave face of the molecule, mainly in the N-terminus, seem to be responsible for the impairment of dimer formation in human annexin A5. Taking into account that chicken annexin A5 presents a high sequence and structural similarity with mammalian annexins absent in birds, as annexins A3 and A4, some of the physiological functions exerted by these proteins may be carried out by chicken annexin A5, even those that could require calcium-dependent membrane aggregation.

Ligand-Receptor Interaction Modulates the Energy Landscape of Enzyme-Instructed Self-Assembly of Small Molecules.

PubMed

Haburcak, Richard; Shi, Junfeng; Du, Xuewen; Yuan, Dan; Xu, Bing

2016-11-30

The concurrence of enzymatic reaction and ligand-receptor interactions is common for proteins, but rare for small molecules and has yet to be explored. Here we show that ligand-receptor interaction modulates the morphology of molecular assemblies formed by enzyme-instructed assembly of small molecules. While the absence of ligand-receptor interaction allows enzymatic dephosphorylation of a precursor to generate the hydrogelator that self-assembles to form long nanofibers, the presence of the ligand-receptor interaction biases the pathway to form precipitous aggregates containing short nanofibers. While the hydrogelators self-assemble to form nanofibers or nanoribbons that are unable to bind with the ligand (i.e., vancomycin), the addition of surfactant breaks up the assemblies to restore the ligand-receptor interaction. In addition, an excess amount of the ligands can disrupt the nanofibers and result in the precipitates. As the first example of the use of ligand-receptor interaction to modulate the kinetics of enzymatic self-assembly, this work not only provides a solution to evaluate the interaction between aggregates and target molecules but also offers new insight for understanding the emergent behavior of sophisticated molecular systems having multiple and parallel processes.

Modification in structure, phase transition, and magnetic property of metallic gallium driven by atom-molecule interactions.

PubMed

Song, Le Xin; Chen, Jie; Zhu, Lin Hong; Xia, Juan; Yang, Jun

2011-09-05

The present work supports a novel paradigm in which the surface structure and stacking behavior of metallic gallium (Ga) were significantly influenced by the preparation process in the presence of organic small molecules (ethanol, acetone, dichloromethane, and diethyl ether). The extent of the effect strongly depends on the polarity of the molecules. Especially, a series of new atom-molecule aggregates consisting of metallic Ga and macrocyclic hosts (cyclodextrins, CDs) were prepared and characterized by various techniques. A comprehensive comparative analysis between free metallic Ga and the Ga samples obtained provides important and at present rare information on the modification in structure, phase transition, and magnetic property of Ga driven by atom-molecule interactions. First, there is a notable difference in microstructure and electronic structure between the different types of Ga samples. Second, differential scanning calorimetry analysis gives us a complete picture (such as the occurrence of a series of metastable phases of Ga in the presence of CDs) that has allowed us to consider that Ga atoms were protected by the shielding effect provided by the cavities of CDs. Third, the metallic Ga distributed in the aggregates exhibits very interesting magnetic property compared to free metallic Ga, such as the uniform zero-field-cooled and field-cooled magnetization processes, the enhanced responses in magnetization to temperature and applied field, and the fundamental change in shape of magnetic hysteresis loops. These significant changes in structural transformation and physical property of Ga provide a novel insight into the understanding of atom-molecule interactions between metallic atoms and organic molecules.

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.

Volcanic ash aggregation in the lab - can we mimic natural processes?

NASA Astrophysics Data System (ADS)

Mueller, Sebastian B.; Kueppers, Ulrich; Jacob, Michael; Ayris, Paul; Cimarelli, Corrado; Dingwell, Donald B.; Guttzeit, Melanie; Hess, Kai-Uwe; Walter, Ulrich

2015-04-01

Explosive volcanic eruptions release large amounts of particles into the atmosphere. Volcanic ash, by definition pyroclasts smaller than 2 mm, can be distributed around the globe by prevailing winds. Ash poses hazards to aviation industry by melting in jet turbines, to human health by entering respiration systems and to society by damaging infrastructure. Under certain circumstances, ash particles can cluster together and build ash aggregates. Aggregates range in size from few mm to few cm and may exhibit complex internal stratigraphy. During growth, weight, density and aerodynamic properties change, leading to a significantly different settling behavior compared to individual ash particles. Although ash aggregation has been frequently observed in the geologic record, the physical and chemical mechanisms generating the aggregates remain poorly understood. During several field campaigns, we collected numerous ash aggregates and analyzed their textural, chemical and mechanical properties. Based on this knowledge, we have designed experiments using the ProCell Lab System® of Glatt Ingenieurtechnik GmbH, Germany. In this device, a continuous fluidized bed can be applied on solid particles and simulate gas-particle flow conditions as they would be expected in volcanic plumes or pyroclastic density currents. The geological record and direct observations have shown that both processes are capable of producing ash aggregates. As starting material we used Na-glass beads as an analogue and volcanic ash from Laacher See Volcano, Eifel Volcanic Field, Germany. We define parameters such as grainsize, specific surface area and concentration of the starting material, degree of turbulence, temperature and moisture in the process chamber and the composition of the liquid phase to influence form, size, stability and production rate of aggregates. We were able to experimentally produce round, unstructured ash pellets up to 5mm in diameter. A detailed textural description highlights