Inhibition of Tau Polymerization with a Cyanine Dye in Two Distinct Model Systems

We report the results of a computational study of TiO2 nanoclusters of various sizes as well as of complex systems with various molecules adsorbed onto the clusters to set the ground for the modeling of charge transfer processes in hybrid organic–inorganic photovoltaics or photocatalytic degradation of pollutants. Despite the large number of existing computational studies of TiO2 clusters and in spite of the higher computing power of the typical available hardware, allowing for calculations of larger systems, there are still studies that use cluster sizes that are too small and not appropriate to address particular problems or certain complex systems relevant in photovoltaic or photocatalytic applications. By means of density functional theory (DFT) calculations, we attempt to find acceptable minimal sizes of the TinO2n+2H4 (n = 14, 24, 34, 44, 54) nanoclusters in correlation with the size of the adsorbed molecule and the rigidity of the backbone of the molecule to model systems and interface processes that occur in hybrid photovoltaics and photocatalysis. We illustrate various adsorption cases with a small rigid molecule based on coumarin, a larger rigid oligomethine cyanine dye with indol groups, and the penicillin V antibiotic having a flexible backbone. We find that the use of the n = 14 cluster to describe adsorption leads to significant distortions of both the cluster and the molecule and to unusual tridentate binding configurations not seen for larger clusters. Moreover, the significantly weaker bonding as well as the differences in the density of states and in the optical spectra suggest that the n = 14 cluster is a poor choice for simulating the materials used in the practical applications envisaged here. As the n = 24 cluster has provided mixed results, we argue that cluster sizes larger than or equal to n = 34 are necessary to provide the reliability required by photovoltaic and photocatalytic applications. Furthermore, the tendency to saturate the key quantities of interest when moving from n = 44 to n = 54 suggests that the largest cluster may bring little improvement at a significantly higher computational cost.

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Tubular J-aggregates of cyanine dyes in the near-infrared

10.33774/chemrxiv-2021-rjmvz ◽

2021 ◽

Author(s):

Austin Bailey ◽

Arundhati Deshmukh ◽

Timothy Atallah ◽

Ulugbek Barotov ◽

Monica Pengshung ◽

...

Keyword(s):

Self Assembly ◽

Near Infrared ◽

Chemical Space ◽

Photophysical Properties ◽

Model Systems ◽

Cyanine Dye ◽

Infrared Emitters ◽

Photosynthetic Complexes ◽

Infrared Wavelengths ◽

Artificial Photosynthetic

Developing improved organic infrared emitters has wide-ranging applicability in fields such as bioimaging or energy harvesting. We synthesize redshifted analogues of C8S3, a well-known cyanine dye that self assembles into tubular aggregates which have attracted widespread attention as artificial photosynthetic complexes. Despite the elongated dye structure, the new pentamethine dyes retain their tubular self-assembly and emit at near-infrared wavelengths. Cryo-electron microscopy and detailed photophysical characterization of the new aggregates reveal similar absorption lineshapes with ~100 nm of redshift, as well as supramolecular morphologies that resemble their trimethine counterparts; the pentamethine aggregates generally show more disorder and decreased superradiance, suggesting that more ordered structures yield more robust photophysical properties. These results provide design principles of superradiant organic emitters, expand the chemical space of near-infrared aggregates, and introduce two additional wavelength-specific antennae as model systems for study.

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Model systems for rhodopsins: the photolysis of protonated retinal Schiff bases, cyanine dye, and artificial cyanine-bacteriorhodopsin

Journal of the American Chemical Society ◽

10.1021/ja00191a015 ◽

1989 ◽

Vol 111 (9) ◽

pp. 3203-3211 ◽

Cited By ~ 7

Author(s):

Noga Friedman ◽

Mordechai Sheves ◽

Michael Ottolenghi

Keyword(s):

Schiff Bases ◽

Model Systems ◽

Cyanine Dye

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Tubular J-aggregates of cyanine dyes in the near-infrared

10.33774/chemrxiv-2021-rjmvz-v2 ◽

2021 ◽

Author(s):

Austin Bailey ◽

Arundhati Deshmukh ◽

Timothy Atallah ◽

Ulugbek Barotov ◽

Monica Pengshung ◽

...

Keyword(s):

Self Assembly ◽

Near Infrared ◽

Chemical Space ◽

Photophysical Properties ◽

Model Systems ◽

Cyanine Dye ◽

Infrared Emitters ◽

Photosynthetic Complexes ◽

Infrared Wavelengths ◽

Artificial Photosynthetic

Developing improved organic infrared emitters has wide-ranging applicability in fields such as bioimaging or energy harvesting. We synthesize redshifted analogues of C8S3, a well-known cyanine dye that self assembles into tubular aggregates which have attracted widespread attention as artificial photosynthetic complexes. Despite the elongated dye structure, the new pentamethine dyes retain their tubular self-assembly and emit at near-infrared wavelengths. Cryo-electron microscopy and detailed photophysical characterization of the new aggregates reveal similar absorption lineshapes with ~100 nm of redshift, as well as supramolecular morphologies that resemble their trimethine counterparts; the pentamethine aggregates generally show more disorder and decreased superradiance, suggesting that more ordered structures yield more robust photophysical properties. These results provide design principles of superradiant organic emitters, expand the chemical space of near-infrared aggregates, and introduce two additional wavelength-specific antennae as model systems for study.

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Nuclear coiled bodies and the nucleolus

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100167834 ◽

1994 ◽

Vol 52 ◽

pp. 20-21

Author(s):

K. Brasch ◽

J. Williams ◽

D. Gallo ◽

T. Lee ◽

R. L. Ochs

Keyword(s):

Mouse Liver ◽

Nuclear Body ◽

Nuclear Bodies ◽

Model Systems ◽

Coiled Body ◽

Rrna Processing ◽

Malignant Cells ◽

Sm Proteins ◽

Coiled Bodies ◽

Unique Protein

Though first described in 1903 by Ramon-y-Cajal as silver-staining “accessory bodies” to nucleoli, nuclear bodies were subsequently rediscovered by electron microscopy about 30 years ago. Nuclear bodies are ubiquitous, but seem most abundant in hyperactive and malignant cells. The best studied type of nuclear body is the coiled body (CB), so termed due to characteristic morphology and content of a unique protein, p80-coilin (Fig.1). While no specific functions have as yet been assigned to CBs, they contain spliceosome snRNAs and proteins, and also the nucleolar protein fibrillarin. In addition, there is mounting evidence that CBs arise from or are generated near the nucleolus and then migrate into the nucleoplasm. This suggests that as yet undefined links may exist, between nucleolar pre-rRNA processing events and the spliceosome-associated Sm proteins in CBs.We are examining CB and nucleolar changes in three diverse model systems: (1) estrogen stimulated chick liver, (2) normal and neoplastic cells, and (3) polyploid mouse liver.

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Microtubule Dynamics and Organelle Transport in Reticulomyxa

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100158510 ◽

1990 ◽

Vol 48 (3) ◽

pp. 194-195

Author(s):

Yih-Tai Chen ◽

Ursula Euteneuer ◽

Ken B. Johnson ◽

Michael P. Koonce ◽

Manfred Schliwa

Keyword(s):

Plasma Membrane ◽

Light Microscopy ◽

Cytoplasmic Dynein ◽

Living Cells ◽

Microtubule Dynamics ◽

Model Systems ◽

Organelle Transport ◽

Biochemical Characteristics ◽

Dependent Transport

The application of video techniques to light microscopy and the development of motility assays in reactivated or reconstituted model systems rapidly advanced our understanding of the mechanism of organelle transport and microtubule dynamics in living cells. Two microtubule-based motors have been identified that are good candidates for motors that drive organelle transport: kinesin, a plus end-directed motor, and cytoplasmic dynein, which is minus end-directed. However, the evidence that they do in fact function as organelle motors is still indirect.We are studying microtubule-dependent transport and dynamics in the giant amoeba, Reticulomyxa. This cell extends filamentous strands backed by an extensive array of microtubules along which organelles move bidirectionally at up to 20 μm/sec (Fig. 1). Following removal of the plasma membrane with a mild detergent, organelle transport can be reactivated by the addition of ATP (1). The physiological, pharmacological and biochemical characteristics show the motor to be a cytoplasmic form of dynein (2).

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Microstructural observations of the “Wustite-Spinel” coexistence following quenching of cation-excess spinels, Ni2(1+x)Ti1-xO4

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100178422 ◽

1990 ◽

Vol 48 (4) ◽

pp. 1058-1059

Author(s):

Ian M. Anderson ◽

Arnulf Muan ◽

C. Barry Carter

Keyword(s):

Film Growth ◽

Spinel Phase ◽

Model Systems ◽

Ion Milling ◽

Coexistence Of Phases ◽

Nonequilibrium Conditions ◽

Diffraction Patterns ◽

Spinel Structures ◽

Highly Porous ◽

Standard Techniques

Oxide mixtures which feature a coexistence of phases with the wüstite and spinel structures are considered model systems for the study of solid-state reaction kinetics, phase boundaries, and thin-film growth, and such systems are especially suited to TEM studies. (In this paper, the terms “wüstite” and “spinel” will refer to phases of those structure types.) The study of wüstite-spinel coexistence has been limited mostly to systems near their equilibrium condition, where the assumptions of local thermodynamic equilibrium are valid. The cation-excess spinels of the type Ni2(1+x)Ti1-xO4, which reportedly exist only above 1375°C4, provide an excellent system for the study of wüstite-spinel coexistence under highly nonequilibrium conditions. The nature of these compounds has been debated in the literature. X-ray and neutron powder diffraction patterns have been used to advocate the existence of a single-phase, non- stoichiometric spinel. TEM studies of the microstructure have been used to suggest equilibrium coexistence of a stoichiometric spinel, Ni2TiO4, and a wüstite phase; this latter study has shown a coexistence of wüstite and spinel phases in specimens thought to have been composed of a single, non- stoichiometric spinel phase. The microstructure and nature of this phase coexistence is the focus of this study. Specimens were prepared by ball-milling a mixture of NiO and TiO2 powders with 10 wt.% TiO2. The mixture was fired in air at 1483°C for 5 days, and then quenched to room temperature. The aggregate thus produced was highly porous, and needed to be infiltrated prior to TEM sample preparation, which was performed using the standard techniques of lapping, dimpling, and ion milling.

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