Emerging Disordered Layered-Herringbone Phase in Organic Semiconductors Unveiled by Electron Crystallography

Reconstitution of solubilized and purified membrane proteins in the presence of phospholipids into vesicles allows their functions to be studied by simple bulk measurements (e.g. diffusion of differently sized solutes) or by conductance measurements after transformation into planar membranes. On the other hand, reconstitution into regular protein-lipid arrays, usually forming at a specific lipid-to-protein ratio, provides the basis for determining the 3-dimensional structure of membrane proteins employing the tools of electron crystallography.To refine reconstitution conditions for reproducibly inducing formation of large and highly ordered protein-lipid membranes that are suitable for both electron crystallography and patch clamping experiments aimed at their functional characterization, we built a flow-dialysis device that allows precise control of temperature and flow-rate (Fig. 1). The flow rate is generated by a peristaltic pump and can be adjusted from 1 to 500 ml/h. The dialysis buffer is brought to a preselected temperature during its travel through a meandering path before it enters the dialysis reservoir. A Z-80 based computer controls a Peltier element allowing the temperature profile to be programmed as function of time.

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Enhanced information from biological materials through technological improvements in cryo-electron microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100124343 ◽

1992 ◽

Vol 50 (1) ◽

pp. 788-789

Author(s):

Marc J.C. de Jong ◽

Wim M. Busing ◽

Max T. Otten

Keyword(s):

Electron Microscopy ◽

Electron Beam ◽

Biological Materials ◽

Electron Crystallography ◽

Cryo Electron Microscopy ◽

Transmission Electron ◽

The Many ◽

Technological Improvements ◽

Beam Damage

Biological materials damage rapidly in the electron beam, limiting the amount of information that can be obtained in the transmission electron microscope. The discovery that observation at cryo temperatures strongly reduces beam damage (in addition to making it unnecessaiy to use chemical fixatives, dehydration agents and stains, which introduce artefacts) has given an important step forward to preserving the ‘live’ situation and makes it possible to study the relation between function, chemical composition and morphology.Among the many cryo-applications, the most challenging is perhaps the determination of the atomic structure. Henderson and co-workers were able to determine the structure of the purple membrane by electron crystallography, providing an understanding of the membrane's working as a proton pump. As far as understood at present, the main stumbling block in achieving high resolution appears to be a random movement of atoms or molecules in the specimen within a fraction of a second after exposure to the electron beam, which destroys the highest-resolution detail sought.

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Direct phase determination in electron crystallography: small organic molecules

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100130468 ◽

1992 ◽

Vol 50 (2) ◽

pp. 1166-1167

Author(s):

Douglas L. Dorset

Keyword(s):

Organic Molecules ◽

Data Sets ◽

Temperature Structure ◽

3D Analysis ◽

Intensity Data ◽

Electron Crystallography ◽

Phase Determination ◽

Measured Intensity ◽

3D Data

The quantitative use of electron diffraction intensity data for the determination of crystal structures represents the pioneering achievement in the electron crystallography of organic molecules, an effort largely begun by B. K. Vainshtein and his co-workers. However, despite numerous representative structure analyses yielding results consistent with X-ray determination, this entire effort was viewed with considerable mistrust by many crystallographers. This was no doubt due to the rather high crystallographic R-factors reported for some structures and, more importantly, the failure to convince many skeptics that the measured intensity data were adequate for ab initio structure determinations.We have recently demonstrated the utility of these data sets for structure analyses by direct phase determination based on the probabilistic estimate of three- and four-phase structure invariant sums. Examples include the structure of diketopiperazine using Vainshtein's 3D data, a similar 3D analysis of the room temperature structure of thiourea, and a zonal determination of the urea structure, the latter also based on data collected by the Moscow group.

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Defocus ramp correction in spot-scan imaging

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100121053 ◽

1992 ◽

Vol 50 (1) ◽

pp. 130-131

Author(s):

Kenneth H. Downing

Keyword(s):

Computer Control ◽

Three Dimensional ◽

Sufficient Accuracy ◽

Objective Lens ◽

Electron Crystallography ◽

Contrast Transfer Function ◽

Tilt Axis ◽

Specimen Height ◽

The Difference ◽

Envelope Functions

Three-dimensional structures of a number of samples have been determined by electron crystallography. The procedures used in this work include recording images of fairly large areas of a specimen at high tilt angles. There is then a large defocus ramp across the image, and parts of the image are far out of focus. In the regions where the defocus is large, the contrast transfer function (CTF) varies rapidly across the image, especially at high resolution. Not only is the CTF then difficult to determine with sufficient accuracy to correct properly, but the image contrast is reduced by envelope functions which tend toward a low value at high defocus.We have combined computer control of the electron microscope with spot-scan imaging in order to eliminate most of the defocus ramp and its effects in the images of tilted specimens. In recording the spot-scan image, the beam is scanned along rows that are parallel to the tilt axis, so that along each row of spots the focus is constant. Between scan rows, the objective lens current is changed to correct for the difference in specimen height from one scan to the next.

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Factors in Photographic Emulsions for Low Dose Electron Crystallography

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s143192760000101x ◽

1980 ◽

Vol 38 ◽

pp. 230-231

Author(s):

T.W. Jeng ◽

W. Chiu

Keyword(s):

Radiation Damage ◽

Low Dose ◽

Damage Effect ◽

Photographic Emulsion ◽

Electron Crystallography ◽

Electron Microscopic ◽

X Ray ◽

Signal Contrast ◽

Diffraction Patterns ◽

Photographic Emulsions

With the advances in preparing biological materials in a thin and highly ordered form, and in maintaining them hydrated under vacuum, electron crystallography has become an important tool for biological structure investigation at high resolution (1,2). However, the electron radiation damage would limit the capability of recording reflections with low intensities in an electron diffraction pattern. It has been demonstrated that the use of a low temperature stage can reduce the radiation damage effect and that one can expose the specimen with a higher dose in order to increase the signal contrast (3). A further improvement can be made by selecting a proper photographic emulsion. The primary factors in evaluating the suitability of photographic emulsion for recording low dose diffraction patterns are speed, fog level, electron response at low electron exposure, linearity, and usable range of exposure. We have compared these factors with three photographic emulsions including Kodak electron microscopic plate (EMP), Industrex AA x-ray film (AA x-ray) and Kodak nuclear track film (NTB3).

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Energetic Control of Redox-Active Polymers Towards Safe Organic Bioelectronic Materials

10.26434/chemrxiv.11366186.v1 ◽

2019 ◽

Author(s):

Alexander Giovannitti ◽

Reem B. Rashid ◽

Quentin Thiburce ◽

Bryan D. Paulsen ◽

Camila Cendra ◽

...

Keyword(s):

Molecular Oxygen ◽

Organic Semiconductors ◽

Side Reaction ◽

Semiconducting Polymers ◽

Side Reactions ◽

Redox Active ◽

Donor Acceptor ◽

Electrochemical Devices ◽

Biological Environment ◽

Device Operation

Avoiding faradaic side reactions during the operation of electrochemical devices is important to enhance the device stability, to achieve low power consumption, and to prevent the formation of reactive side‑products. This is particularly important for bioelectronic devices which are designed to operate in biological systems. While redox‑active materials based on conducting and semiconducting polymers represent an exciting class of materials for bioelectronic devices, they are susceptible to electrochemical side‑reactions with molecular oxygen during device operation. We show that this electrochemical side reaction yields hydrogen peroxide (H2O2), a reactive side‑product, which may be harmful to the local biological environment and may also accelerate device degradation. We report a design strategy for the development of redox-active organic semiconductors based on donor-acceptor copolymers that prevent the formation of H2O2 during device operation. This study elucidates the previously overlooked side-reactions between redox-active conjugated polymers and molecular oxygen in electrochemical devices for bioelectronics, which is critical for the operation of electrolyte‑gated devices in application-relevant environments.

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Quantitative Image Analysis of Fractal-like Thin Films of Organic Semiconductors

10.26434/chemrxiv.6223610.v1 ◽

2018 ◽

Author(s):

Weikun Zhu ◽

Erfan Mohammadi ◽

Ying Diao

Keyword(s):

Thin Film ◽

Thin Films ◽

Image Analysis ◽

Fractal Dimension ◽

Organic Semiconductors ◽

Film Growth ◽

Electronic Device ◽

Significant Control ◽

Semiconductor Thin Films ◽

Two Parameters

Morphology modulation offers significant control over organic electronic device performance. However, morphology quantification has been rarely carried out via image analysis. In this work, we designed a MATLAB program to evaluate two key parameters describing morphology of small molecule semiconductor thin films: fractal dimension and film coverage. We then employ this program in a case study of meniscus-guided coating of 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene (C8-BTBT) under various conditions to analyze a diverse and complex morphology set. The evolution of morphology in terms of fractal dimension and film coverage was studied as a function of coating speed. We discovered that combined fractal dimension and film coverage can quantitatively capture the key characteristics of C8-BTBT thin film morphology; change of these two parameters further inform morphology transition. Furthermore, fractal dimension could potentially shed light on thin film growth mechanisms.

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Design and Synthesis of Two-Dimensional Covalent Organic Frameworks with Four-Arm Cores: Prediction of Remarkable Ambipolar Charge-Transport Properties

10.26434/chemrxiv.7766786.v2 ◽

2019 ◽

Author(s):

Simil Thomas ◽

Hong Li ◽

Raghunath R. Dasari ◽

Austin Evans ◽

William Dichtel ◽

...

Keyword(s):

Charge Transport ◽

Organic Semiconductors ◽

Density Functional ◽

Polymer Networks ◽

Two Dimensional ◽

Covalent Organic Frameworks ◽

X Ray Diffraction ◽

Zinc Porphyrin ◽

Design And Synthesis ◽

Predicted Values

We have considered three two-dimensional (2D) π-conjugated polymer networks (i.e., covalent organic frameworks, COFs) materials based on pyrene, porphyrin, and zinc-porphyrin cores connected via diacetylenic linkers. Their electronic structures, investigated at the density functional theory global-hybrid level, are indicative of valence and conduction bands that have large widths, ranging between 1 and 2 eV. Using a molecular approach to derive the electronic couplings between adjacent core units and the electron-vibration couplings, the three π-conjugated 2D COFs are predicted to have ambipolar charge-transport characteristics with electron and hole mobilities in the range of 65-95 cm2V-1s-1. Such predicted values rank these 2D COFs among the highest-mobility organic semiconductors. In addition, we have synthesized the zinc-porphyrin based 2D COF and carried out structural characterization via powder X-ray diffraction and surface area analysis, which demonstrates the feasability of these electroactive networks.

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