Name: photoelectron imaging of anions illustrated by 310 nm detachment of f−
Uploaded: 2018-07-27T14:45:00.000+00:00
Duration: 6 min 53 s
Description: Watch this Scientific Journal Video about Photoelectron Imaging of Anions Illustrated by 310 Nm Detachment of Fâˆ' at JoVE.com

This material is based upon work supported by the National Science Foundation under CHE - 1566157

NOTE: A general experimental protocol is presented here, specific to the WUSTL instrument. Specific instrument settings for the F&#8722; image presented in Figure 4a can be found in Table 1-2.
1. Ion Generation
<ol>
	<li>To generate anions, apply a backing gas or gas mixture (for F&#8722;, 40 psig. of O2) behind the pulsed nozzle and operate the nozzle at 10 Hz.
	<ol>
		<li>Set the nozzle duration on digital delay generator 1 (DDG1), channel A (A1) and trigger the pulsed nozzle driver to inject the gas into discharge.</li>
		<li>Apply a high voltage discharge pulse V1. The timing and duration of the pulse are controlled by channel C (C1) on DDG1.</li>
		<li>As the escape of O2 gas can lead to increased laboratory fire risk, ensure that all gas lines are leak tight. Since high gas pressures can lead to failure of gas lines, ensure that the pressure is kept below maximum operating pressure. Ensure that power supplies are properly grounded and switched off when cables are being attached or removed.</li>
	</ol>
	</li>
</ol>
2. Ion Extraction, Separation and Detection
<ol>
	<li>To extract anions from the source, apply a high voltage extraction pulse (V2) to the ion extraction plate.
	<ol>
		<li>Set the timing and duration of the ion extraction pulse using DDG1 channel D (D1).</li>
	</ol>
	</li>
	<li>To monitor the anion mass spectrum, put the instrument into ion mode.
	<ol>
		<li>Connect the detector voltage divider to the imaging detector MCPs.</li>
		<li>Apply voltage V11 to the detector anode (phosphor screen).</li>
		<li>Connect the ion detector voltage divider output to the oscilloscope channel 1 input.</li>
		<li>Connect the MCP power supply to the voltage divider input and gradually increase voltage. An input voltage V9 provides V7 to the entry side and V8 to the exit side of the MCP. 
		CAUTION: Do not exceed maximum allowable voltage for MCPs.</li>
	</ol>
	</li>
	<li>Separate the anions by TOF-MS.
	<ol>
		<li>Set the acceleration stack voltage V3.</li>
		<li>Using DDG1 channel E (E1), set the timing and duration for the potential switch high voltage pulse (V3).</li>
		<li>Externally trigger the oscilloscope from DDG1 channel F (F1) to set the TOF-MS time scale.</li>
	</ol>
	</li>
	<li>Adjust the discharge and extraction pulse magnitudes (V1-V2), discharge, extraction, potential switch and nozzle timing and duration through channels A-E on DDG1 to produce ion signal on the oscilloscope.</li>
</ol>
3. Ion Yield and Resolution Optimization.
NOTE: Steps 3.1 and 3.2 should be repeated iteratively to obtain the optimum resolution and ion yield. (Tables 1-2 show the settings used to generate the F&#8722; image shown in the results section).
<ol>
	<li>To optimize the number of anions of a given species, adjust the ion source settings.
	<ol>
		<li>Adjust the pressure of O2 gas behind the nozzle using the regulator on the gas cylinder.</li>
		<li>Adjust the pulsed nozzle duration of operation (A1).</li>
		<li>Adjust the magnitude of the discharge pulse voltage (V1).</li>
		<li>Adjust the timing and duration of the discharge pulse voltage (C1).</li>
		<li>Adjust the timing and duration of the ion extraction pulse (D1).</li>
		<li>Adjust the duration the potential switch is at high voltage (E1).</li>
		<li>Adjust the voltage on central element of the einzel lens (V4). The ion peaks on the oscilloscope should increase in intensity. 
		CAUTION: Ensure O2 pressure is kept below maximum operating pressure.</li>
	</ol>
	</li>
	<li>Adjust the TOF-MS settings to optimize the mass spectral resolution and ion separation
	<ol>
		<li>Adjust the ion extraction voltage (V2) to achieve Wiley-McLaren focusing. The ion peaks on the oscilloscope should narrow.</li>
		<li>Adjust the acceleration stack voltage V3.</li>
	</ol>
	</li>
</ol>
4. Photoelectron Production and Detection
<ol>
	<li>Switch the spectrometer to the imaging mode.
	<ol>
		<li>Reduce the voltage applied to the ion detector voltage divider (V9) to zero.</li>
		<li>Disconnect the ion detector voltage divider from the MCPs.</li>
		<li>Connect the MCP and imaging power supplies to the imaging high voltage pulse.</li>
		<li>Connect the imaging high voltage pulse to the imaging MCPs</li>
	</ol>
	</li>
	<li>Apply a permanent voltage to phosphor screen (V11) and MCPs (V9).</li>
	<li>Synchronize the arrival time of laser pulses from the nanosecond (ns) dye laser with the arrival time of the ion of interest within the VMI lens.
	<ol>
		<li>Connect the fast photodiode to oscilloscope channel 2.</li>
		<li>Externally trigger the Nd:YAG laser flash lamps and Q switch using DDG2 channels H (H2) and G (G2). Adjust the timing of the laser trigger (H2) until the photodiode output is close to but preceding the ion signal of interest.</li>
		<li>Apply voltage to the imaging repeller (V5) and extractor (V6) electrodes.</li>
		<li>Set the camera to long exposure and adjust the laser trigger timing (H2) to maximize the number of electron detection events observed on the PC screen. 
		CAUTION: Class IV laser radiation will permanently damage eyesight. Wear appropriate eye protection. Do not look directly into the beam even when wearing eye protection. Avoid specular reflections.</li>
	</ol>
	</li>
	<li>Apply a high voltage pulse to the MCP timed to coincide with arrival of the photon pulse to amplify electron signal within the photoelectron production window.
	<ol>
		<li>Set the imaging pulse voltage (V10).</li>
		<li>Set the imaging pulse timing and duration using DDG2 channel F (F2) such that the imaging pulse is centered on the arrival time of the photon pulse.</li>
	</ol>
	</li>
</ol>
5. Image Focusing
<ol>
	<li>Set the camera to short exposure.
	<ol>
		<li>Trigger the CCD camera to open at the start of an experimental cycle using DDG2 channel E (E2).</li>
	</ol>
	</li>
	<li>Collect a background-subtracted image
	<ol>
		<li>Collect several frames with the laser pulse coincident with the anion of interest.</li>
		<li>Collect several frames with the laser pulse not coincident with any anion.</li>
		<li>Subtract the frames collected off coincidence from the frames collected on coincidence.</li>
		<li>Repeat step 5.2 and accumulate an image.</li>
	</ol>
	</li>
	<li>Adjust the imaging repeller (V5) and extraction (V6) electrode voltages. Generate a new image by repeating step 5.2. The best focusing condition is achieved when the image features are at their narrowest.</li>
</ol>
6. Image Collection
<ol>
	<li>With the camera in short exposure mode, switch to centroided collection.</li>
	<li>Repeat step 5.2 at the optimum focusing condition to accumulate a sub-pixel resolution image.</li>
</ol>
7. Data Extraction
NOTE: The data manipulations performed in this section are performed using specifically written programs in the MatLab platform.
<ol>
	<li>Locate the center of the image by determining the center of mass (intensity) of the image, using the inherent symmetry of the image to find the center of inversion, or (in the case of low signal to noise) iteratively minimizing the width of the transitions in the spectrum by selecting different trial centers.
	<ol>
		<li>Inverse Abel transform the image to recover the 3D velocity distribution.</li>
	</ol>
	</li>
	<li>Generate photoelectron spectra
	<ol>
		<li>Integrate the intensity as a function of angle for all radii (this is the spectrum in the radial and hence momentum or velocity domain). In practice this is acheived by summation over all radii. 
		<img alt="Equation 1" src="/files/ftp_upload/57989/57989eq01v2.jpg" /> 
		where I(r) is the radial intensity and I(r,&#952;) is the intensity at point r, &#952;.</li>
		<li>Calibrate the spectrum for electron kinetic energy by comparison with an image recorded under the same conditions with transitions of known eBE. 
		eKE = eKEcal&#215;(r/rcal)2 
		where eKEref is the kinetic energy of a known transition in the reference spectrum, rref is the radius of the ring in the reference image corresponding to this transition and eKE is the kinetic energy associated with radius r in the experimental image.</li>
		<li>Convert the radial spectrum to the energy domain via Jacobian transformation. The energy corresponding to a given r is determined as in 7.2.2. The intensity I(r) is divided by &#8730;eKE.</li>
	</ol>
	</li>
	<li>Angular Distribution of electrons.
	<ol>
		<li>Select a transition in the spectrum.</li>
		<li>For different small angular ranges, integrate over the radial range associated with the transition and plot against &#952;. In practice the integration is acheived by summation over all radii in the range r0 -FWHM/2 to +FWHM/2. 
		<img alt="Equation 2" src="/files/ftp_upload/57989/57989eq02v2.jpg" /> 
		where I(&#952;) is the angular intensity, r0 is the radial value of the transition maximum and FWHM is the full width at half maximum across the radial range of the transition.</li>
	</ol>
	</li>
</ol>

The authors have no competing financial interests or other conflicts of interest.

Two factors are particularly critical to the success of the described protocol. The best possible velocity mapping conditions must be determined and more crucially, a sufficient and relatively time invariant yield of the desired anion must be produced. Regarding the VMI focusing steps, steps 5.2 and 5.3 should be repeated in tandem with image analysis to determine the condition which gives the sharpest (narrowest) image features. Fine tuning of the electrode voltages (V5 and V6) is influenced by the size and location of ...

Anion photoelectron imaging1 is a variant on photoelectron spectroscopy and represents a powerful probe of atomic/molecular electronic structure and the interactions between electrons and neutral species. The information obtained is essential in developing the understanding of bound and metastable (electron-molecule scattering resonances) negative ion states, doorway states for chemical reduction, dissociative attachment processes and ion-molecule interactions. Furthermore, the results provide vital tests of high level ab initio theoretical methods, particularly those designed to deal with highly correlated systems and/or non-stationary states.
The technique combines ion production, mass spectrometry and charged particle imaging2,3,4 to sensitively probe electronic (and for small molecules, vibrational) structure. Working with anionic species allows good mass selectivity via time of flight mass spectrometry (TOF-MS). Visible/near ultraviolet (UV) photons are sufficiently energetic to remove the excess electron, allowing the use of table top laser sources. An additional benefit of the use of anions is the ability to photoexcite low-lying, unstable anionic states which represent energy regimes under which the electrons and neutral atoms/molecules strongly interact. The use of velocity mapped imaging5 (VMI) affords uniform detection efficiency, even at low electron kinetic energies, monitors all ejected photoelectrons and simultaneously reveals the magnitude and direction of their velocities.
The experimental results are photoelectron images which contain photoelectron spectra (details of parent anion internal energy distributions and the energies of daughter neutral internal states) and photoelectron angular distributions (related to the electron orbital prior to the detachment). A particularly interesting application of the technique is found in fs time-resolved studies. An initial ultrafast laser pulse (pump) excites to a dissociative anion electronic state, and a second temporally delayed ultrafast pulse (probe) then detaches electrons from the excited anion. The control of the pump-probe time difference follows the evolution of energy states of the system and the changing nature of the orbitals of the system on the timescale of the atomic motion. Examples include the photodissociation of I2&#8722; and other interhalogen species6,7,8,9, the fragmentation and/or electron accommodation in I&#8722;&#183;uracil10,11,12,13, I&#8722;&#183;thymine13,14, I&#8722;&#183;adenine15, I&#8722;&#183;nitromethane16,17 and I&#8722;&#183;acetonitrile17 cluster anions and the revelation of the hitherto unexpectedly long timescale for the production of Cu&#8722; atomic anions after the photoexcitation of CuO2&#8722;18.
Figure 1 shows the Washington University in St. Louis (WUSTL) anion photoelectron imaging spectrometer19. The instrument consists of three differentially pumped regions. Ions are produced in the source chamber which operates at a pressure of 10&#8722;5 Torr and contains a discharge ion source20, and electrostatic ion extraction plate. Ions are separated by mass in a Wiley-McLaren TOF-MS21 (the pressure in the TOF-Tube is 10&#8722;8 Torr). Ion detection and probing takes place in the detection region (pressure of 10&#8722;9 Torr) which contains a VMI lens5 and a charged particle detector. The main components of the instrument are schematically illustrated in Figure 1b where the shaded region represents all the elements contained within the vacuum system. Gas is introduced through the pulsed nozzle into the discharge. To offset the high inlet pressure, the source chamber is maintained under vacuum using an oil-based diffusion pump. The discharge region is illustrated in more detail in Figure 2a. A high potential difference is applied between the electrodes, which are insulated from the face of the nozzle by a series of Teflon spacers. In fact, the Teflon acts as the source of fluorine atoms for the results shown later.
The discharge produces a mixture of anions, cations and neutral species. The ion extraction plate, ion acceleration stack, potential switch and microchannel plate (MCP) detector (Figure 1b) form the 2 m long Wiley McLaren TOF-MS. Ions are extracted by the application of a (negative) voltage pulse to the ion extraction plate and then all ions are accelerated to the same kinetic energy. Variation of the extraction pulse magnitude focuses the arrival time in the VMI lens while the einzel lens reduces the spatial cross section of the ion beam. Anions are re-referenced to ground using a potential switch22, the timing of which acts as a mass discriminator. Anion selection is achieved by synchronizing the arrival of a visible/near uv photon pulse with the arrival time of the anion in the VMI lens. The ion separation and detection regions use oil free turbopumps to protect the imaging detector.
Anions and photons interact to produce photoelectrons throughout the spatial volume of the Steinmetz solid, representing the overlap between the ion and laser beams. The VMI lens (Figure 2b) consists of three open electrodes, the purpose of which is to ensure that all photoelectrons reach the detector and that the momentum space distribution of the photoelectrons is maintained. To achieve this, different voltages are applied to the extractor and repeller such that, regardless of the spatial point of origin, electrons with the same initial velocity vector are detected at the same point on the detector. The detector consists of a set of chevron-matched MCPs which act as electron multipliers. Each channel has a diameter on the order of a few microns, localizing the gain and preserving the initial impact position. A phosphor screen behind the MCPs indicates the position via the amplified electron pulse as a flash of light which is recorded using a charge coupled device (CCD) camera.
The timing and duration of the various voltage pulses required are controlled using a pair of digital delay generators (DDG, Figure 3). The whole experiment is repeated on a shot by shot basis with a repetition rate of 10 Hz. For each shot, several ions and photons interact producing a few detection events per camera frame. Several thousand frames are accumulated into an image. The image center represents the momentum space origin and hence the distance from the center (r) is proportional to the speed of an electron. Angle &#952;, (relative to the photon polarization direction) represents the direction of an electron&#39;s velocity. An image contains the distribution of detection event densities. Thus, it can also be viewed as representing the probability density for detection (at a given point) of an electron. Invoking the Born interpretation of the wave function (&#968;) an image represents |&#968;|2 for the photoelectron23.
The 3D electron probability density is cylindrically symmetric about the polarization of the electric vector (&#949;p) of the radiation with consequent scrambling of information. Reconstruction of the original distribution is achieved mathematically24,25,26,27. The radial distribution (of electrons) in the reconstruction is the momentum (velocity) domain photoelectron spectrum which is converted into the energy domain via application of the appropriate Jacobian transformation.
The anion photoelectron imaging spectrometer (Figure 1) used in these experiments is a custom-built instrument28. The settings in Table 1 and Table 2 for the protocol are specific to this instrument for the production of F&#8722; and imaging of its photoelectron distribution. Several similar versions of the design are used in various research laboratories6,29,30,31,32,33,34,35,36,37,38,39,40,41,42, but no two instruments are exactly alike. Additionally, instrument settings are strongly interdependent and highly sensitive to small changes in conditions and instrument dimensions.

<table><tbody><tr><td>Digital Delay Generators</td><td>Berkeley Nucleonics Corp.</td><td>565-8c</td><td>DDG1</td></tr><tr><td>Digital Delay Generators</td><td>Berkeley Nucleonics Corp.</td><td>577-8c</td><td>DDG2</td></tr><tr><td>HV Power Supplies</td><td>Stanford Research Systems</td><td>PS325</td><td>V3</td></tr><tr><td>HV Power Supplies</td><td>Stanford Research Systems</td><td>PS325</td><td>V2</td></tr><tr><td>HV Power Supplies</td><td>Stanford Research Systems</td><td>PS325</td><td>V5</td></tr><tr><td>HV Power Supplies</td><td>Burle Inc.</td><td>PF1053</td><td>V9</td></tr><tr><td>HV Power Supplies</td><td>Burle Inc.</td><td>PF1053</td><td>V4</td></tr><tr><td>HV Power Supplies</td><td>Burle Inc.</td><td>PF1053</td><td>V10</td></tr><tr><td>HV Power Supplies</td><td>Burle Inc.</td><td>PF1054</td><td>V9,V11</td></tr><tr><td>HV Power Supplies</td><td>Bertan</td><td>205B-05R</td><td>V6</td></tr><tr><td>HV Pulsers</td><td>Directed Energy Inc.</td><td>PVX-4150</td><td>V2</td></tr><tr><td>HV Pulsers</td><td>Directed Energy Inc.</td><td>PVX-4140</td><td>V1</td></tr><tr><td>HV Pulsers</td><td>Directed Energy Inc.</td><td>PVX-4140</td><td>V11</td></tr><tr><td>HV Pulsers</td><td>Directed Energy Inc.</td><td>PVX-4140</td><td>V3</td></tr><tr><td>Pulsed Nozzle Driver</td><td>Parker Hannifin (General Valve)</td><td>Iota-One</td><td></td></tr><tr><td>Pulsed Nozzle</td><td>Parker Hannifin (General Valve)</td><td>Series 9</td><td></td></tr><tr><td>Camera</td><td>Imperx</td><td>VGA120</td><td></td></tr><tr><td>Imaging Detector</td><td>Beam Imaging Systems</td><td>BOS40</td><td></td></tr><tr><td>Oscilloscope</td><td>LeCroy</td><td>Wavejet 334</td><td></td></tr><tr><td>Photodiode</td><td>ThorLabs</td><td>DET10A</td><td></td></tr><tr><td>Diffusion Pump</td><td>Leybold</td><td>DIP 8000</td><td></td></tr><tr><td>2&amp;times;Turbo Pump</td><td>Leybold</td><td>TMP361</td><td></td></tr><tr><td>Rotary Pump</td><td>Leybold</td><td>D40B</td><td></td></tr><tr><td>2&amp;times;Rotary Pump</td><td>Leybold</td><td>D16B</td><td></td></tr><tr><td>Oxygen Gas</td><td>Praxair</td><td>OX 5.0RS</td><td></td></tr><tr><td>Tunable Laser</td><td>Spectra Physics Sirah Dye Laser</td><td>Cobra-Stretch</td><td></td></tr><tr><td>Pump laser for Dye Laser</td><td>Sepctra Physics Nd:YAG</td><td>INDI-10</td><td></td></tr></tbody></table>

photoelectron imaging of anions illustrated by 310 nm detachment of f&#8722;

Anion photoelectron imaging is a very efficient method for the study of energy states of bound negative ions, neutral species and interactions of unbound electrons with neutral molecules/atoms. State-of-the-art in vacuo anion generation techniques allow application to a broad range of atomic, molecular, and cluster anion systems. These are separated and selected using time-of-flight mass spectrometry. Electrons are removed by linearly polarized photons (photo detachment) using table-top laser sources which provide ready access to excitation energies from the infra-red to the near ultraviolet. Detecting the photoelectrons with a velocity mapped imaging lens and position sensitive detector means that, in principle, every photoelectron reaches the detector and the detection efficiency is uniform for all kinetic energies. Photoelectron spectra extracted from the images via mathematical reconstruction using an inverse Abel transformation reveal details of the anion internal energy state distribution and the resultant neutral energy states. At low electron kinetic energy, typical resolution is sufficient to reveal energy level differences on the order of a few millielectron-volts, i.e., different vibrational levels for molecular species or spin-orbit splitting in atoms. Photoelectron angular distributions extracted from the inverse Abel transformation represent the signatures of the bound electron orbital, allowing more detailed probing of electronic structure. The spectra and angular distributions also encode details of the interactions between the outgoing electron and the residual neutral species subsequent to excitation. The technique is illustrated by the application to an atomic anion (F&#8722;), but it can also be applied to the measurement of molecular anion spectroscopy, the study of low lying anion resonances (as an alternative to scattering experiments) and femtosecond (fs) time resolved studies of the dynamic evolution of anions.

By centroiding43 the data recorded on the 640&#215;480 pixel CCD array of the camera, a grid resolution of 6400&#215;4800 is possible. However, extraction of the spectra and angular distributions involves inverse Abel transformation of the data which requires the image intensity to vary relatively smoothly. As a compromise, the centroided data is &#34;binned&#34; by summing n&#215;n blocks of points. Similar treatment is also necessary for the display of imaging re...

Watch this Scientific Journal Video about Photoelectron Imaging of Anions Illustrated by 310 Nm Detachment of Fâˆ' at JoVE.com

Photoelectron Imaging of Anions Illustrated by 310 Nm Detachment of F&#8722;

Here, we present a protocol for photoelectron imaging of anionic species. Anions generated in vacuo and separated by mass spectrometry are probed using velocity mapped photoelectron imaging, providing details of anion and neutral energy levels, anion and neutral structure and the nature of the anion electronic state.

Anion photoelectron imaging is a very efficient method for the study of energy states of bound negative ions, neutral species and interactions of unbound ...

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8.6K Views.  Washington University in St. Louis. Here, we present a protocol for photoelectron imaging of anionic species. Anions generated in vacuo and separated by mass spectrometry are probed using velocity mapped photoelectron imaging, providing details of anion and neutral energy levels, anion and neutral structure and the nature of the anion electronic state.

Video: Photoelectron Imaging of Anions Illustrated by 310 Nm Detachment of F−

Electron Channeling Contrast Imaging for Rapid III-V Heteroepitaxial Characterization

Misfit dislocations in heteroepitaxial layers of GaP grown on Si(001) substrates are characterized through use of electron channeling contrast imaging (ECCI) in a scanning electron microscope (SEM). ECCI allows for imaging of defects and crystallographic features under specific diffraction conditions, similar to that possible via plan-view transmission electron microscopy (PV-TEM). A particular advantage of the ECCI technique is that it requires little to no sample preparation, and indeed can use large area, as-produced samples, making it a considerably higher throughput characterization method than TEM. Similar to TEM, different diffraction conditions can be obtained with ECCI by tilting and rotating the sample in the SEM. This capability enables the selective imaging of specific defects, such as misfit dislocations at the GaP/Si interface, with high contrast levels, which are determined by the standard invisibility criteria. An example application of this technique is described wherein ECCI imaging is used to determine the critical thickness for dislocation nucleation for GaP-on-Si by imaging a range of samples with various GaP epilayer thicknesses. Examples of ECCI micrographs of additional defect types, including threading dislocations and a stacking fault, are provided as demonstration of its broad, TEM-like applicability. Ultimately, the combination of TEM-like capabilities &#8211; high spatial resolution and richness of microstructural data &#8211; with the convenience and speed of SEM, position ECCI as a powerful tool for the rapid characterization of crystalline materials.

The use of electron channeling contrast imaging in a scanning electron microscope to characterize defects in III-V/Si heteroexpitaxial thin films is described. This method yields similar results to plan-view transmission electron microscopy, but in significantly less time due to lack of required sample preparation.

Misfit dislocations in heteroepitaxial layers of GaP grown on Si(001) substrates are characterized through use of electron channeling contrast imaging ...

Engineering

Experimental Methods for Trapping Ions Using Microfabricated Surface Ion Traps

Ions trapped in a quadrupole Paul trap have been considered one of the strong physical candidates to implement quantum information processing. This is due to their long coherence time and their capability to manipulate and detect individual quantum bits (qubits). In more recent years, microfabricated surface ion traps have received more attention for large-scale integrated qubit platforms. This paper presents a microfabrication methodology for ion traps using micro-electro-mechanical system (MEMS) technology, including the fabrication method for a 14 &#181;m-thick dielectric layer and metal overhang structures atop the dielectric layer. In addition, an experimental procedure for trapping ytterbium (Yb) ions of isotope 174 (174Yb+) using 369.5 nm, 399 nm, and 935 nm diode lasers is described. These methodologies and procedures involve many scientific and engineering disciplines, and this paper first presents the detailed experimental procedures. The methods discussed in this paper can easily be extended to the trapping of Yb ions of isotope 171 (171Yb+) and to the manipulation of qubits.

This paper presents a microfabrication methodology for surface ion traps, as well as a detailed experimental procedure for trapping ytterbium ions in a room-temperature environment.

Ions trapped in a quadrupole Paul trap have been considered one of the strong physical candidates to implement quantum information processing. This is due ...

An Experimental Protocol for Femtosecond NIR/UV - XUV Pump-Probe Experiments with Free-Electron Lasers

This protocol describes key steps in performing and analyzing femtosecond pump-probe experiments that combine a femtosecond optical laser with a free-electron laser. This includes methods to establish the spatial and temporal overlap between the optical and free-electron laser pulses during the experiment, as well as important aspects of the data analysis, such as corrections for arrival time jitter, which are necessary to obtain high-quality pump-probe data sets with the best possible temporal resolution. These methods are demonstrated for an exemplary experiment performed at the FLASH (Free-electron LASer Hamburg) free-electron laser in order to study ultrafast photochemistry in gas-phase molecules by means of velocity map ion imaging. However, most of the strategies are also applicable to similar pump-probe experiments using other targets or other experimental techniques.

This protocol describes the key steps for performing and analyzing pump-probe experiments combining a femtosecond optical laser with a free-electron laser in order to study ultrafast photochemical reactions in gas-phase molecules.

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We discuss in this article the experimental measurements of the molecules in liquid crystal (LC) phase using the time-resolved infrared (IR) vibrational spectroscopy and time-resolved electron diffraction. Liquid crystal phase is an important state of matter that exists between the solid and liquid phases and it is common in natural systems as well as in organic electronics. Liquid crystals are orientationally ordered but loosely packed, and therefore, the internal conformations and alignments of the molecular components of LCs can be modified by external stimuli. Although advanced time-resolved diffraction techniques have revealed picosecond-scale molecular dynamics of single crystals and polycrystals, direct observations of packing structures and ultrafast dynamics of soft materials have been hampered by blurry diffraction patterns. Here, we report time-resolved IR vibrational spectroscopy and electron diffractometry to acquire ultrafast snapshots of a columnar LC material bearing a photoactive core moiety. Differential-detection analyses of the combination of time-resolved IR vibrational spectroscopy and electron diffraction are powerful tools for characterizing structures and photoinduced dynamics of soft materials.

Here, we present the protocols of differential-detection analyses of time-resolved infrared vibrational spectroscopy and electron diffraction which enable observations of the deformations of local structures around photoexcited molecules in a columnar liquid crystal, giving an atomic perspective on the relationship between the structure and the dynamics of this photoactive material.

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Single Molecule Fluorescence Microscopy on Planar Supported Bilayers

In the course of a single decade single molecule microscopy has changed from being a secluded domain shared merely by physicists with a strong background in optics and laser physics to a discipline that is now enjoying vivid attention by life-scientists of all venues 1. This is because single molecule imaging has the unique potential to reveal protein behavior in situ in living cells and uncover cellular organization with unprecedented resolution below the diffraction limit of visible light 2. Glass-supported planar lipid bilayers (SLBs) are a powerful tool to bring cells otherwise growing in suspension in close enough proximity to the glass slide so that they can be readily imaged in noise-reduced Total Internal Reflection illumination mode 3,4. They are very useful to study the protein dynamics in plasma membrane-associated events as diverse as cell-cell contact formation, endocytosis, exocytosis and immune recognition. Simple procedures are presented how to generate highly mobile protein-functionalized SLBs in a reproducible manner, how to determine protein mobility within and how to measure protein densities with the use of single molecule detection. It is shown how to construct a cost-efficient single molecule microscopy system with TIRF illumination capabilities and how to operate it in the experiment.

Preparation of protein-functionalized planar glass-supported lipid bilayers, determination of protein mobility within and measurement of protein densities is shown here. A roadmap to building a noise-reduced Total Internal Reflection microscope is outlined, which allows visualizing single bilayer-resident fluorochromes with high spatiotemporal resolution.

In the course of a single decade single molecule microscopy has changed from being a secluded domain shared merely by physicists with a strong background ...

Bioengineering

Sample Preparation and Experimental Design for In Situ Multi-Beam Transmission Electron Microscopy Irradiation Experiments

There is a need to understand materials exposed to overlapping extreme environments such as high temperature, radiation, or mechanical stress. When these stressors are combined there may be synergistic effects that enable unique microstructural evolution mechanisms to activate. Understanding of these mechanisms is necessary for the input and refinement of predictive models and critical for engineering of next generation materials. The basic physics and underlying mechanisms require advanced tools to be investigated. The in situ ion irradiation transmission electron microscope (I&#179;TEM) is designed to explore these principles.
To quantitatively probe the complex dynamic interactions in materials, careful preparation of samples and consideration of experimental design is required. Particular handling or preparation of samples can easily introduce damage or features that obfuscate the measurements. There is no one correct way to prepare a sample; however, many mistakes can be made. The most common errors and things to consider are highlighted within. The I&#179;TEM has many adjustable variables and a large potential experimental space, therefore it is best to design experiments with a specific scientific question or questions in mind.
Experiments have been performed on large number of sample geometries, material classes, and with many irradiation conditions. The following are a subset of examples that demonstrate unique in situ capabilities utilizing the I3TEM. Au nanoparticles prepared by drop casting have been used to investigate the effects of single ion strikes. Au thin films have been used in studies on the effects of multibeam irradiation on microstructure evolution. Zr films have been exposed to irradiation and mechanical tension to examine creep. Ag nanopillars were subjected to simultaneous high temperature, mechanical compression, and ion irradiation to study irradiation induced creep as well. These results impact fields including: structural materials, nuclear energy, energy storage, catalysis, and microelectronics in space environments.

Sample preparation techniques are outlined with specific considerations for in situ ion irradiation TEM experiments. Ion species, energy, and fluence are discussed with methods for how to select and compute them. Finally, procedures for conducting an experiment are described and accompanied by the representative results.

There is a need to understand materials exposed to overlapping extreme environments such as high temperature, radiation, or mechanical stress. When these ...

Single-Molecule Imaging of Lateral Mobility and Ion Channel Activity in Lipid Bilayers using Total Internal Reflection Fluorescence (TIRF) Microscopy

High-resolution imaging techniques have shown that many ion channels are not static, but subject to highly dynamic processes, including the transient association of pore-forming and auxiliary subunits, lateral diffusion, and clustering with other proteins. However, the relationship between lateral diffusion and function is poorly understood. To approach this problem, we describe how lateral mobility and activity of individual channels in supported lipid membranes can be monitored and correlated using total internal reflection fluorescence (TIRF) microscopy. Membranes are fabricated on an ultrathin hydrogel substrate using the droplet interface bilayer (DIB) technique. Compared to other types of model membranes, these membranes have the advantage of being mechanically robust and suitable for highly sensitive analytical techniques. This protocol measures Ca2+ ion flux through single channels by observing the fluorescence emission of a Ca2+-sensitive dye in close proximity to the membrane. In contrast to classical single-molecule tracking approaches, no fluorescent fusion proteins or labels, which can interfere with lateral movement and function in the membrane, are required. Possible changes in ion flux associated with conformational changes of the protein are only due to protein lateral motion in the membrane. Representative results are shown using the mitochondrial protein translocation channel TOM-CC and the bacterial channel OmpF. In contrast to OmpF, the gating of TOM-CC is very sensitive to molecular confinement and the nature of lateral diffusion. Hence, supported droplet-interface bilayers are a powerful tool to characterize the link between lateral diffusion and the function of ion channels.

Single-Molecule Imaging of Lateral Mobility and Ion Channel Activity in Lipid Bilayers using Total Internal Reflection Fluorescence TIRF Microscopy

This protocol describes how to use TIRF microscopy to track individual ion channels and determine their activity in supported lipid membranes, thereby defining the interplay between lateral membrane movement and channel function. It describes how to prepare the membranes, record the data, and analyze the results.

High-resolution imaging techniques have shown that many ion channels are not static, but subject to highly dynamic processes, including the transient ...

Biochemistry

Examining the Conformational Dynamics of Membrane Proteins in situ with Site-directed Fluorescence Labeling

Two electrode voltage clamp electrophysiology (TEVC) is a powerful tool to investigate the mechanism of ion transport1 for a wide variety of membrane proteins including ion channels2, ion pumps3, and transporters4. Recent developments have combined site-specific fluorophore labeling alongside TEVC to 
concurrently examine the conformational dynamics at specific residues and function of these proteins on the surface of single cells.
We will describe a method to study the conformational dynamics of membrane proteins by simultaneously monitoring fluorescence and current changes using voltage-clamp fluorometry. This approach can be used to examine the molecular motion of membrane proteins site-specifically following cysteine replacement and site-directed fluorophore labeling5,6. Furthermore, this method provides an approach to determine distance constraints between specific residues7,8. 
This is achieved by selectively attaching donor and acceptor fluorophores to two mutated cysteine residues of interest.
In brief, these experiments are performed following functional expression of the desired protein on the surface of Xenopus leavis oocytes. The large surface area of these oocytes enables facile functional measurements and a robust fluorescence signal5. It is also possible to readily change the extracellular conditions such as pH, ligand or cations/anions, which can provide further information on the mechanism of membrane proteins4. Finally, recent developments 
have also enabled the manipulation of select internal ions following co-expression with a second protein9.
Our protocol is described in multiple parts. First, cysteine scanning mutagenesis proceeded by fluorophore labeling is completed at residues located at the interface of the transmembrane and extracellular domains. Subsequent experiments are designed to identify residues which demonstrate large changes in fluorescence intensity (&lt;5%)3 upon a conformational change of the protein. Second, these changes in fluorescence intensity are compared to the kinetic parameters of 
the membrane protein in order to correlate the conformational dynamics to the function of the protein10. This enables a rigorous biophysical analysis of the molecular motion of the target protein. Lastly, two residues of the holoenzyme can be labeled with a donor and acceptor fluorophore in order to determine distance constraints using donor photodestruction methods. It is also possible to monitor the relative movement of protein subunits following labeling with a donor and acceptor fluorophore.

Examining the Conformational Dynamics of Membrane Proteins in situ with Site-directed Fluorescence Labeling

We will describe a method which measures the kinetics of ion transport of membrane proteins alongside site-specific analysis of conformational changes using fluorescence on single cells. This technique is adaptable to ion channels, transporters and ion pumps and can be utilized to determine distance constraints between protein subunits.

Two electrode voltage clamp electrophysiology (TEVC) is a powerful tool to investigate the mechanism of ion transport1 for a wide variety of membrane ...

Biology

Imaging Plasma Membrane Deformations With pTIRFM

To gain novel insights into the dynamics of exocytosis, our group focuses on the changes in lipid bilayer shape that must be precisely regulated during the fusion of vesicle and plasma membranes. These rapid and localized changes are achieved by dynamic interactions between lipids and specialized proteins that control membrane curvature. The absence of such interactions would not only have devastating consequences for vesicle fusion, but a host of other cellular functions that involve control of membrane shape. In recent years, the identity of a number of proteins with membrane-shaping properties has been determined. What remains missing is a roadmap of when, where, and how they act as fusion and content release progress.
Our understanding of the molecular events that enable membrane remodeling has historically been limited by a lack of analytical methods that are sensitive to membrane curvature or have the temporal resolution to track rapid changes. PTIRFM satisfies both of these criteria. We discuss how pTIRFM is implemented to visualize and interpret rapid, submicron changes in the orientation of chromaffin cell membranes during dense core vesicle (DCV) fusion. The chromaffin cells we use are isolated from bovine adrenal glands. The membrane is stained with a lipophilic carbocyanine dye,1,1&#39;-dioctadecyl-3,3,3&#39;,3&#39;-tetramethylindodicarbocyanine, 4-chlorobenzenesulfonate, or&#160;diD. DiD intercalates in the membrane plane with a &#34;fixed&#34; orientation and is therefore sensitive to the polarization of the evanescent field. The diD-stained cell membrane is sequentially excited with orthogonal polarizations of a 561&#160;nm laser (p-pol, s-pol). A 488&#160;nm laser is used to visualize vesicle constituents and time the moment of fusion. Exocytosis is triggered by locally perfusing cells with a depolarizing KCl solution. Analysis is performed offline using custom-written software to understand how diD emission intensity changes relate to fusion pore dilation.

Polarization-based Total Internal Reflection Fluorescence Microscopy (pTIRFM) enables real-time detection of cell membrane dynamics. This article describes the implementation of pTIRFM for the study of membrane remodeling during regulated exocytosis. The technique is generalizable to other processes in cell biology that directly or indirectly involve changes in membrane shape.

To gain novel insights into the dynamics of exocytosis, our group focuses on the changes in lipid bilayer shape that must be precisely regulated during ...

Fluorescence Imaging with One-nanometer Accuracy (FIONA)

Fluorescence imaging with one-nanometer accuracy (FIONA) is a simple but useful technique for localizing single fluorophores with nanometer precision in the x-y plane. Here a summary of the FIONA technique is reported and examples of research that have been performed using FIONA are briefly described. First, how to set up the required equipment for FIONA experiments, i.e., a total internal reflection fluorescence microscopy (TIRFM), with details on aligning the optics, is described. Then how to carry out a simple FIONA experiment on localizing immobilized Cy3-DNA single molecules using appropriate protocols, followed by the use of FIONA to measure the 36 nm step size of a single truncated myosin Va motor labeled with a quantum dot, is illustrated. Lastly, recent effort to extend the application of FIONA to thick samples is reported. It is shown that, using a water immersion objective and quantum dots soaked deep in sol-gels and rabbit eye corneas (&#62;200 &#181;m), localization precision of 2-3 nm can be achieved.

Fluorescence Imaging with One-nanometer Accuracy FIONA

Single fluorophores can be localized with nanometer precision using FIONA. Here a summary of the FIONA technique is reported, and how to carry out FIONA experiments is described.

Fluorescence imaging with one-nanometer accuracy (FIONA) is a simple but useful technique for localizing single fluorophores with nanometer precision in ...

Photoelectron Imaging of Anions Illustrated by 310 Nm Detachment of F⁻

Summary

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Sample Preparation and Experimental Design for In Situ Multi-Beam Transmission Electron Microscopy Irradiation Experiments

Single-Molecule Imaging of Lateral Mobility and Ion Channel Activity in Lipid Bilayers using Total Internal Reflection Fluorescence (TIRF) Microscopy

Examining the Conformational Dynamics of Membrane Proteins in situ with Site-directed Fluorescence Labeling

Imaging Plasma Membrane Deformations With pTIRFM

Fluorescence Imaging with One-nanometer Accuracy (FIONA)