The authors thank Evgeny Savelyev, C&#233;dric Bomme, Nora Schirmel, Harald Redlin, Stefan D&#252;sterer, Erland M&#252;ller, Hauke H&#246;ppner, Sven Toleikis, Jost M&#252;ller, Marie Kristin Czwalinna, Rolf Treusch, Thomas Kierspel, Terence Mullins, Sebastian Trippel, Joss Wiese, Jochen K&#252;pper, Felix Brau&#946;e, Faruk Krecinic, Arnaud Rouz&#233;e, Piotr Rudawski, Per Johnsson, Kasra Amini, Alexandra Lauer, Michael Burt, Mark Brouard, Lauge Christensen, Jan Th&#248;gersen, Henrik Stapelfeldt, Nora Berrah, Maria M&#252;ller, Anatoli Ulmer, Simone Techert,&#160;Artem Rudenko, Daniela Rupp, and Melanie Schnell, who participated in the FLASH beamtime during which the specific data shown and discussed here were acquired and who contributed to the analysis and interpretation. The work of the scientific and technical teams at FLASH, who have made the experiment possible, is also gratefully acknowledged. D.R. acknowledges support from the Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U.S. Department of Energy, Grant No. DE-FG02-86ER13491. The experiments at FLASH were also supported by the Helmholtz Gemeinschaft through the Helmholtz Young Investigator Program. We acknowledge the Max Planck Society for funding the development and the initial operation of the CAMP end-station within the Max Planck Advanced Study Group at CFEL and for providing this equipment for CAMP@FLASH. The installation of CAMP@FLASH was partially funded by the BMBF grants 05K10KT2, 05K13KT2, 05K16KT3 and 05K10KTB from FSP-302

<ol>
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The authors declare no competing interests.

Due to the complexity of the experimental setups, pump-probe experiments with free-electron lasers require a high level of expertise and experience and need very careful preparation and detailed discussions with the scientific teams that operate the free-electron laser, the optical laser, and the end-station, both before and during the experiment. While performing the actual experiment, precise determination of spatial and temporal overlap and close monitoring of all diagnostics and timing systems, as described in this protocol, are essential.
Note that most of the methods described here are only applicable for a specific photon energy range of the FEL since they rely on effects that strongly depend on the photon energy. For example, the determination of the &#34;rough&#34; temporal overlap using scattered light directed on a photodiode was found to work well for photon energies up to ~250 eV. At higher photon energies, the signal generated by the FEL pulses becomes so small that it is hard to detect. In that case, an open-ended SMA cable that can be brought very close (less than a millimeter) to or even into the FEL beam was found to produce a more reliable signal to perform the procedure described in step 3.1) of the protocol. Similarly, the best target for determining the &#34;fine&#34; timing, described in step 3.2), is strongly dependent on the photon energy. For FEL pulses in the XUV and soft X-ray region above 65.7 eV and ~57 eV photon energy (corresponding to the 4d ionization thresholds in xenon and CH3I, respectively), Xe and CH3I were found to be suitable targets for the procedure described in step 3.2. The method using CH3I was found to work for photon energies up to 2 keV (above which it has not yet been tested), while the method using Xe has been tested up to 250 eV. For photon energies below 50 eV, the bond softening process in H2 can be used19. At photon energies above 400 eV, a similar process in N2 is also suitable20. Alternative approaches involve the change in reflectivity of a solid sample25,26,30 or the formation of side bands in the photoelectron spectrum31,32.
In order to achieve the best temporal resolution, it is necessary to sort the experimental data on a shot-by-shot basis in the data analysis to compensate for the arrival time jitter between the FEL and the optical laser pulses, as described in step 5. However, the quality of the pump-probe data and, in particular, the achievable temporal resolution, strongly depends on the performance of the FEL during the experiment and on the pulse durations of the optical laser pulses and the FEL pulses that can be provided during that time. For the exemplary data shown here, the pulse duration of the UV pulses was estimated to be 150 fs (FWHM) and the FEL pulse duration was estimated to be 120 fs (FWHM). Although the total arrival time-jitter of approximately 90 fs (rms) before jitter-correction could be reduced to approximately 27 fs (rms) using the procedure described here12, the resulting improvement of the total temporal resolution of the experiment was rather small because of the relatively long pulse durations of the FEL and the optical laser. Both can, however, be reduced substantially, in which case the impact of the jitter correction scheme will be more significant. For example, a new optical laser is currently being installed at FLASH, which will have a pulse duration (in the near-infrared) below 15 fs, while new FEL operation modes are also being tested that can produce FEL pulses with pulse durations of a few femtoseconds or even below. These developments will soon enable pump-probe experiments combining FEL and optical laser pulses with an overall temporal resolution of only a few tens of femtoseconds.
While the increased availability of short and intense XUV and X-ray pulses produced by FELs has spawned a number of NIR/UV - XUV pump-probe experiments such as the one described here, similar pump-probe experiments can also be performed with high harmonic generation (HHG) sources33,34,35. The main limitation of the FEL-based experiments is typically the achievable temporal resolution, which is fundamentally limited by the synchronization between the FEL and the optical laser or by the precision with which the relative timing between the pump and the probe pulses can be measured. This is not the case for a HHG-based pump-probe experiment, where the XUV and NIR pulses are intrinsically synchronized with sub-cycle precision and which can therefore, in general, have a much higher temporal resolution. The major advantage of the FEL-based experiments, on the other hand, is the several orders of magnitude higher photon fluence, which enables experiments, e.g., on dilute targets that are not be feasible with current HHG sources, especially at higher photon energies in the soft X-ray regime. For the foreseeable future, pump-probe experiments with FELs and HHG will therefore remain complementary, with some overlap in the XUV region where both can be used for similar investigations. Some of the steps to perform these experiments are also similar, and some of the methods described here can therefore also be applied for HHG-based pump-probe experiments.

The availability of short and intense extreme ultraviolet (XUV) and X-ray pulses from free-electron lasers (FELs)1,2 has opened up new opportunities for femtosecond pump-probe experiments exploiting the site- and element-specificity of the inner-shell photo-absorption process3,4,5,6. Such experiments can be used, e.g., to investigate molecular dynamics and charge transfer processes in liquids7 and gas-phase molecules8,9,10,11,12, and for real-time observations of catalytic reactions and ultrafast surface chemistry13,14 with a temporal resolution of 100 femtoseconds or below. If the pump-probe experiment is performed by combining a synchronized optical femtosecond laser with the FEL, which was the case in all of the examples mentioned above, the intrinsic arrival-time jitter between the optical laser and the FEL pulses has to be measured on a shot-by-shot basis and corrected for in the data analysis in order to achieve the best temporal resolution possible.
Within a large collaboration, several pump-probe experiments combining optical lasers with a free-electron laser have recently been performed9,10,11,12, both at the FLASH XUV FEL15,16 and the LCLS X-ray FEL17 facilities, and an experimental protocol for performing and analyzing these experiments has been developed, which is presented in the following. The method is demonstrated for an exemplary experiment performed at the FLASH free-electron laser in order to study ultrafast photochemistry in gas-phase molecules by means of velocity map ion imaging11,12. However, most of the strategies are also applicable to similar pump-probe experiments using other targets or other experimental techniques and can also be adapted to other FEL facilities. While some of the individual steps presented here or variations thereof have already been discussed in the literature18,19,20, this protocol provides a comprehensive description of the key steps, including some that take advantage of the most recent technical improvements in the synchronization and in the timing diagnostics, which have considerably improved the stability and the temporal resolution for pump-probe experiments12,21.
The following protocol assumes a pump-probe end-station, such as the CAMP instrument at FLASH22, equipped with an ion time-of-flight, an ion momentum imaging, or a velocity map imaging (VMI) ion spectrometer; an effusive or supersonic gas jet; and a synchronized near-infrared (NIR) or ultraviolet (UV) femtosecond laser, whose pulses can be overlapped collinearly or near-collinearly with the free-electron laser beam, as sketched schematically in Figure 1. Furthermore, an appropriate suite of diagnostics tools such as a removable beam viewing screen (e.g. a paddle coated with Ce:YAG powder or a thin Ce:YAG crystal) in the interaction region, a fast photodiode sensitive to both FEL and laser pulses, and a bunch arrival-time monitor (BAM)23,24 or &#34;timing tool&#34;25,26,27 are required, all of which are usually integrated in the pump-probe end-station or are provided by the FEL facility, if requested before the experiment. Finally, the shot-by-shot jitter correction assumes that the experimental data is recorded and accessible on a shot-by-shot basis and linked to the shot-by-shot measurements of the bunch arrival-time time jitter by using a unique &#34;bunch ID&#34; or by another equivalent scheme.
At FLASH, the specific systems that are crucial for pump-probe experiments are:
<ul>
	<li>The active, all-optical feedback and stabilization system of the pump-probe laser to the master laser oscillator, which includes a balanced optical cross-correlator that stabilizes the pump-probe laser&#39;s oscillator output to the master laser oscillator, and a cross-correlator (&#34;drift correlator&#34;) to correct for slow drifts of the laser amplifier with respect to the oscillator21.</li>
	<li>The bunch arrival-time monitors (BAMs) that measure the shot-to-shot variations in the electron bunch arrival time at various positions in the accelerator with respect to the master laser oscillator23,24. They can be used for an active-feedback loop to stabilize the timing of the electron bunches with respect to the master laser oscillator, thus reducing slow drifts in the arrival time. Moreover, the BAM located closed to the experiment (BAM 4DBC3) can be used for a shot-to-shot jitter correction in the data analysis, which is in detail in step 5.1 of the experimental protocol.</li>
	<li>The pump-probe laser streak camera, which measures the relative timing between the pump-probe laser output and the dipole radiation generated by the electron bunch at the end of the accelerator before it is guided into the beam dump28.</li>
	<li>The focus camera, which images the &#34;virtual&#34; laser focus by using the part of the laser beam that is leaking through the last turning mirror behind the focusing lens in order to parasitically monitor slow spatial drifts of the optical laser.</li>
</ul>
Similar systems are available at other FEL facilities and are crucial for performing a reliable pump-probe experiment.

<table>
	<tbody>
		<tr>
			<td>Xenon</td>
			<td>Linde</td>
			<td></td>
			<td>minican</td>
		</tr>
		<tr>
			<td>CH3I (methyl iodide)</td>
			<td>Sigma Aldrich</td>
			<td>67692</td>
			<td>or other suitable sample</td>
		</tr>
		<tr>
			<td>FEL pump-probe endstation</td>
			<td>CAMP@FLASH or LAMP@LCLS</td>
			<td></td>
			<td>or a similar endstation at another FEL facility</td>
		</tr>
		<tr>
			<td>fast XUV photodiode</td>
			<td>Opto Diode Corp.</td>
			<td>AXUVHS11</td>
			<td></td>
		</tr>
		<tr>
			<td>bias T</td>
			<td>Tektronix</td>
			<td>PSPL5575A</td>
			<td></td>
		</tr>
		<tr>
			<td>fast ( &#8805;10 GHz) oscilloscope</td>
			<td>Tektronix</td>
			<td>TDS6124C</td>
			<td></td>
		</tr>
	</tbody>
</table>

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.

If the FEL and the optical laser pulses are spatially overlapped in the interaction region of the ion spectrometer, the temporal overlap, i.e., the delay value T0, at which FEL and laser pulses arrive exactly at the same time, can be found by varying the delay between FEL and NIR pulses and by analyzing the ratio of the Xe2+ to Xe3+ ion yield as a function of delay, as explained above in section 3.2.1. When the NIR pulse arrives after the FEL pulse (which needs to have a photon energy of 67.5 eV or higher), the Xe3+ ion yield is increased due to post-ionization of excited, metastable Xe2+ ion that are created during the Auger decay process following the Xe(4d) inner-shell ionization18, as shown in Figure 2. Plotting the ratio of the Xe2+ to Xe3+ ion yield as a function of delay thus yields a step function, which can be fitted to extract the exact value of T0.
A similar step function can be obtained by varying the delay between FEL and laser pulses and by analyzing the ion time-of-flight traces or ion momentum images of highly charged iodine ions, such as I3+ or I4+, created in the ionization of CH3I, as explained above in step 3.2.2). In this case, a low-energy contribution will appear as an additional peak at center of the highly charged iodine peaks in the time-of-flight spectrum or as a bright spot at the center of the corresponding momentum images, as shown in Figure 3. The low-energy ions are created when the CH3I molecules are first dissociated by the laser pulse and the ion fragment is then post-ionized by the FEL pulse9,10. This method can be used if either NIR or UV pulses are used for the pump-probe experiment, as long as the FEL photon energy is higher than 57 eV, which is the iodine 4d inner-shell ionization threshold in CH3I.
In order to correct for the jitter in the relative arrival time of the FEL pulses with respect to the laser pulses, the shot-by-shot data recorded by the bunch arrival-time monitor (BAM), shown in Figure 4, can be used to sort the recorded pump-probe data in the post-analysis, as explained above in section 5. This typically improves the temporal resolution and overall quality of the pump-probe data considerably, as shown in Figure 4 and, in more detail, in Savelyev et al. 201712.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/57055/57055fig1.jpg" /> 
Figure 1: Experimental Setup. Sketch of the experimental setup for a UV-pump XUV-probe experiment on gas-phase molecules. The UV (266 nm) laser beam is produced as the third harmonic of an 800-nm Titanium:Sapphire (Ti:Sa) beam using Beta Barium Borate (BBO) crystals and compressed using a prism compressor. It is collinearly overlapped with the XUV FEL beam using a drilled mirror and focused inside a supersonic gas beam at the center of a double-sided velocity map imaging spectrometer22,29. Ion and electron momentum distributions are recorded at opposite ends of the spectrometer using a MCP/phosphor screen assembly followed by a CCD camera. <a href="https://cloudflare.jove.com/files/ftp_upload/57055/57055fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/57055/57055fig2.jpg" /> 
Figure 2: Delay-dependence of the Xe ion yield. Xe ion time-of-flight spectrum (decoupled MCP signal recorded by a fast digitizer) at 83 eV photon energy and with the NIR laser pulses arriving 1 &#956;s before (top, black trace) and after (bottom, red trace) the FEL pulses. The change in the Xe2+ to Xe3+ ratio is clearly visible. <a href="https://cloudflare.jove.com/files/ftp_upload/57055/57055fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/57055/57055fig3.jpg" /> 
Figure 3: Delay-dependence of the iodine ion yield and momentum. (A) Zoom-in on the I4+ peak in the ion time-of-flight spectrum of CH3I recorded at 727 eV photon energy and with the UV laser pulses arriving before (red line) and after (black line) the FEL pulses. The blue and green line, respectively, show the time-of-flight spectrum for FEL and UV laser pulse alone. This figure has been modified from Boll et al. 201610. (B) Ion momentum image of I3+ ions from CH3I recorded at 107 eV photon energy and with the UV laser pulses arriving before the FEL pulses. (C) Same as (B), but with the UV pulses arriving after the FEL pulses. The color scale in (B) and (C) shows the ion yield in arbitrary units. <a href="https://cloudflare.jove.com/files/ftp_upload/57055/57055fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/57055/57055fig4.jpg" /> 
Figure 4: Relative arrival time jitter of the FEL pulses with respect to the optical laser pulses. (A) Shot-by-shot bunch arrival-time monitor (BAM) data for all FEL shots recorded during an exemplary delay scan. The reference value BAM0 was set to the mean BAM value for this scan. (B) Ion yield of low kinetic-energy I3+ ions produced in a UV-XUV pump-probe experiment on difluoroiodobenzene before correction of the shot-to-shot arrival jitter. The red line shows a least-squares fit of a cumulative distribution function (Gauss error function) to the experimental data. The fit parameter &#963; is a measure of the total temporal resolution of the pump-probe experiment. (C) Same as in (B) but with the single-shot images resorted into new delay bins using the BAM data. The error bars represent one standard deviation. Figure adapted from Savelyev et al. 201712. <a href="https://cloudflare.jove.com/files/ftp_upload/57055/57055fig4large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about An Experimental Protocol for Femtosecond NIR/UV - XUV Pump-Probe Experiments with Free-Electron Lasers at JoVE.com

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

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.

This protocol describes key steps in performing and analyzing femtosecond pump-probe experiments that combine a femtosecond optical laser with a ...

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15.9K Views.  Kansas State University. 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.

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

Conducting Miller-Urey Experiments

In 1953, Stanley Miller reported the production of biomolecules from simple gaseous starting materials, using an apparatus constructed to simulate the primordial Earth&#39;s atmosphere-ocean system. Miller introduced 200 ml of water, 100 mmHg of H2, 200 mmHg of CH4, and 200 mmHg of NH3 into the apparatus, then subjected this mixture, under reflux, to an electric discharge for a week, while the water was simultaneously heated. The purpose of this manuscript is to provide the reader with a general experimental protocol that can be used to conduct a Miller-Urey type spark discharge experiment, using a simplified 3 L reaction flask. Since the experiment involves exposing inflammable gases to a high voltage electric discharge, it is worth highlighting important steps that reduce the risk of explosion. The general procedures described in this work can be extrapolated to design and conduct a wide variety of electric discharge experiments simulating primitive planetary environments.

The Miller-Urey experiment was a pioneering study regarding the abiotic synthesis of organic compounds with possible relevance to the origins of life. Simple gases were introduced into a glass apparatus and subjected to an electric discharge, simulating the effects of lightning in the primordial Earth&#8217;s atmosphere-ocean system. The experiment was conducted for one week, after which, the samples collected from it were analyzed for the chemical building blocks of life.

In 1953, Stanley Miller reported the production of biomolecules from simple gaseous starting materials, using an apparatus constructed to simulate the ...

Metal-silicate Partitioning at High Pressure and Temperature: Experimental Methods and a Protocol to Suppress Highly Siderophile Element Inclusions

Estimates of the primitive upper mantle (PUM) composition reveal a depletion in many of the siderophile (iron-loving) elements, thought to result from their extraction to the core during terrestrial accretion. Experiments to investigate the partitioning of these elements between metal and silicate melts suggest that the PUM composition is best matched if metal-silicate equilibrium occurred at high pressures and temperatures, in a deep magma ocean environment. The behavior of the most highly siderophile elements (HSEs) during this process however, has remained enigmatic. Silicate run-products from HSE solubility experiments are commonly contaminated by dispersed metal inclusions that hinder the measurement of element concentrations in the melt. The resulting uncertainty over the true solubility and metal-silicate partitioning of these elements has made it difficult to predict their expected depletion in PUM. Recently, several studies have employed changes to the experimental design used for high pressure and temperature solubility experiments in order to suppress the formation of metal inclusions. The addition of Au (Re, Os, Ir, Ru experiments) or elemental Si (Pt experiments) to the sample acts to alter either the geometry or rate of sample reduction respectively, in order to avoid transient metal oversaturation of the silicate melt. This contribution outlines procedures for using the piston-cylinder and multi-anvil apparatus to conduct solubility and metal-silicate partitioning experiments respectively. A protocol is also described for the synthesis of uncontaminated run-products from HSE solubility experiments in which the oxygen fugacity is similar to that during terrestrial core-formation. Time-resolved LA-ICP-MS spectra are presented as evidence for the absence of metal-inclusions in run-products from earlier studies, and also confirm that the technique may be extended to investigate Ru. Examples are also given of how these data may be applied.

We present a procedure to determine the metal-silicate partitioning of siderophile elements, emphasizing techniques that suppress the formation of metal inclusions in experiments for the noble metals. The results of these experiments are used to demonstrate the effect of core-formation on the highly siderophile element composition of the mantle.

Estimates of the primitive upper mantle (PUM) composition reveal a depletion in many of the siderophile (iron-loving) elements, thought to result from ...

Protocol for the Synthesis of Ortho-trifluoromethoxylated Aniline Derivatives

Molecules bearing trifluoromethoxy (OCF3) group often show desired pharmacological and biological properties. However, facile synthesis of trifluoromethoxylated aromatic compounds remains a formidable challenge in organic synthesis. Conventional approaches often suffer from poor substrate scope, or require use of highly toxic, difficult-to-handle, and/or thermally labile reagents. Herein, we report a user-friendly protocol for the synthesis of methyl 4-acetamido-3-(trifluoromethoxy)benzoate using 1-trifluoromethyl-1,2-benziodoxol-3(1H)-one (Togni reagent II). Treating methyl 4-(N-hydroxyacetamido)benzoate (1a) with Togni reagent II in the presence of a catalytic amount of cesium carbonate (Cs2CO3) in chloroform at RT afforded methyl 4-(N-(trifluoromethoxy)acetamido)benzoate (2a). This intermediate was then converted to the final product methyl 4-acetamido-3-(trifluoromethoxy)benzoate (3a) in nitromethane at 120 &#176;C. This procedure is general and can be applied to the synthesis of a broad spectrum of ortho-trifluoromethoxylated aniline derivatives, which could serve as useful synthetic building blocks for the discovery and development of new pharmaceuticals, agrochemicals, and functional materials.

Protocol for the Synthesis of Ortho-trifluoromethoxylated Aniline Derivatives

An operationally simple procedure for the synthesis of ortho-trifluoromethoxylated aniline derivatives via a two-step sequence of O-trifluoromethylation of N-aryl-N-hydroxyacetamide followed by thermally induced intramolecular OCF3-migration is reported.

Molecules bearing trifluoromethoxy (OCF3) group often show desired pharmacological and biological properties. However, facile synthesis of ...

A Protocol for the Production of Gliadin-cyanoacrylate Nanoparticles for Hydrophilic Coating

This article presents a protocol for the production of protein-based nanoparticles that changes the hydrophobic surface to hydrophilic by a simple spray coating. These nanoparticles are produced by the polymerization reaction of alkyl cyanoacrylate on the surface of cereal protein (gliadin) molecules. Alkyl cyanoacrylate is a monomer that instantly polymerizes at RT when it is applied to the surface of materials. Its polymerization reaction is initiated by the trace amounts of weakly basic or nucleophilic species on the surface, including moisture. Once polymerized, the polymerized alkyl cyanoacrylates show a strong affinity with the object materials because nitrile groups are in the backbone of poly (alkyl cyanoacrylate). Proteins also work as initiator for this polymerization because they contain amine groups that can initiate the polymerization of cyanoacrylate. If aggregated protein is used as an initiator, protein aggregate is surrounded by the hydrophobic poly(alkyl cyanoacrylate) chains after the polymerization reaction of alkyl cyanoacrylate. By controlling the experimental condition, particles in the nanometer range are produced. The produced nanoparticles readily adsorb to the surface of most materials including glass, metals, plastics, wood, leather, and fabrics. When the surface of a material is sprayed with the produced nanoparticle suspension and rinsed with water, the micellar structure of nanoparticle changes its conformation, and the hydrophilic proteins are exposed to the air. As a result, the nanoparticle-coated surface changes to hydrophilic.

This article presents a protocol for the production of protein-based nanoparticles that changes the hydrophobic surface to hydrophilic. The produced nanoparticle is an assembly of gliadin-cyanoacrylate diblock copolymers. Spray coating with the produced nanoparticle changes the surface of target material to a hydrophilic surface.

This article presents a protocol for the production of protein-based nanoparticles that changes the hydrophobic surface to hydrophilic by a simple spray ...

Original Experimental Approach for Assessing Transport Fuel Stability

The study of fuel oxidation stability is an important issue for the development of future fuels. Diesel and kerosene fuel systems have undergone several technological changes to fulfill environmental and economic requirements. These developments have resulted in increasingly severe operating conditions whose suitability for conventional and alternative fuels needs to be addressed. For example, fatty acid methyl esters (FAMEs) introduced as biodiesel are more prone to oxidation and may lead to deposit formation. Although several methods exist to evaluate fuel stability (induction period, peroxides, acids, and insolubles), no technique allows one to monitor the real-time oxidation mechanism and to measure the formation of oxidation intermediates that may lead to deposit formation. In this article, we developed an advanced oxidation procedure (AOP) based on two existing reactors. This procedure allows the simulation of different oxidation conditions and the monitoring of the oxidation progress by the means of macroscopic parameters, such as total acid number (TAN) and advanced analytical methods like gas chromatography coupled to mass spectrometry (GC-MS) and Fourier Transform Infrared - Attenuated Total Reflection (FTIR-ATR). We successfully applied AOP to gain an in-depth understanding of the oxidation kinetics of a model molecule (methyl oleate) and commercial diesel and biodiesel fuels. These developments represent a key strategy for fuel quality monitoring during logistics and on-board utilization.

Oxidation stability of transport fuels has become a concern for future fuel development. This work presents an original methodology developed by IFP Energies Nouvelles for assessing fuel stability using two different reactors. This methodology was successfully applied to gain an in-depth understanding of the oxidation kinetics and pathways of model molecules and commercial fuels.

The study of fuel oxidation stability is an important issue for the development of future fuels. Diesel and kerosene fuel systems have undergone several ...

A Protocol for Safe Lithiation Reactions Using Organolithium Reagents

Organolithium reagents are powerful tools in the synthetic chemist&#39;s toolbox. However, the extreme pyrophoric nature of the most reactive reagents warrants proper technique, thorough training, and proper personal protective equipment. To aid in the training of researchers using organolithium reagents, a thorough, step-by-step protocol for the safe and effective use of tert-butyllithium on an inert gas line or within a glovebox is described. As a model reaction, preparation of lithium tert-butyl amide by the reaction of tert-butyl amine with one equivalent of tert-butyl lithium is presented.

The safe and proper use of organolithium reagents is described.

Organolithium reagents are powerful tools in the synthetic chemist&#39;s toolbox. However, the extreme pyrophoric nature of the most reactive reagents ...

An Optimized Protocol for the Efficient Radiolabeling of Gold Nanoparticles by Using a 125I-labeled Azide Prosthetic Group

Here, we demonstrate a detailed protocol for the radiosynthesis of a 125I-labeled azide prosthetic group and its application to the efficient radiolabeling of DBCO-group-functionalized gold nanoparticles using a copper-free click reaction. Radioiodination of the stannylated precursor (2) was carried out by using [125I]NaI and chloramine T as an oxidant at room temperature for 15 min. After HPLC purification of the crude product, the purified 125I-labeled azide (1) was obtained with high radiochemical yield (75 &plusmn; 10%, n = 8) and excellent radiochemical purity (&gt;99%). For the synthesis of radiolabeled 13-nm-sized gold nanoparticles, the DBCO-functionalized gold nanoparticles (3) were prepared by using a thiolated polyethylene glycol polymer. A copper-free click reaction between 1 and 3 gave the 125I-labeled gold nanoparticles (4) with more than 95% of radiochemical yield as determined by radio-thin-layer chromatography (radio-TLC). These results clearly indicate that the present radiolabeling method using a strain-promoted copper-free click reaction will be useful for the efficient and convenient radiolabeling of DBCO-group-containing nanomaterials.

An Optimized Protocol for the Efficient Radiolabeling of Gold Nanoparticles by Using a 125I-labeled Azide Prosthetic Group

A detailed procedure for the synthesis of a 125I-labeled azide and the radiolabeling of dibenzocyclooctyne (DBCO)-group-conjugated, 13-nm-sized gold nanoparticles using a copper-free click reaction is described.

Here, we demonstrate a detailed protocol for the radiosynthesis of a 125I-labeled azide prosthetic group and its application to the efficient ...

Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene

The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the results of femtosecond X-ray free electron laser (XFEL) experiments. An increasing number of experimental observations have shown that although nuclear motion can be negligible, given a short enough incident pulse duration, electronic motion cannot be ignored. The current and widely accepted models assume that although electrons undergo dynamics driven by interaction with the pulse, their motion could largely be considered &#39;random&#39;. This would then allow the supposedly incoherent contribution from the electronic motion to be treated as a continuous background signal and thus ignored. The original aim of our experiment was to precisely measure the change in intensity of individual Bragg peaks, due to X-ray induced electronic damage in a model system, crystalline C60. Contrary to this expectation, we observed that at the highest X-ray intensities, the electron dynamics in C60 were in fact highly correlated, and over sufficiently long distances that the positions of the Bragg reflections are significantly altered. This paper describes in detail the methods and protocols used for these experiments, which were conducted both at the Linac Coherent Light Source (LCLS) and the Australian Synchrotron (AS) as well as the crystallographic approaches used to analyse the data.

We describe an experiment designed to probe the electronic damage induced in nanocrystals of Buckminsterfullerene (C60) by intense, femtosecond pulses of X-rays. The experiment found that, surprisingly, rather than being stochastic, the X-ray induced electron dynamics in C60 are highly correlated, extending over hundreds of unit cells within the crystals1.

The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the ...

Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography

This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The devices are patterned from epoxy glue using soft lithography and are suitable for in situ X-ray diffraction experiments at room temperature. The sample wells are lidded on both sides with polymeric polyimide foil windows that allow diffraction data collection with low X-ray background. This fabrication method is undemanding and inexpensive. After the sourcing of a SU-8 master wafer, all fabrication can be completed outside of a cleanroom in a typical research lab environment. The chip design and fabrication protocol utilize capillary valving to microfluidically split an aqueous reaction into defined nanoliter sized droplets. This loading mechanism avoids the sample loss from channel dead-volume and can easily be performed manually without using pumps or other equipment for fluid actuation. We describe how isolated nanoliter sized drops of protein solution can be monitored in situ by dynamic light scattering to control protein crystal nucleation and growth. After suitable crystals are grown, complete X-ray diffraction datasets can be collected using goniometer based in situ fixed target serial X-ray crystallography at room temperature. The protocol provides custom scripts to process diffraction datasets using a suite of software tools to solve and refine the protein crystal structure. This approach avoids the artefacts possibly induced during cryo-preservation or manual crystal handling in conventional crystallography experiments. We present and compare three protein structures that were solved using small crystals with dimensions of approximately 10-20 &#181;m grown in chip. By crystallizing and diffracting in situ, handling and hence mechanical disturbances of fragile crystals is minimized. The protocol details how to fabricate a custom X-ray transparent microfluidic chip suitable for in situ serial crystallography. As almost every crystal can be used for diffraction data collection, these microfluidic chips are a very efficient crystal delivery method.

Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography

This protocol describes in detail how to fabricate and operate microfluidic devices for X-ray diffraction data collection at room temperature. Additionally, it describes how to monitor protein crystallization by dynamic light scattering and how to process and analyze obtained diffraction data.

This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The ...

The MPLEx Protocol for Multi-omic Analyses of Soil Samples

Mass spectrometry (MS)-based integrated metaproteomic, metabolomic, and lipidomic (multi-omic) studies are transforming our ability to understand and characterize microbial communities in environmental and biological systems. These measurements are even enabling enhanced analyses of complex soil microbial communities, which are the most complex microbial systems known to date. Multi-omic analyses, however, do have sample preparation challenges, since separate extractions are typically needed for each omic study, thereby greatly amplifying the preparation time and amount of sample required. To address this limitation, a 3-in-1 method for the simultaneous extraction of metabolites, proteins, and lipids (MPLEx) from the same soil sample was created by adapting a solvent-based approach. This MPLEx protocol has proven to be both simple and robust for many sample types, even when utilized for limited quantities of complex soil samples. The MPLEx method also greatly enabled the rapid multi-omic measurements needed to gain a better understanding of the members of each microbial community, while evaluating the changes taking place upon biological and environmental perturbations.

A protocol is presented for simultaneously extracting metabolites, proteins, and lipids from a single soil sample, allowing reduced sample preparation times and enabling multi-omic mass spectrometry analyses of samples with limited quantities.

Mass spectrometry (MS)-based integrated metaproteomic, metabolomic, and lipidomic (multi-omic) studies are transforming our ability to understand and ...