Name: elemental-sensitive detection of the chemistry in batteries through soft x-ray absorption spectroscopy and resonant inelastic x-ray scattering
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The Advanced Light Source (ALS) of the Lawrence Berkeley National Laboratory (LBNL) is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Q.L. thanks the China Scholarship Council (CSC) for financial support through the collaboration based on China 111 project No. B13029. R.Q. thanks the support from LBNL LDRD program. S.S. and Z.Z. thank the support from the ALS Doctoral fellowship.

1. Experimental Planning
Note: While sXES could be performed with lab-based equipment, sXAS and RIXS are synchrotron-based experiments, which requires access to the beamtime of a synchrotron facility. The procedure for applying for beamtime and running experiments could be different at different facilities, but they all follow a similar basic procedure.
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	<li>Check the facility website for the beamline directory (e.g., https://als.lbl.gov/beamlines/), or contact the scientists i...

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B. 25 (1), 17104 (2016).</li><li>Yang, W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Key+electronic+states+in+lithium+battery+materials+probed+by+soft+X-ray+spectroscopy.">Key electronic states in lithium battery materials probed by soft X-ray spectroscopy.</a> Journal of Electron Spectroscopy and Related Phenomena. 190, 64-74 (2013).</li><li>Qiao, R., Yang, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Interactions+at+the+electrode-electrolyte+interfaces+in+batteries+studied+by+quasi-in-situ+soft+x-ray+absorption+spectroscopy.">Interactions at the electrode-electrolyte interfaces in batteries studied by quasi-in-situ soft x-ray absorption spectroscopy.</a> Journal of Electron Spectroscopy and Related Phenomena. , (2017).</li><li>Lin, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Synchrotron+X-ray+Analytical+Techniques+for+Studying+Materials+Electrochemistry+in+Rechargeable+Batteries.">Synchrotron X-ray Analytical Techniques for Studying Materials Electrochemistry in Rechargeable Batteries.</a> Chem Rev. , (2017).</li><li>Liu, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Why+LiFePO4+is+a+safe+battery+electrode:+Coulomb+repulsion+induced+electron-state+reshuffling+upon+lithiation.">Why LiFePO4 is a safe battery electrode: Coulomb repulsion induced electron-state reshuffling upon lithiation.</a> Phys Chem Chem Phys. 17 (39), 26369-26377 (2015).</li><li>Liu, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Polymers+with+tailored+electronic+structure+for+high+capacity+lithium+battery+electrodes.">Polymers with tailored electronic structure for high capacity lithium battery electrodes.</a> Adv Mater. 23 (40), 4679-4683 (2011).</li><li>Wu, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Toward+an+Ideal+Polymer+Binder+Design+for+High-Capacity+Battery+Anodes.">Toward an Ideal Polymer Binder Design for High-Capacity Battery Anodes.</a> Journal of the American Chemical Society. 135 (32), 12048-12056 (2013).</li><li>Wang, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rhombohedral+prussian+white+as+cathode+for+rechargeable+sodium-ion+batteries.">Rhombohedral prussian white as cathode for rechargeable sodium-ion batteries.</a> J Am Chem Soc. 137 (7), 2548-2554 (2015).</li><li>Qiao, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Distinct+Solid-Electrolyte-Interphases+on+Sn+(100)+and+(001)+Electrodes+Studied+by+Soft+X-Ray+Spectroscopy.">Distinct Solid-Electrolyte-Interphases on Sn (100) and (001) Electrodes Studied by Soft X-Ray Spectroscopy.</a> Advanced Materials Interfaces. 1 (100), (2014).</li><li>Shan, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bivalence+Mn5O8+with+hydroxylated+interphase+for+high-voltage+aqueous+sodium-ion+storage.">Bivalence Mn5O8 with hydroxylated interphase for high-voltage aqueous sodium-ion storage.</a> Nat Commun. 7, 13370 (2016).</li><li>Qiao, R., Chuang, Y. 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M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Na-Ion+Intercalation+and+Charge+Storage+Mechanism+in+2D+Vanadium+Carbide.">Na-Ion Intercalation and Charge Storage Mechanism in 2D Vanadium Carbide.</a> Advanced Energy Materials. , 1700959 (2017).</li><li>Zhuo, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+excess+lithium+in+LiMn2O4+and+Li1.15Mn1.85O4+electrodes+revealed+by+quantitative+analysis+of+soft+X-ray+absorption+spectroscopy.">Effect of excess lithium in LiMn2O4 and Li1.15Mn1.85O4 electrodes revealed by quantitative analysis of soft X-ray absorption spectroscopy.</a> Applied Physics Letters. 110, 093902 (2017).</li><li>Qiao, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transition-metal+redox+evolution+in+LiNi+0.5+Mn+0.3+Co+0.2+O+2+electrodes+at+high+potentials.">Transition-metal redox evolution in LiNi 0.5 Mn 0.3 Co 0.2 O 2 electrodes at high potentials.</a> Journal of Power Sources. 360, 294-300 (2017).</li><li>Qiao, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Revealing+and+suppressing+surface+Mn(II)+formation+of+Na0.44MnO2+electrodes+for+Na-ion+batteries.">Revealing and suppressing surface Mn(II) formation of Na0.44MnO2 electrodes for Na-ion batteries.</a> Nano Energy. 16, 186-195 (2015).</li><li>Qiao, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+evidence+of+gradient+Mn(II)+evolution+at+charged+states+in+LiNi0.5Mn1.5O4+electrodes+with+capacity+fading.">Direct evidence of gradient Mn(II) evolution at charged states in LiNi0.5Mn1.5O4 electrodes with capacity fading.</a> Journal of Power Sources. 273, 1120-1126 (2015).</li><li>Wu, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modification+of+Transition-Metal+Redox+by+Interstitial+Water+in+Hexacyanometallate+Electrodes+for+Sodium-Ion+Batteries.">Modification of Transition-Metal Redox by Interstitial Water in Hexacyanometallate Electrodes for Sodium-Ion Batteries.</a> Journal of the American Chemical Society. , (2017).</li><li>Liu, X., et al. <a target="_blank" 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The formidable challenge of improving the performance of energy storage materials requires advances of incisive tools to directly probe the chemical evolutions in battery compounds upon electrochemical operation. Soft X-ray core-level spectroscopy, such as sXAS, sXES, and RIXS, is a tool-of-choice for detecting the critical valence states of both the anions and cations involved in LIBs and SIBs.
Core-level spectroscopy techniques involve the strong excitation of core electrons to unoccupied st...

Developing high-performance batteries is one of the crucial requirements for realizing modern energy applications with environmentally benign resources and devices. Developing high-efficiency, low-cost, and sustainable energy storage devices has become critical for both electric vehicles (EVs) and the electric grid, with a projected energy storage market expansion of ten times in this decade. The ubiquitous Li-ion battery (LIB) technology remains a promising candidate for high energy-density and high power energy storage solutions1, while Na-ion batteries (SIBs) hold the promise of realizing low-cost and stable storage for green-grid applications2. However, the overall level of battery technology is well below what is required to meet the need of this new phase of mid-to-large scale energy storage1,3.
The pressing challenge of developing high-performance energy-storage system arises from the complex mechanical and electronic characteristics of the battery operations. Extensive efforts have focused on material synthesis and mechanical properties. However, the evolution of the chemical states of particular elements in battery electrodes is often under active debate for newly developed battery materials. In general, both LIBs and SIBs operate with evolving electronic states triggered by the transportation of the electrons and ions during the charge and discharge process, leading to the oxidation and reduction (redox) reactions of specific element(s). As the bottleneck for many performance parameters, battery cathodes have been paid much attention in research and developments4,5. A practical battery cathode material is often a 3d transition-metal (TM) oxide with particular structural channels for ion diffusion. Conventionally, the redox reaction is limited to the TM elements; however, recent results indicate that oxygen could possibly be utilized in reversible electrochemical cycling6. The redox mechanism is one of the most critical pieces of information for understanding an electrochemical operation, and a direct probe of the chemical states of battery electrodes with elemental sensitivity is thus highly desirable.
Synchrotron-based, soft X-ray spectroscopy is an advanced technique that detects the valence electron states in the vicinity of the Fermi level in battery materials7. Because of the high sensitivity of soft X-ray photons to the electrons of a specific element and orbital, soft X-ray spectroscopy could be utilized as a direct probe of the critical electron states in battery electrodes8, or at the interfaces in batteries9. Furthermore, compared with hard X-rays, soft X-rays are lower in energy and cover excitations of the low-Z elements, e.g., C, N, O, and of the 2p-to-3d excitation in the 3d TMs10.
The excitations of soft x-ray spectroscopy first involve electron transitions from a particular core state to an unoccupied state by absorbing energy from soft X-ray photons. The intensity of such soft X-ray absorption spectroscopy thus corresponds to the density of state (DOS) of the unoccupied (conduction-band) states with the existence of the excited core-holes. The X-ray absorption coefficient can be measured by detecting the total number of photons or electrons emitted during the decay process. The total electron yield (TEY) counts the total number of emitted electrons, and is thus a photon-in-electron-out (PIEO) detection mode. TEY has a shallow probe depth of several nanometers, and therefore is relatively surface sensitive, due to the shallow escape depth of electrons. However, as a photon-in-photon-out (PIPO) detection mode, the total fluorescence yield (TFY) measures the total number of emitted photons in the sXAS process. Its probe depth is about hundreds of nanometers, which is deeper than that of TEY. Due to the difference in probe depths, the contrast between TEY and TFY could provide important information for a comparison between the surface and bulk of the material.
sXES is a PIPO technique, corresponding to the decay of the exited state to fill the core hole, leading to the emission of X-ray photons at characteristic energies. If the core electron is excited to the continuum electron state far away from the sXAS threshold, it is a non-resonant X-ray fluorescence process corresponding to the decay of occupied (valence-band) electrons to the core holes, i.e., sXES reflects the DOS of the valence-band states. Otherwise, if the core electron is resonantly excited to exactly the absorption threshold, the resulting emission spectra feature strong excitation energy dependence. For this case, the spectroscopy experiments are denoted as resonant inelastic x-ray scattering (RIXS).
Because sXAS and sXES corresponds to the unoccupied (conduction-band) and occupied (valence-band) electron states, respectively, they provide complementary information on the electron states involved in the reduction and oxidation reactions in the battery electrodes upon electrochemical operation11. For low-Z elements, especially C12,13, N14, and O15,16,17, sXAS has been widely used for studying the critical electron states corresponding to both the electron transfer12,13 and chemical compositions15,16,17. For 3d TMs, sXAS of TM L-edges has been successfully demonstrated to be an effective probe of the TM redox reactions of V18, Mn19,20,21,22,23, Fe23,24,25,26, Co20,27, and Ni20,28. Because the TM-L sXAS features are dominated by the well-defined multiplet effect, which are sensitive to the different TM oxidation18,19,20,21,22,24,25,26,27,28 and spin states14,29, the TM sXAS data could enable even quantitative analysis of the TM redox couples in LIB and SIB electrodes27.
Compared with the popular employment of sXAS for battery material studies, RIXS is less often utilized due to the complexity of both the experiments and data interpretation for obtaining meaningful information related to battery performance10. However, due to the extremely high chemical-state selectivity of RIXS, RIXS is potentially a much more sensitive probe of the chemical state evolution in battery materials with inherent elemental sensitivity. Recent sXES and RIXS reports by Jeyachandran et al., have showcased the high sensitivity of RIXS to specific chemical configurations in the ion-solvation systems beyond sXAS30,31. With the recent rapid developments of high-efficiency RIXS systems32,33,34, RIXS has quickly shifted from a fundamental physics tool to a powerful technique for battery research, and occasionally becomes the tool-of-choice for specific studies of both the cation and anion evolution in battery compounds.
In this work, the detailed protocols for sXAS, sXES, and RIXS experiments are introduced. We cover the details of experimental planning, technical procedures for carrying out experiments, and more importantly, data processing for different spectroscopic techniques. Furthermore, three representative results in battery material studies are presented to demonstrate the applications of these three soft X-ray spectroscopy techniques. We note that the technical details of these experiments could be different at different end-stations and/or facilities. Additionally, ex-situ and in-situ experiments have very different setup procedures on sample handling due to the stringent requirements of ultra-high vacuum for soft X-ray spectroscopy35. But the protocol here represents the typical procedure and could serve as a common reference for soft X-ray spectroscopy experiments in various experimental systems at different facilities.

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			<td height="21" style="height:21px;width:216px;">Material</td>
			<td style="width:144px;"></td>
			<td style="width:119px;"></td>
			<td style="width:355px;"></td>
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			<td height="21" style="height:21px;">Electrode active materials</td>
			<td style="width:144px;">various</td>
			<td style="width:119px;"></td>
			<td>Synthesized in-house or obtained from various suppliers.</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;">Lithium foil</td>
			<td style="width:144px;">Sigma-Aldrich</td>
			<td>320080</td>
			<td style="width:355px;">Anode for half cells. Store and handle in an inert atmosphere glovebox under Ar. (www.sigmaaldrich.com)</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;">Sodium foil</td>
			<td style="width:144px;">Sigma-Aldrich</td>
			<td style="width:119px;">282065</td>
			<td style="width:355px;">Anode for half cells. Store and handle in an inert atmosphere glovebox under Ar. (www.sigmaaldrich.com)</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;">Electrolyte solutions</td>
			<td style="width:144px;">BASF</td>
			<td style="width:119px;">Contact vendor for desired formulations</td>
			<td style="width:355px;">http://www.catalysts.basf.com/p02/USWeb-Internet/catalysts/en/content/microsites/catalysts/prods-inds/batt-mats/electrolytes</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Synthetic flake graphite</td>
			<td style="width:144px;">Timcal</td>
			<td style="width:119px;">SFG-6</td>
			<td style="width:355px;">Conductive additive for electrodes. (www.timcal.com)</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">Indium foil</td>
			<td style="width:144px;">Sigma-Aldrich</td>
			<td style="width:119px;">357308</td>
			<td style="width:355px;">Used if collecting Carbon and Oxygen signals of power samples</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Argon gas</td>
			<td style="width:144px;">Air Products</td>
			<td style="width:119px;">Custom order, contact vendors</td>
			<td style="width:355px;">Argon used to fill glovebox where to assemble and store air-sensitive samples. (http://www.airproducts.com/products/gases.aspx)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Eqiupment</td>
			<td style="width:144px;"></td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;width:216px;">CCD</td>
			<td style="width:144px;">iKon-L</td>
			<td style="width:119px;">DO936N</td>
			<td style="width:355px;">Used to capture the emission photons when carrying out the sXES or RiXS experiment (http://www.andor.com/scientific-cameras/ikon-xl-and-ikon-large-ccd-series/ikon-l-936)</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Inert atmosphere glovebox</td>
			<td style="width:144px;">MBRAUN</td>
			<td style="width:119px;">MB200B</td>
			<td style="width:355px;">Used during air-sensitive samples assembly and storage. (http://www.mbraun.com/products/glovebox-workstations/mb200b-mod)</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Battery Charge &#38; Discharge Tester</td>
			<td style="width:144px;">Bio-Logic</td>
			<td style="width:119px;">VMP3</td>
			<td style="width:355px;">Used to electrochemical cycling of battery materials. (https://www.bio-logic.net/en/)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Swagelok cell</td>
			<td style="width:144px;">MTI</td>
			<td style="width:119px;">EQ-HSTC</td>
			<td style="width:355px;">Used to contain the battery for electrochemical cycling</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sample holder</td>
			<td style="width:144px;">manufactured in lab</td>
			<td style="width:119px;"></td>
			<td>Used to hold the samples in the experiment</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">Hardware tools</td>
			<td style="width:144px;">various</td>
			<td style="width:119px;"></td>
			<td style="width:355px;">Including tweezers, scissors (used to assemble samples), tongs (used to transfer sample holders), etc.&#160;</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Carbon and Copper tape</td>
			<td style="width:144px;">3M</td>
			<td style="width:119px;">Custom order, contact vendors</td>
			<td>Used to paste the samples onto sample holders</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Igor Pro</td>
			<td style="width:144px;">WaveMetrics</td>
			<td style="width:119px;">7.06</td>
			<td style="width:355px;">Used to process the experiment data. (https://www.wavemetrics.com/index.html)</td>
		</tr>
	</tbody>
</table>

elemental-sensitive detection of the chemistry in batteries through soft x-ray absorption spectroscopy and resonant inelastic x-ray scattering

Energy storage has become more and more a limiting factor of today's sustainable energy applications, including electric vehicles and green electric grid based on volatile solar and wind sources. The pressing demand of developing high-performance electrochemical energy storage solutions, i.e., batteries, relies on both fundamental understanding and practical developments from both the academy and industry. The formidable challenge of developing successful battery technology stems from the different requirements for different energy-storage applications. Energy density, power, stability, safety, and cost parameters all have to be balanced in batteries to meet the requirements of different applications. Therefore, multiple battery technologies based on different materials and mechanisms need to be developed and optimized. Incisive tools that could directly probe the chemical reactions in various battery materials are becoming critical to advance the field beyond its conventional trial-and-error approach. Here, we present detailed protocols for soft X-ray absorption spectroscopy (sXAS), soft X-ray emission spectroscopy (sXES), and resonant inelastic X-ray scattering (RIXS) experiments, which are inherently elemental-sensitive probes of the transition-metal 3d and anion 2p states in battery compounds. We provide the details on the experimental techniques and demonstrations revealing the key chemical states in battery materials through these soft X-ray spectroscopy techniques.

The sample holder and pasted samples are shown in Figure 1. Figure 7a is a typical RIXS image collected at a particular excitation energy with the spectrometer set to the interested edges. The image shown here was collected on a battery electrode material, LiNi0.33Co0.33Mn0.33O2, with an excitation energy of 858 eV and the detector set at about 500-900 eV range to cover...

Watch this Scientific Journal Video about Elemental-sensitive Detection of the Chemistry in Batteries through Soft X-ray Absorption Spectroscopy and Resonant Inelastic X-ray Scattering at JoVE.com

Elemental-sensitive Detection of the Chemistry in Batteries through Soft X-ray Absorption Spectroscopy and Resonant Inelastic X-ray Scattering

Here, we present a protocol for typical experiments of soft X-ray absorption spectroscopy (sXAS) and resonant inelastic X-ray scattering (RIXS) with applications in battery material studies.

Energy storage has become more and more a limiting factor of today's sustainable energy applications, including electric vehicles and green electric grid ...

The overall goal of this protocol is to apply soft X-ray absorption spectroscopy and resonant inelastic X-ray scattering to battery material studies. This method is about utilizing soft X-ray spectroscopy, including X-ray absorption and resonant inelastic X-ray scattering, the so-called RIXS, as unique tools to answer the key questions in battery field. The main advantage of this technique is it can directly probe the chemical reactions in various battery material and develop this field beyond the conventional trial-and-error approach.Though this method can provide insight into battery materials, it can also be applied to other systems, such as catalysts, solar cells, and semiconductors. Visual demonstration of this method is critical as synchrotron based soft X-ray spectroscopy is difficult to learn without it. This protocol provides a detailed visual example of a typical experiment.To begin, cut the battery material samples to fit the sample holder, ensuring that each sample is larger than the beam spot. Fix the samples on the sample holder with double-sided conductive tape. For some powder samples, use indium foil to stick if necessary.Then, vent the sample load lock with nitrogen gas. Use a sample grabber, such as large tweezers, to load the sample holder into the load lock. Close and evaluate the load lock.Once the load lock pressure is sufficiently low, open the valve between the load lock and the main chamber. Using the transfer arm, transfer the sample holder to the main manipulator in the main chamber. Close the valve to the load lock, then open the valve between the main chamber and the beam line.Locate the beam spot by observing visible light fluorescence on a reference sample or on a phosphor applied to the sample holder. Position a sample in the beam spot using the sample manipulator controls. Connect the X-ray beam flux monitor signal cables to the measurement computer.Adjust the beam line monochromator slits to tune the energy resolution of the incident X-ray beam. Then, set the incident beam energy to the absorption edge of the element or elements of interest. Fix the monochromator mechanism in place.Measure the beam flux intensity and identify the undulator gap value that provides the maximum possible beam flux. To begin the sXAS data collection process, ensure that the sample current signal used to measure the total electron yield is directed to the measurement computer. Turn on the power supplies and controllers of the electron multiplier or photo diode used to measure the total fluorescence yield.Ensure that the signal is directed to the computer. Then, in the data acquisition software, select Single Motor Scan. Open the Scan Setup menu and set the incident X-ray photon scan range to span the sXAS edge of interest.Click Start Scan to simultaneously record the total electron yield, total fluorescence yield, and the beam flux while scanning the incident X-ray photon energy. Follow the same beam alignment and data collection procedure to acquire sXAS data for additional samples. If a reference sample has been scanned, adjust the scan range accordingly for any shift observed in the sXAS values.After collecting sXAS data, turn on the spectrometer for the sXES and RIXS system and cool down the soft X-ray detector, then open the motor controls. Set the spectrograph parameters to cover the energy range of the elements and edges of interest. Next, select CCD Instrument Scan and open the Scan Setup.For sXES, set a single value about 20 to 30 electron volts above the calibrated sXAS absorption edge. For RIXS, set the scan range to span the sXAS absorption edge. Select Apply Cosmic Ray Filter so that cosmic ray signals will be removed from the raw RIXS 2D images after initial data collection.Start the scan to collect fluorescent signals in 2D image form for each excitation energy. This RIXS image was collected from a lithium-ion battery material sample over the energy range of the Oxygen-K edge and the Manganese, Cobalt, and Nickel-L edges. A full range sXES covering all four edges simultaneously was collected in 10 seconds.A RIXS map of the Nickel-L edge was generated from the raw RIXS image data. Analysis of this map showed that the Nickel-L RIXS features were dominated by d-d excitations. Transition metal redox states in sodium-ion and lithium-ion battery materials were analyzed by quantitative fitting of sXAS spectra.The surface manganese valence distribution in layered sodium-manganese oxide electrodes at different electrochemical states was determined by quantitative fitting of sXAS spectra to a linear combination of Manganese II, III, and IV cation reference spectra. The redox process of a spinel lithium-nickel-manganese oxide electrode was identified as sequential single-electron transfers by a similar quantitative fitting approach using total fluorescence yield. Intermediate charge states of lithium-iron-phosphate electrodes were identified by quantitative fitting based on sXAS spectra of the electrodes at 0%and 100%charge.We have been making efforts to utilize synchrotron-based soft X-ray spectroscopy to characterize battery materials with unprecedented results. After its development, the technique paved the way for the researchers in the field of battery materials. The researchers can use it to explore the fundamental mechanula of the battery material.After watching this video, you should have a good understanding of how to perform soft X-ray spectroscopy at a synchrotron light source.

elemental-sensitive-detection-chemistry-batteries-through-soft-x-ray

Research

JoVE Journal

Chemistry

Preparing Adherent Cells for X-ray Fluorescence Imaging by Chemical Fixation

X-ray fluorescence imaging allows us to non-destructively measure the spatial distribution and concentration of multiple elements simultaneously over large or small sample areas. It has been applied in many areas of science, including materials science, geoscience, studying works of cultural heritage, and in chemical biology. In the case of chemical biology, for example, visualizing the metal distributions within cells allows us to study both naturally-occurring metal ions in the cells, as well as exogenously-introduced metals such as drugs and nanoparticles. Due to the fully hydrated nature of nearly all biological samples, cryo-fixation followed by imaging under cryogenic temperature represents the ideal imaging modality currently available. However, under the circumstances that such a combination is not easily accessible or practical, aldehyde based chemical fixation remains useful and sometimes inevitable. This article describes in as much detail as possible in the preparation of adherent mammalian cells by chemical fixation for X-ray fluorescent imaging.

Here, we present a protocol on how to determine the quantity and distribution of metals in a sample using synchrotron X-ray fluorescence. We focus on adherent cells, and describe the chemical fixation method to prepare this sample. We then describe how to mount and image the sample using synchrotron X-rays.

X-ray fluorescence imaging allows us to non-destructively measure the spatial distribution and concentration of multiple elements simultaneously over ...

X-ray Powder Diffraction in Conservation Science: Towards Routine Crystal Structure Determination of Corrosion Products on Heritage Art Objects

The crystal structure determination and refinement process of corrosion products on historic art objects using laboratory high-resolution X-ray powder diffraction (XRPD) is presented in detail via two case studies.
The first material under investigation was sodium copper formate hydroxide oxide hydrate, Cu4Na4O(HCOO)8(OH)2&#8729;4H2O (sample 1) which forms on soda glass/copper alloy composite historic objects (e.g., enamels) in museum collections, exposed to formaldehyde and formic acid emitted from wooden storage cabinets, adhesives, etc. This degradation phenomenon has recently been characterized as &#34;glass induced metal corrosion&#34;.
For the second case study, thecotrichite, Ca3(CH3COO)3Cl(NO3)2&#8729;6H2O (sample 2), was chosen, which is an efflorescent salt forming needlelike crystallites on tiles and limestone objects which are stored in wooden cabinets and display cases. In this case, the wood acts as source for acetic acid which reacts with soluble chloride and nitrate salts from the artifact or its environment.
The knowledge of the geometrical structure helps conservation science to better understand production and decay reactions and to allow for full quantitative analysis in the frequent case of mixtures.

Modern high resolution X-ray powder diffraction (XRPD) in the laboratory is used as an efficient tool to determine crystal structures of long-known corrosion products on historic objects.

The crystal structure determination and refinement process of corrosion products on historic art objects using laboratory high-resolution X-ray powder ...

Quantifying X-Ray Fluorescence Data Using MAPS

The quantification of X-ray fluorescence (XRF) microscopy maps by fitting the raw spectra to a known standard is crucial for evaluating chemical composition and elemental distribution within a material. Synchrotron-based XRF has become an integral characterization technique for a variety of research topics, particularly due to its non-destructive nature and its high sensitivity. Today, synchrotrons can acquire fluorescence data at spatial resolutions well below a micron, allowing for the evaluation of compositional variations at the nanoscale. Through proper quantification, it is then possible to obtain an in-depth, high-resolution understanding of elemental segregation, stoichiometric relationships, and clustering behavior.
This article explains how to use the MAPS fitting software developed by Argonne National Laboratory for the quantification of full 2-D XRF maps. We use as an example results from a Cu(In,Ga)Se2 solar cell, taken at the Advanced Photon Source beamline 2-ID-D at Argonne National Laboratory. We show the standard procedure for fitting raw data, demonstrate how to evaluate the quality of a fit and present the typical outputs generated by the program. In addition, we discuss in this manuscript certain software limitations and offer suggestions for how to further correct the data to be numerically accurate and representative of spatially resolved, elemental concentrations.

Here, we demonstrate the use of the X-ray fluorescence fitting software, MAPS, created by Argonne National Laboratory for the quantification of fluorescence microscopy data. The quantified data that results is useful for understanding the elemental distribution and stoichiometric ratios within a sample of interest.

The quantification of X-ray fluorescence (XRF) microscopy maps by fitting the raw spectra to a known standard is crucial for evaluating chemical ...

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 ...

Essential Metal Uptake in Gram-negative Bacteria: X-ray Fluorescence, Radioisotopes, and Cell Fractionation

We demonstrate a scalable method for the separation of the bacterial periplasm from the cytoplasm. This method is used to purify periplasmic protein for the purpose of biophysical characterization, and measure substrate transfer between periplasmic and cytoplasmic compartments. By carefully limiting the time that the periplasm is separated from the cytoplasm, the experimenter can extract the protein of interest and assay each compartment individually for substrate without carry-over contamination between compartments. The extracted protein from fractionation can then be further analyzed for three-dimensional structure determination or substrate-binding profiles. Alternatively, this method can be performed after incubation with a radiotracer to determine total percent uptake, as well as distribution of the tracer (and hence metal transport) across different bacterial compartments. Experimentation with a radiotracer can help differentiate between a physiological substrate and artefactual substrate, such as those caused by mismetallation.
X-ray fluorescence can be used to discover the presence or absence of metal incorporation in a sample, as well as measure changes that may occur in metal incorporation as a product of growth conditions, purification conditions, and/or crystallization conditions. X-ray fluorescence also provides a relative measure of abundance for each metal, which can be used to determine the best metal energy absorption peak to use for anomalous X-ray scattering data collection. Radiometal uptake can be used as a method to validate the physiological nature of a substrate detected by X-ray fluorescence, as well as support the discovery of novel substrates.

A protocol for the extraction of a periplasmic transition metal chaperone in the context of its native binding partners, and biophysical characterization of its substrate contents by X-ray fluorescence and radiometal uptake is presented.

We demonstrate a scalable method for the separation of the bacterial periplasm from the cytoplasm. This method is used to purify periplasmic protein for ...

Analysis of Minerals Produced by hFOB 1.19 and Saos-2 Cells Using Transmission Electron Microscopy with Energy Dispersive X-ray Microanalysis

This video presents the use of transmission electron microscopy with energy dispersive X-ray microanalysis (TEM-EDX) to compare the state of minerals in vesicles released by two human bone cell lines: hFOB 1.19 and Saos-2. These cell lines, after treatment with ascorbic acid (AA) and &#946;-glycerophosphate (&#946;-GP), undergo complete osteogenic transdifferentiation from proliferation to mineralization and produce matrix vesicles (MVs) that trigger apatite nucleation in the extracellular matrix (ECM).
Based on Alizarin Red-S (AR-S) staining and analysis of the composition of minerals in cell lysates using ultraviolet (UV) light or in vesicles using TEM imaging followed by EDX quantitation and ion mapping, we can infer that osteosarcoma Saos-2 and osteoblastic hFOB 1.19 cells reveal distinct mineralization profiles. Saos-2 cells mineralize more efficiently than hFOB 1.19 cells and produce larger mineral deposits that are not visible under UV light but are similar to hydroxyapatite (HA) in that they have more Ca and F substitutions.
The results obtained using these techniques allow us to conclude that the process of mineralization differs depending on the cell type. We propose that, at the cellular level, the origin and properties of vesicles predetermine the type of minerals.

We present a protocol to compare the state of minerals in vesicles released by two human bone cell lines: hFOB 1.19 and Saos-2. Their mineralization profiles were analyzed by Alizarin Red-S (AR-S) staining, ultraviolet (UV) light visualization, transmission electron microscopy (TEM) imaging and energy dispersive X-ray microanalysis (EDX).

This video presents the use of transmission electron microscopy with energy dispersive X-ray microanalysis (TEM-EDX) to compare the state of minerals in ...

Ligand-Mediated Nucleation and Growth of Palladium Metal Nanoparticles

The size, size distribution and stability of colloidal nanoparticles are greatly affected by the presence of capping ligands. Despite the key contribution of capping ligands during the synthesis reaction, their role in regulating the nucleation and growth rates of colloidal nanoparticles is not well understood. In this work, we demonstrate a mechanistic investigation of the role of trioctylphosphine (TOP) in Pd nanoparticles in different solvents (toluene and pyridine) using in situ SAXS and ligand-based kinetic modeling. Our results under different synthetic conditions reveal the overlap of nucleation and growth of Pd nanoparticles during the reaction, which contradicts the LaMer-type nucleation and growth model. The model accounts for the kinetics of Pd-TOP binding for both, the precursor and the particle surface, which is essential to capture the size evolution as well as the concentration of particles in situ. In addition, we illustrate the predictive power of our ligand-based model through designing the synthetic conditions to obtain nanoparticles with desired sizes. The proposed methodology can be applied to other synthesis systems and therefore serves as an effective strategy for predictive synthesis of colloidal nanoparticles.

The main goal of this work is to elucidate the role of capping agents in regulating the size of palladium nanoparticles by combining in situ small angle x-ray scattering (SAXS) and ligand-based kinetic modeling.

The size, size distribution and stability of colloidal nanoparticles are greatly affected by the presence of capping ligands. Despite the key contribution ...

Improving High Viscosity Extrusion of Microcrystals for Time-resolved Serial Femtosecond Crystallography at X-ray Lasers

High-viscosity micro-extrusion injectors have dramatically reduced sample consumption in serial femtosecond crystallographic experiments (SFX) at X-ray free electron lasers (XFELs). A series of experiments using the light-driven proton pump bacteriorhodopsin have further established these injectors as a preferred option to deliver crystals for time-resolved serial femtosecond crystallography (TR-SFX) to resolve structural changes of proteins after photoactivation. To obtain multiple structural snapshots of high quality, it is essential to collect large amounts of data and ensure clearance of crystals between every pump laser pulse. Here, we describe in detail how we optimized the extrusion of bacteriorhodopsin microcrystals for our recent TR-SFX experiments at the Linac Coherent Light Source (LCLS). The goal of the method is to optimize extrusion for a stable and continuous flow while maintaining a high density of crystals to increase the rate at which data can be collected in a TR-SFX experiment. We achieve this goal by preparing lipidic cubic phase with a homogenous distribution of crystals using a novel three-way syringe coupling device followed by adjusting the sample composition based on measurements of the extrusion stability taken with a high-speed camera setup. The methodology can be adapted to optimize the flow of other microcrystals. The setup will be available for users of the new Swiss Free Electron Laser facility.

The success of a time-resolved serial femtosecond crystallography experiment is dependent on efficient sample delivery. Here, we describe protocols to optimize the extrusion of bacteriorhodopsin microcrystals from a high viscosity micro-extrusion injector. The methodology relies on sample homogenization with a novel three-way coupler and visualization with a high-speed camera.

High-viscosity micro-extrusion injectors have dramatically reduced sample consumption in serial femtosecond crystallographic experiments (SFX) at X-ray ...

Biological Samples Preparation for Speciation at Cryogenic Temperature using High-Resolution  X-Ray Absorption Spectroscopy

The study of elements with X-ray absorption spectroscopy (XAS) is of particular interest when studying the role of metals in biological systems. Sample preparation is a key and often complex procedure, particularly for biological samples. Although X-ray speciation techniques are widely used, no detailed protocol has been yet disseminated for users of the technique. Further, chemical state modification is of concern, and cryo-based techniques are recommended to analyze the biological samples in their near-native hydrated state to provide the maximum preservation of chemical integrity of the cells or tissues. Here, we propose a cellular preparation protocol based on cryo-preserved samples. It is demonstrated in a high energy resolution fluorescence detected X-ray absorption spectroscopy study of selenium in cancer cells and a study of iron in phytoplankton. This protocol can be used with other biological samples and other X-ray techniques that can be damaged by irradiation.

This protocol presents a detailed procedure to prepare biological cryosamples for synchrotron-based X-ray absorption spectroscopy experiments. We describe all the steps required to optimize sample preparation and cryopreservation with examples of the protocol with cancer and phytoplankton cells. This method provides a universal standard of sample cryo-preparation.

The study of elements with X-ray absorption spectroscopy (XAS) is of particular interest when studying the role of metals in biological systems. Sample ...

In situ Grazing Incidence Small Angle X-ray Scattering on Roll-To-Roll Coating of Organic Solar Cells with Laboratory X-ray Instrumentation

We present an in-house, in situ Grazing Incidence Small Angle X-ray Scattering (GISAXS) experiment, developed to probe the drying kinetics of roll-to-roll slot-die coating of the active layer in organic photovoltaics (OPVs), during deposition. For this demonstration, the focus is on the combination of P3HT:O-IDTBR and P3HT:EH-IDTBR, which have different drying kinetics and device performance, despite their chemical structure only varying slightly by the sidechain of the small molecule acceptor. This article provides a step-by-step guide to perform an in situ GISAXS experiment and demonstrates how to analyze and interpret the results. Usually, performing this type of in situ X-ray experiments to investigate the drying kinetics of the active layer in OPVs relies on access to synchrotrons. However, by using and further developing the method described in this paper, it is possible to perform experiments with a coarse temporal and spatial resolution, on a day-to-day basis to gain fundamental insight in the morphology of drying inks.

This paper is a demonstration and a guideline to perform and analyze in-house (with a laboratory X-ray instrument) in situ GISAXS experiments of drying inks on roll-to-roll slot-die coated, non-fullerene organic photovoltaics.

We present an in-house, in situ Grazing Incidence Small Angle X-ray Scattering (GISAXS) experiment, developed to probe the drying kinetics of roll-to-roll ...