Name: x-ray powder diffraction in conservation science: towards routine crystal structure determination of corrosion products on heritage art objects
Uploaded: 2016-06-08T14:00:00
Description: Watch this Scientific Journal Video about X-ray Powder Diffraction in Conservation Science: Towards Routine Crystal Structure Determination of Corrosion Products on Heritage Art Objects at JoVE.com

The authors gratefully acknowledge Ms. Christine Stefani for performing the XRPD measurements. Marian Schu&#776;ch and Rebekka Kuiter (State Academy of Art and Design Stuttgart) are acknowledged for the pictures of the tile (Fig. 7).

1. Sample Preparation
<ol>
	<li>Collection of material
	<ol>
		<li>Carefully pick a small amount (less than 1 mg) of sample 1 under a digital microscope using a scalpel and tweezers from settings of opaque blue-green cabochons on a historic clasp, belonging to the collection of the Rosgartenmuseum Konstanz (RMK-1964.79) (Figure 6).</li>
		<li>Carefully scratch a few mg of sample 2 with a scalpel from the surface of a glazed ceramic tile, dating at early modern times, manufactured in So...

<ol>
	<li>Bradley, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> The interface between science and conservation, Occacional Paper 116. , (1997).</li><li>Dinnebier, R. E., Billinge, S. J. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Powder Diffraction:Theory and Practice. , (2008).</li><li>Debye, P., Scherrer, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Interferenzen+an+regellos+orientierten+Teilchen+im+Roentgenlicht.">Interferenzen an regellos orientierten Teilchen im Roentgenlicht.</a> Phys. Zeit. 17, 277-283 (1916).</li><li>Hull, A. 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Chem. 54 (6), 2638-2642 (2015).</li><li>Wahlberg, N., 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=Crystal+Structure+of+Thecotrichite,+an+Efflorescent+Salt+on+Calcareous+Objects+Stored+in+Wooden+Cabinets.">Crystal Structure of Thecotrichite, an Efflorescent Salt on Calcareous Objects Stored in Wooden Cabinets.</a> Cryst. Growth Des. 15 (6), 2795-2800 (2015).</li><li>Eggert, G., Fischer, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gef&#228;hrliche+Nachbarschaft:+Durch+Glas+induzierte+Metallkorrosion+an+Museums-Exponaten+-+Das+GIMME-Projekt.">Gef&#228;hrliche Nachbarschaft: Durch Glas induzierte Metallkorrosion an Museums-Exponaten - Das GIMME-Projekt.</a> Restauro. 1, 38-43 (2012).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> TOPAS (current version 5.0). , (2015).</li><li>Coelho, A. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Indexing+of+powder+diffraction+patterns+by+iterative+use+of+singular+value+decomposition.">Indexing of powder diffraction patterns by iterative use of singular value decomposition.</a> J. Appl. Crystallogr. 36 (1), 86-95 (2003).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> International Tables for Crystallography Volume A: Space-group symmetry. , (2006).</li><li>Pawley, G. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Unit-cell+refinement+from+powder+diffraction+scans.">Unit-cell refinement from powder diffraction scans.</a> J. Appl. Crystallogr. 14, 357-361 (1981).</li><li>Cheary, R. W., Coelho, A. A., Cline, J. 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A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Whole-profile+structure+solution+from+powder+diffraction+data+using+simulated+annealing.">Whole-profile structure solution from powder diffraction data using simulated annealing.</a> J. Appl. Crystallogr. 33 (3), 899-908 (2000).</li><li>Macrae, C. 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=Mercury:+visualization+and+analysis+of+crystal+structures.">Mercury: visualization and analysis of crystal structures.</a> J. Appl. Crystallogr. 39 (3), 453-457 (2006).</li><li>Mittemeijer, E. J., Welzel, U. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Modern Diffraction Methods. , (2012).</li></ol>

XRPD is a suitable technique for conservation research as it is non-destructive, fast and easy-to-use. XRPD data can be used in routine qualitative analysis, owing to the fact that the powder pattern is a fingerprint signature to the corresponding crystal structure. The biggest advantage of XRPD over other analytic techniques is the ability of performing simultaneous qualitative and quantitative analysis of crystalline constituents in mixtures by using the Rietveld refinement method5. Moreover, the presence of...

Conservation science applies scientific (often chemical) methods in the conservation of artifacts. This includes investigations of the production of artifacts (&#39;technical art history&#39;: How was it made at that time?) and their decay pathways as a prerequisite to develop proper conservation treatments. Oftentimes these studies deal with metal organic salts like carbonates, formates and acetates. Some of them have been deliberately manufactured using suitable compounds (e.g., vinegar), others derive from deterioration reactions with the atmosphere (carbon dioxide or carbonyl compounds from indoor air pollution)1. As a matter of fact, the crystal structures of many of these corrosion materials are still unknown. This is an unfortunate fact, since 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 case of mixtures.
Under the condition that the material of interest forms single crystals of sufficient size and quality, single crystal diffraction is the method of choice for the determination of the crystal structure. If these boundary conditions are not fulfilled, powder diffraction is the closest alternative. The biggest drawback of powder diffraction as compared to single crystal diffraction lies in the loss of the orientational information of the reciprocal d-vector d* (scattering vector). In other words, the intensity of a single diffraction spot is smeared over the surface of a sphere. This can be considered a projection of the three-dimensional diffraction (= reciprocal) space onto the one dimensional 2&#952;-axis of the powder pattern. As a consequence, scattering vectors of different direction but equal or similar length, overlap systematically or accidentally making it difficult or even impossible to separate these reflections2 (Figure 1). This is also the main reason why powder diffraction, despite its early invention just four years after the first single crystal experiment3,4, was mainly used for phase identification and quantification for more than half a century. Nevertheless, the information content of a powder pattern is huge as can be easily deduced from Figure 2. The real challenge, however, is to reveal as much information as possible in a routine way.
A crucial step towards this goal, without any doubt, was the idea from Hugo Rietveld in 19695 who invented a local optimization technique for crystal structure refinement from powder diffraction data. The method does not refine single intensities but the entire powder pattern against a model of increasing complexity, thus taking the peak overlap intrinsically into account. From that time on, scientists using powder diffraction techniques were no longer limited to data analysis by methods developed for single crystal investigation. Several years after the invention of the Rietveld method, the power of the powder diffraction method for ab-initio structure determinations was recognized. Nowadays, almost all branches of natural sciences and engineering use powder diffraction to determine more and more complex crystal structures, although the method can still not be regarded as routine. Within the last decade, a new generation of powder diffractometers in the laboratory was designed providing high resolution, high energy and high intensity. Better resolution immediately leads to better peak separation while higher energies fight absorption. The benefit of a better peak profile description based on fundamental physical parameters (Figure 3) are more accurate intensities of Bragg reflection allowing for more detailed structural investigations. With modern equipment and software even microstructural parameters like domain sizes and microstrain are routinely deduced from powder diffraction data.
All algorithms for crystal structure determination from powder diffraction data use single peak intensities, the entire powder pattern or a combination of both. The conventional single crystal reciprocal space techniques often fail due to an unfavorable ratio between available observations and structural parameters. This situation changed dramatically with the introduction of the &#34;charge flipping&#34; technique6 (Figure 4) and the development of global optimization methods in direct space, of which the simulated annealing technique7 (Figure 5) is the most prominent representative. In particular, the introduction of chemical knowledge into the structure determination process using rigid bodies or the known connectivity of molecular compounds concerning bond lengths and angles strongly reduces the number of necessary parameters. In other words, instead of three positional parameters for every single atom, only the external (and few internal) degrees of freedom of groups of atoms need to be determined. It is this reduction of structural complexity which makes the powder method a real alternative to single crystal analysis.
Two pioneering case studies of the authors8,9 proved that it is possible to solve complicated crystal structures of complex corrosion products using powder diffraction data. The superiority of the crystallographic studies compared to other approaches was demonstrated among others by the fact that in both cases the reported formulas had to be corrected after considering the solved crystal structures.
The occurrence of both materials under investigation in museums is related to their storage in wooden cabinets or exposed to other sources of carbonyl pollutants. 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 from wooden storage cabinets, adhesives, etc. This degradation phenomenon has recently been characterized as &#34;glass induced metal corrosion&#34;10. For the second case study, thecotrichite, Ca3(CH3COO)3Cl(NO3)2&#8729;6H2O (sample 2), was chosen. Thecotrichite is a frequently observed efflorescent salt forming needlelike crystallites on tiles and limestone museum objects, which are stored in oak 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.
In the following part of the text, the individual steps of the structure determination process using powder diffraction data applied to corrosion products from conservation science are presented in detail.

<table border="0" cellpadding="0" cellspacing="0" width="573">
	<tbody>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Stadi-P&#160;</td>
			<td style="width:71px;">Stoe &#38; Cie GmbH</td>
			<td style="width:119px;"></td>
			<td style="width:167px;">Powder Diffractometer</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Mythen 1-K (450 &#956;m)</td>
			<td style="width:71px;">Dectris Ltd.</td>
			<td style="width:119px;"></td>
			<td>Position Sensitive Detector</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Mark tube borosilicate glass No. 50, 0.5 mm diameter</td>
			<td style="width:71px;">Hilgenberg GmbH</td>
			<td align="right">4007605</td>
			<td>Low absorbing capillaries</td>
		</tr>
		<tr height="126">
			<td height="126" style="height:126px;width:216px;">Topas 5.0</td>
			<td style="width:71px;">Bruker AXS Advanced X-ray Solutions GmbH</td>
			<td style="width:119px;"></td>
			<td>Powder Diffraction Evaluation Software</td>
		</tr>
	</tbody>
</table>

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.

High resolution XRPD was used to determine the previously unknown crystal structures of two long-known corrosion products on historic objects. The samples were taken from two museum objects and carefully grinded before they were sealed in transmission and capillary sample holders (Figures 6, 7). Standard measurements using a state of the art laboratory high resolution powder diffractometer in transmission and Debye-Scherrer geometry using monochromatic X-rays were perform...

Watch this Scientific Journal Video about X-ray Powder Diffraction in Conservation Science: Towards Routine Crystal Structure Determination of Corrosion Products on Heritage Art Objects at JoVE.com

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

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 ...

The overall goal of this method is to gain knowledge of the crystal structure of micro and nano crystal and corrosion products to better understand production and decay reactions of heritage art objects and to allow for full quantitative analysis of mixtures. This method can help answer key questions in the field of conservation science such as how the art object has been produced and why is it corroded. The main advantage of this technique is that it does not require single crystals but only small amounts of micro crystal and powder.Though this method can provide insight into conservation science it can also be applied to other fields such as material science, inorganic chemistry or metallogy. We found that the idea for this method when we investigated at a gradation phenomenon which recently has been characterized as glass induced metal corrosion. Demonstrating sample preparation and data collection will be Ms.Stefani, a chemical technical assistant from our laboratory.Under a digital microscope carefully pick less than one milligram of sample one from opaque blue green cabochons on a historic clasp using a fine needle. Following this, grind the sample carefully with a pestle in a small agate mortar. Distribute the sample between two thin x-ray transparent polyamide foils and mount them on a transmission sample holder with an eight millimeter diameter central opening.Fix the transmission sample holder on the theta circle of a diffractometer. Measure the sample for 20 hours from five to 85 degrees two theta, with a step width of 0.015 degrees two theta in transmission mode. Turn rotation on in order to achieve better particle statistics.The next step is to perform an automatic peak search using the first and second derivatives of Sovietske Golle polynomials of low order. First start the software program by double clicking the icon and then click Load Scan Files. Using the pull down menu select xy data files and then double click on the appropriate file.Now expand the range of the file. Click on the Emission Profile tab, select Load Emission Profile and choose the desired profile. Next click the Automatically Insert Peaks button and unclick Remove K Alpha 2 Peaks, after setting the Peak Width to 0.12 set the Noise Threshold to 1.74 and press the Add Peaks button.Zoom in on the pattern, move to the desired section of peaks and then open the peak details window. Set the peaks by pressing the left mouse button. Next click on Peaks Phase.Mark all peaks yellow by clicking on Position and then left click in the yellow marked column, copy the selection and select Create Indexing Range. Deselect the range and select Range Indexing. Then select all bravais lattices.Following this press the Run button. And Yes to keep indexing solutions. Press the Solutions button and then highlight the first solution by left clicking button one.Now right click on the highlighted solution and copy the selection. Deselect Range Indexing and then select the range. At this point press Add hkl Phase, expand the range and then expand hkl Phase.Under Indexing Details, choose Paste Indexing Details. Under Background, change Order to eight and then select 1/X Bkg term. Next click Instrument.After setting the primary and secondary radii to 217.5 mm, select Receiving Slit Width under Point detector. Under Full Axial Model, set the source, sample, and RS length to six mm. Now click Corrections and choose 0 error.Choose LP factor and set the value to 27.3. Then click Miscellaneous and set Convolution Steps to 2. Select Start X and set the value to eight, then choose Finish X and set the value to 75.Under Click Peaks Phase choose Delete Peaks Phase and click Yes. At this point click hkl Phase and choose Microstructure. After selecting Cry size L choose Cry size G, select Strain L, choose Strain G and then press the Run button.Finally create a list of brag peaks suitable for charge flipping. For crystal structure determination use the method of charge flipping supported by the inclusion of the tangent formula to find the positions of most of the heavier atoms. First under File select Close All and click Yes.Under Launch, select Launch Kernel. From the Launch pull down menu, select Set INP file and then select the prepared input file. Now press the Run button and after approximately 20, 000 cycles press the Stop button and click OK.Following this press the temporary output window displaying selected atoms button and then press the Cloud options dialog button.Set N to pick to 45. Choose width symmetry and press the Pick button. Copy the temporary output, save it to a text file and close the charge flipping graphics window.The next step is to apply the global optimization method of simulated annealing to find the positions of all missing non hydrogen atoms. From the launch pull down menu select Set INP file and then choose the prepared input file. Press the Run button and after several thousand cycles press the Stop button and click Yes.The final step is to turn off simulated annealing and switch to the Reitfeld refinement mode by commenting out the appropriate command. Under Launch choose Set INP file and select the prepared input text file. Finally press the Run button and click Yes.High resolution X-ray powder diffraction was used to determine the crystal structures of two long known corrosion products on historic objects. Standard measurements using a state of the art laboratory high resolution powder diffractometer in transmission and Debye Scherrer geometry using monochromatic x-rays were performed. Crystal structure determination of sample one was performed by iteratively combining reciprocal and direct space methods with Difference Fourier analysis.The determination of the crystal structures of these compounds confirms the exact composition, improves our understanding of the decay mechanisms and allows full quantitative phase analysis of corrosion products. Once mastered this technique can be done within one day if it is performed properly. Following this procedure other methods like DTA, Raman Spectroscopy and EDX can be performed in order to get complimentary and additional information concerning composition, bonding, possible phase transitions and stability.After watching this video you should have a good understanding of how to prepare samples, record appropriate powder diffraction data, perform data reduction and determine the crystal structure of micro crystalline material. After its development this technique will pave the way for researchers in the field of conservation science and it is non destructive, fast and easy to use.

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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 ...

From Constructs to Crystals &#8211; Towards Structure Determination of &#946;-barrel Outer Membrane Proteins

Membrane proteins serve important functions in cells such as nutrient transport, motility, signaling, survival and virulence, yet constitute only ~1% percent of known structures. There are two types of membrane proteins, &#945;-helical and &#946;-barrel. While &#945;-helical membrane proteins can be found in nearly all cellular membranes, &#946;-barrel membrane proteins can only be found in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. One common bottleneck in structural studies of membrane proteins in general is getting enough pure sample for analysis. In hopes of assisting those interested in solving the structure of their favorite &#946;-barrel outer membrane protein (OMP), general protocols are presented for the production of target &#946;-barrel OMPs at levels useful for structure determination by either X-ray crystallography and/or NMR spectroscopy. Here, we outline construct design for both native expression and for expression into inclusion bodies, purification using an affinity tag, and crystallization using detergent screening, bicelle, and lipidic cubic phase techniques. These protocols have been tested and found to work for most OMPs from Gram-negative bacteria; however, there are some targets, particularly for mitochondria and chloroplasts that may require other methods for expression and purification. As such, the methods here should be applicable for most projects that involve OMPs from Gram-negative bacteria, yet the expression levels and amount of purified sample will vary depending on the target OMP.

From Constructs to Crystals &amp;#8211; Towards Structure Determination of &amp;#946;-barrel Outer Membrane Proteins

&#946;-barrel outer membrane proteins (OMPs) serve many functions within the outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts. Here, we hope to alleviate a known bottleneck in structural studies by presenting protocols for the production of &#946;-barrel OMPs in sufficient quantities for structure determination by X-ray crystallography or NMR spectroscopy.

Membrane proteins serve important functions in cells such as nutrient transport, motility, signaling, survival and virulence, yet constitute only ~1% ...

High Pressure Single Crystal Diffraction at PX^2

In this report we describe detailed procedures for carrying out single crystal X-ray diffraction experiments with a diamond anvil cell (DAC) at the GSECARS 13-BM-C beamline at the Advanced Photon Source. The DAC program at 13-BM-C is part of the Partnership for Extreme Xtallography (PX^2) project. BX-90 type DACs with conical-type diamond anvils and backing plates are recommended for these experiments. The sample chamber should be loaded with noble gas to maintain a hydrostatic pressure environment. The sample is aligned to the rotation center of the diffraction goniometer. The MARCCD area detector is calibrated with a powder diffraction pattern from LaB6. The sample diffraction peaks are analyzed with the ATREX software program, and are then indexed with the RSV software program. RSV is used to refine the UB matrix of the single crystal, and with this information and the peak prediction function, more diffraction peaks can be located. Representative single crystal diffraction data from an omphacite (Ca0.51Na0.48)(Mg0.44Al0.44Fe2+0.14Fe3+0.02)Si2O6 sample were collected. Analysis of the data gave a monoclinic lattice with P2/n space group at 0.35 GPa, and the lattice parameters were found to be: a = 9.496 &#177;0.006 &#197;, b = 8.761 &#177;0.004 &#197;, c = 5.248 &#177;0.001 &#197;, &#946; = 105.06 &#177;0.03&#186;, &#945; = &#947; = 90&#186;.

In this report, we describe detailed procedures for carrying out single crystal X-ray diffraction experiments with a diamond anvil cell at the GSECARS 13-BM-C beamline at the Advanced Photon Source. ATREX and RSV programs are used to analyze the data.

In this report we describe detailed procedures for carrying out single crystal X-ray diffraction experiments with a diamond anvil cell (DAC) at the ...

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 ...

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 ...

Nanothermite with Meringue-like Morphology: From Loose Powder to Ultra-porous Objects

The goal of the protocol described in this article is to prepare aluminothermic compositions (nanothermites) in the form of porous, monolithic objects. Nanothermites are combustible materials made up of inorganic fuel and an oxidizer. In nanothermite foams, aluminum is the fuel and aluminum phosphate and tungsten trioxide are the oxidizing moieties. The highest flame propagation velocities (FPVs) in nanothermites are observed in loose powders and FPVs are strongly decreased by pelletizing nanothermite powders. From a physical standpoint, nanothermite loose powders are metastable systems. Their properties can be altered by unintentional compaction induced by shocks or vibrations or by the segregation of particles over time by settling phenomena, which originates from the density differences of their components. Moving from a powder to an object is the challenge that must be overcome to integrate nanothermites in pyrotechnic systems. Nanothermite objects must have both a high open porosity and good mechanical strength. Nanothermite foams meet both of these criteria, and they are prepared by dispersing a nano-sized aluminothermic mixture (Al/WO3) in orthophosphoric acid. The reaction of aluminum with the acid solution gives the AlPO4 &#34;cement&#34; in which Al and WO3 nanoparticles are embedded. In nanothermite foams, aluminum phosphate plays the dual role of binder and oxidizer. This method can be used with tungsten trioxide, which is not altered by the preparation process. It could probably be extended to some oxides, which are commonly used for the preparation of high performance nanothermites. The WO3-based nanothermite foams described in this article are particularly insensitive to impact and friction, which makes them far safer to handle than loose Al/WO3 powder. The fast combustion of these materials has interesting applications in pyrotechnic igniters. Their use in detonators as primers would require the incorporation of a secondary explosive in their composition.

This manuscript describes the synthesis of combustible aluminophosphate matrices by the reaction of orthophosphoric acid (H3PO4) with aluminum nanopowder. When this reaction is carried out with excess aluminum in the presence of tungsten trioxide nanopowder, it leads to a solid, porous nanothermite foam.

The goal of the protocol described in this article is to prepare aluminothermic compositions (nanothermites) in the form of porous, monolithic objects. ...

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 ...

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.

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 ...

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 ...