Crystallography
1. Introduction
2. experimental, 3. results and discussion.
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laboratory notes \(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)
| JOURNAL OF APPLIED CRYSTALLOGRAPHY |
Use of a confocal optical device for centring a diamond anvil cell in single-crystal X-ray diffraction experiments
a EastChem School of Chemistry and Centre for Science at Extreme Conditions, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3FJ, United Kingdom, b Micro-Epsilon UK Ltd, No. 1 Shorelines Building, Shore Road, Birkenhead CH41 1AU, United Kingdom, and c Bruker AXS GmbH, Oestliche Rheinbrueckenstrasse 49, 76187 Karlsruhe, Germany * Correspondence e-mail: [email protected]
High-pressure crystallographic data can be measured using a diamond anvil cell (DAC), which allows the sample to be viewed only along a cell vector which runs perpendicular to the diamond anvils. Although centring a sample perpendicular to this direction is straightforward, methods for centring along this direction often rely on sample focusing, measurements of the direct beam or short data collections followed by refinement of the crystal offsets. These methods may be inaccurate, difficult to apply or slow. Described here is a method based on precise measurement of the offset in this direction using a confocal optical device, whereby the cell centre is located at the mid-point of two measurements of the distance between a light source and the external faces of the diamond anvils viewed along the forward and reverse directions of the cell vector. It is shown that the method enables a DAC to be centred to within a few micrometres reproducibly and quickly.
Keywords: diamond anvil cells ; high-pressure experiments ; sample alignment .
| ( ) A and ( ) components of a Merrill–Bassett DAC. Reproduced with permission from Moggach (2008 ). |
2.1. Sample preparation
Single-crystal X-ray diffraction data were collected on a Bruker AXS D8 Venture three-circle (2 θ , ω and φ with χ fixed at 54.74°) diffractometer incorporating an Incoatec Mo K α ( λ = 0.71073 Å) microsource.
| A diffractometer configuration showing the confocal device mounted on the diffractometer stage. The inset shows a steel ball mounted on a goniometer head as used for the sensor alignment. |
2.2. Centring procedure
Initial centring of the crystal along the cell vector can also be performed using the video camera. An initial reading is taken on the video camera stage micrometer, and the camera focus is then adjusted so that the sample is in focus. A second micrometer reading is taken and the video camera is moved back to the average of the two micrometer readings. The image focus is then re-established using the goniometer head adjustor screw parallel to the viewing direction of the video camera. The cell can be rotated by 180° in φ to check that the sample remains in focus; if not, the procedure can be iterated until the sample is in focus when viewed along both forward and reverse directions along the cell vector. The success of this method relies on both diamonds having the same thickness.
| The user interface for the confocal device. The red and blue traces refer to the raw and optically corrected readings, respectively. |
2.3. Alignment of the sensor
2.4. validation of centring using diffraction.
Strategy for short data collections used for validation of centring | = 0° and χ = 54.74° in all runs. | Run | Scan angle (°) | Fixed angle (°) | 1 | 13.00 to −17.00 in ω | φ = 270.00 | 2 | 13.00 to −17.00 in ω | φ = 90.00 | 3 | 65.00 to 115.00 in φ | ω = 0.00 | | 2.5. Data collections Strategy for diffraction data collections | Run | 2θ (°) | φ (°) | ω range (°) | 1 | 11.00 | 270.00 | 7.00 to 22.00 | 2 | 11.00 | 270.00 | 15.00 to −45.00 | 3 | −11.00 | 270.00 | 345.00 to 360.00 | 4 | −11.00 | 270.00 | 353.00 to 320.00 | 5 | 11.00 | 270.00 | 187.00 to 220.00 | 6 | 11.00 | 270.00 | 195.00 to 180.00 | 7 | −11.00 | 270.00 | 165.00 to 225.00 | 8 | −11.00 | 270.00 | 173.00 to 158.00 | 9 | 11.00 | 90.00 | 7.00 to 22.00 | 10 | 11.00 | 90.00 | 15.00 to −45.00 | 11 | −11.00 | 90.00 | 345.00 to 360.00 | 12 | −11.00 | 90.00 | 353.00 to 320.00 | 13 | 11.00 | 90.00 | 187.00 to 220.00 | 14 | 11.00 | 90.00 | 195.00 to 180.00 | 15 | −11.00 | 90.00 | 165.00 to 225.00 | 16 | −11.00 | 90.00 | 173.00 to 158.00 | | 3.1. Centring procedure using the optical sensorAlthough diamonds are optically transparent, it is sometimes not possible to obtain a clear view of a sample from both sides of a DAC. This may be because a crystal has been grown in situ and the crystalline region of the sample is obscured; a sample may have fragmented; the sensitivity of a sample may mean that it needed to be loaded quickly with contaminated mother liquor as a pressure-transmitting medium; the medium may partially dissolve the sample and become coloured; optical effects in partially vitrified media may also occur; or, sadly, the outer faces of the diamonds may be dirty. In short, there are many reasons why a clear view of a sample might not be obtained, which can make methods of centring based on focusing the sample image from two opposite directions difficult to apply. Moreover, even when a clear image can be obtained, assessment of whether an image is focused or not can be somewhat subjective and dependent on the quality of the lighting and optics on the viewing device being used. Our aim in incorporating the optical sensor into the centring procedure for a DAC was to replace focus-based centring methods with one which is both based on numerical measurements and less sensitive to the characteristics of the sample. Although the method has been applied to DACs, it could in principle be used for any experiment where the view of the sample is restricted, for example when a sample is surrounded by other material, such as can occur in a capillary. | The shift required between the mid-point of the diamond culets (dark grey) and the centre of the crystal (light grey) is ( − )/2, where is the gasket depth (typically measured during indenting) and the thickness of the crystal. | Although in-house high-pressure work is usually still carried out using conventional manual goniometer heads, motorized heads are becoming much more common for ambient-pressure measurements. Very convenient procedures are available that allow a user to select the centre of a sample with a mouse click or even rely on image-recognition algorithms to identify the sample. Application of this approach to high-pressure work would be very attractive because the precision of adjustments on motorized heads is finer than that on manual heads, provided the weight of the cell can be accommodated. Use of a motorized goniometer head would be immediately applicable to centring perpendicular to the cell vector. The numerical feedback provided by the confocal centring procedure described here would also provide the distance adjustments required for centring along the cell vector, introducing the potential for essentially automated DAC centring. 3.2. Data collection tests Crystal and data for glyphosate collected at different offsets (in µm) along the cell vector | along the X-ray beam from source to sample, vertical and pointing up, and making a right-handed set. The DAC was mounted so that the cell vector would lie along if all the setting angles were at zero, so that the values of the offset in this table correspond to displacements along the cell vector. | Empirical formula: C H NO P | Crystal system: Monoclinic | Space group: 2 / | Resolution limit: 0.7 Å | | | offset | | | 0 (centred) | 30 | 60 | −30 | −60 | Unit cell | (Å) | 8.6274 (12) | 8.6261 (13) | 8.6232 (11) | 8.6262 (12) | 8.6274 (13) | (Å) | 7.7307 (5) | 7.7305 (6) | 7.7303 (5) | 7.7299 (5) | 7.7301 (6) | (Å) | 9.4613 (7) | 9.4604 (7) | 9.4606 (6) | 9.4620 (7) | 9.4631 (7) | α (°) | 90.00 | 90.00 | 90.00 | 90.00 | 90.00 | β (°) | 109.406 (8) | 109.414 (8) | 109.414 (7) | 109.417 (8) | 109.407 (9) | γ (°) | 90.00 | 90.00 | 90.00 | 90.00 | 90.00 | (Å ) | 595.18 (11) | 594.99 (11) | 594.79 (10) | 595.04 (11) | 595.24 (11) | | Domain translation | (mm) | −0.004 (5) | −0.004 (5) | −0.005 (5) | −0.013 (5) | −0.009 (5) | | (mm) | 0.004 (10) | 0.027 (9) | 0.051 (10) | −0.0045 (11) | −0.053 (9) | | (mm) | 0.000 (5) | 0.002 (5) | −0.004 (5) | −0.004 (5) | 0.000 (5) | | (%) | 2.56 | 2.65 | 2.85 | 2.78 | 2.60 | (%) | 5.44 | 5.39 | 6.41 | 6.48 | 6.42 | (%) | 4.17 | 4.37 | 4.34 | 4.56 | 4.30 | Total No. of reflections | 2693 | 2772 | 2672 | 2724 | 2520 | No. of unique reflections | 339 | 356 | 352 | 362 | 362 | Reflections with ≥ 2σ( ) | 296 | 299 | 300 | 292 | 293 | Completeness (%) | 27.0 | 26.8 | 26.7 | 26.9 | 25.7 | Average /σ( ) | 27.70 | 27.49 | 26.98 | 26.95 | 24.61 | | | Scale variation graphs for Mo X-ray radiation measurement with different offsets applied. | ‡ Current address: Renishaw plc, New Mills, Wotton-under-Edge GL12 8JR, United Kingdom. AcknowledgementsFunding information. We thank the Engineering and Physical Sciences Research Council (grant number EP/R042845/1 to Simon Parsons) and the University of Edinburgh for funding. This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence , which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited. Follow J. Appl. Cryst. | |
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IMAGES
VIDEO
COMMENTS
An optical instrument is said to be diffraction-limited if it has reached this limit of resolution performance. Other factors may affect an optical system's performance, such as lens imperfections or aberrations, but these are caused by errors in the manufacture or calculation of a lens, whereas the diffraction limit is the maximum resolution ...
separation due to diffraction, then diffraction limits the imagequality. The "f-number"of a lens is defined as f/D. To minimize diffraction, you want a small f-number, i.e., a large aperture*. d Photosensor: 7 mm 5 mm Pixel *This assumes a 'perfect lens'. In practice, lens aberrations limit the resolution if D is toobig. Photosensor ...
The Airy Disk. When light passes through any size aperture (every lens has a finite aperture), diffraction occurs. The resulting diffraction pattern, a bright region in the center, together with a series of concentric rings of decreasing intensity around it, is called the Airy disk (see Figure 1).The diameter of this pattern is related to the wavelength (λ) of the illuminating light and the ...
The Rayleigh criterion for the diffraction limit to resolution states that two images are just resolvable when the center of the diffraction pattern of one is directly over the first minimum of the diffraction pattern of the other. See Figure 2b. The first minimum is at an angle of θ = 1.22 λ D θ = 1.22 λ D, so that two point objects are ...
2. sin2. I =. (5) (6) where I0 is the intensity from a single source. Since the slits are spaced d apart, the total size of the diffraction grating is a = Nd. Now say we place a screen at a distance L from the slits with L ≫ a. Then the height y up this screen is. y = L tanθ ≈ Lθ ≈ L sinθ, and so d y ∆ = 2π + δ λ L.
Figure 14.1.2 Superposition of two sinusoidal waves. We see that the wave has a maximum amplitude when sin( x + φ ) = 1 , or x = π /2 − φ The interference there is constructive. On the other hand, destructive interference occurs at x = π − φ = 2.61 rad, wheresin( π ) = 0 . The light sources must be coherent.
point being imaged as a diffraction spot of a finite size. Diffraction spots from nearby points may overlap with each other and become indistinguishable. The present experiment studies the diffraction resolution limit of a microscope objective. The theory of microscope resolution was developed by German physicist Ernst Karl Abbe (1840 - 1905).
Just what is the limit? To answer that question, consider the diffraction pattern for a circular aperture, which has a central maximum that is wider and brighter than the maxima surrounding it (similar to a slit) [see Figure 27.26(a)]. It can be shown that, for a circular aperture of diameter D D, the first minimum in the diffraction pattern occurs at θ = 1. 22 λ / D θ = 1. 22 λ / D ...
The classical optical diffraction limit can be overcome by exploiting the quantum properties of light in several theoretical studies; however, they mostly rely on an entangled light source. Recent experiments have demonstrated that quantum properties are preserved in many fluorophores, which makes it possible to add a new dimension of information for super-resolution fluorescence imaging.
Figure 17.7 Young's double-slit experiment. Here, light of a single wavelength passes through a pair of vertical slits and produces a diffraction pattern on the screen—numerous vertical light and dark lines that are spread out horizontally. Without diffraction and interference, the light would simply make two lines on the screen.
Dr. Kurt Thorn (UCSF) begins this iBiology video with a historical summary of the work of Ernst Abbe (1840-1905) who formalized the definition of resolution in 1873 after conducting a groundbreaking experiment, referred to as the Abbe Diffraction experiment. Dr. Thorn describes the experiment in which a sample, which is theoretically represented as a diffraction grating with a repeating ...
We have already encountered the limited resolution in extracting the structure of inhomogeneous objects via scattering experiments (Section 2.5). The microscope obeys the limits. Unlike magnification, resolution is ... effect of a diffraction phenomenon" [3]. Thus, a given image field is formed by the interference between plane waves ...
First we remark that the way the diffraction limit is traditionally studied is in fact a mixture model. In particular we assume that, experimentally, we can measure photons that are sampled from the true diffracted image. However we only observe a finite number of them because our experiment has finite exposure time, and indeed
The angular resolution of many optical instruments such as telescopes is also limited due to diffraction e.g. at the input aperture. That resolution limit can be estimated to be roughly the wavelength divided by the aperture diameter. Apertures are not always circular. Figures 6 and 7 show an example case, where a laser beam is truncated with a ...
In 1873, the German physicist Ernst Abbe realized that the resolution of optical imaging instruments, including telescopes and microscopes, is fundamentally limited by the diffraction of light.
Experiment 9: Interference and Diffraction Answer these questions on a separate sheet of paper and turn them in before the lab 1. Measuring the Wavelength of Laser Light In the first part of this experiment you will shine a red laser through a pair of narrow slits (a = 40 µm) separated by a known distance (you will use both d = 250 µm and 500 ...
The distance — the diffraction limit — is proportional to the wavelength and inversely proportional to the angular distribution of the light observed. ... Although the experiments shown in ...
For completeness, Bragg diffraction is a limit for a large number of atoms with X-rays or neutrons, and is rarely valid for electron diffraction or with solid particles in the size range of less than 50 nanometers. [23] ... In the case of Young's double-slit experiment, this would mean that if the transverse coherence length is smaller than the ...
Diffraction data were collected using the strategy shown in Table 2, which is based on that described by Dawson et al. (2004) but with runs split so that shading is minimized at the beginning of each run. Data were collected with the cell in its centred position and in positions deliberately displaced by ±30 and ±60 µm along the cell vector.