Direct phase determination in electron crystallography: small organic molecules

1992 ◽  
Vol 50 (2) ◽  
pp. 1166-1167
Author(s):  
Douglas L. Dorset
Keyword(s):  
Organic Molecules ◽  
Data Sets ◽  
Temperature Structure ◽  
3D Analysis ◽  
Intensity Data ◽  
Electron Crystallography ◽  
Phase Determination ◽  
Measured Intensity ◽  
3D Data

The quantitative use of electron diffraction intensity data for the determination of crystal structures represents the pioneering achievement in the electron crystallography of organic molecules, an effort largely begun by B. K. Vainshtein and his co-workers. However, despite numerous representative structure analyses yielding results consistent with X-ray determination, this entire effort was viewed with considerable mistrust by many crystallographers. This was no doubt due to the rather high crystallographic R-factors reported for some structures and, more importantly, the failure to convince many skeptics that the measured intensity data were adequate for ab initio structure determinations.We have recently demonstrated the utility of these data sets for structure analyses by direct phase determination based on the probabilistic estimate of three- and four-phase structure invariant sums. Examples include the structure of diketopiperazine using Vainshtein's 3D data, a similar 3D analysis of the room temperature structure of thiourea, and a zonal determination of the urea structure, the latter also based on data collected by the Moscow group.

The Pseudo-Atom Approximation in Direct Phase Determination of Protein Structures.

1997 ◽  
Vol 3 (S2) ◽  
pp. 1025-1026
Author(s):  
Douglas L. Dorset
Keyword(s):  
Fourier Transform ◽  
High Resolution ◽  
Protein Structures ◽  
Direct Methods ◽  
Direct Solution ◽  
Phase Problem ◽  
Electron Crystallography ◽  
Phase Determination ◽  
The Fourier Transform

In principle, the availability of high-resolution micrographs in electron crystallography is a direct solution of the phase problem that has been used to great advantage for the study of proteins. However, as the resolution of the determination increases, the Fourier transform of the micrograph becomes a less accurate phase source. Hence, alternative direct methods for phase determination have been evaluated, if only to extend the resolution of most reliable lower resolution phases to the limit of the electron diffraction pattern. The first demonstration of its feasibility was published in a study of bacteriorhodopsin extending 15 Å image phases to beyond 3 Å by maximum entropy and likelihood procedures i. Later studies demonstrated that convolutional methods also can be effective.In protein crystallography, there is always an interest in carrying out a true ab initio determinations, if only because of the challenge to traditional direct methods that become statistically less reliable as the number of atoms in the unit cell increases.

Multi-Wavelength Fluorescence-Quenching Model for Determination of Cu2+ Conditional Stability Constants and Ligand Concentrations of Fulvic Acid

2003 ◽  
Vol 57 (4) ◽  
pp. 454-460 ◽  
Author(s):  
Michael D. Hays ◽  
David K. Ryan ◽  
Stephen Pennell
Keyword(s):  
Fulvic Acid ◽  
Data Sets ◽  
Conditional Stability ◽  
Intensity Data ◽  
Fluorescence Excitation ◽  
Ph Values ◽  
Synchronous Fluorescence Spectra ◽  
Multi Wavelength ◽  
Conditional Stability Constants

In this work, a multi-wavelength model (MWM) is developed. It uses fluorescence bands in the fulvic acid (FA) spectrum that quench upon binding of inorganic Cu2+ to FA. Quenching data at pH values of 5, 6, and 7 are placed in sets, containing fluorescence measures at select wavelengths versus added copper ( CM). Intensity data of wavelength set 1 are obtained from 25 nm constant offset synchronous fluorescence spectra (SyF), in which are observed distinct peaks (λex = 415 nm, λem = 440 nm; and λex = 471 nm, λem = 496 nm). Wavelength set 2 intensity data are obtained from the FA fluorescence excitation and emission maxima (λex = 335 nm, λem = 450 nm; and λex = 471 nm, λem = 496 nm). Application of MWM shows that the multi-wavelength data sets characterize ligands of different binding strength (log Kx) and concentration ( CLx). Corresponding to pH values of 5, 6, and 7, mean and standard deviation values for wavelength set 1 are log K415/440 = 4.66 (0.12), 5.03 (0.12), and 5.05 (0.08), log K471/496 = 4.93 (0.06), 5.27 (0.11), and 5.39 (0.09), C415/440 = 3.1 (1.5), 10.9 (4.5), and 7.9 (3.9) μM, C471/496 = 14.3 (3.0), 1.7 (0.6), and 1.4 (0.5) μM. And for wavelength set 2, log K335/450 = 4.50 (0.03), 4.96 (0.27), and 5.22 (0.08), log K471/496 = 5.02 (0.04), 5.42 (0.32), and 5.71 (0.09), C335/450 = 8.8 (0.5), 21.9 (7.9), and 18.7 (0.3) μM, C471/496 = 21.0 (2.5), 7.17 (1.2), and 7.09 (0.3) μM. The ability of the 415/440 nm SyF transect to characterize the main excitation and emission maximum of FA at 335/440 nm is evaluated. Relatively low concentration values returned by the model for this transect (415/440 nm) suggest that it is not entirely illustrative of the maximum. The model predictive capability is verified at pH 6 with two fluorescing Cu2+ chelating organic compounds, L-tyrosine and salicylic acid. This test confirms that the model is capable of providing good estimates of equilibrium binding parameters from multi-wavelength measurements of a mixed ligand system.

Direct phase determination and refinement in the electron crystallography of small structures

1993 ◽  
Vol 51 ◽  
pp. 684-685
Author(s):  
Douglas L. Dorset ◽  
Mary P. McCourt
Keyword(s):  
Electron Diffraction ◽  
Scattering Theory ◽  
Heavy Atom ◽  
Intensity Data ◽  
Phase Information ◽  
Diffraction Intensity ◽  
Phase Determination ◽  
X Ray ◽  
Primary Extinction

The use of electron diffraction intensity data for quantitative determination of crystal structures was largely pioneered by Vainshtein, Pinsker and their co-workers, as recently reviewed, and was shown to produce results consistent with more typical X-ray structure analyses. Despite these encouraging results for a number of representative inorganic and organic materials, it is accurate to say that the technique has not been widely accepted by the crystallographic community. This is probably because, in several of the early analyses, contemporary X-ray structure results were used to provide heavy atom positions, thus providing much of the crystallographic phase information. Since it is also known that correct phases, combined with even scrambled structure factor amplitudes, will lead to a Fourier map that appears to be ’correct’, it is commonly (but incorrectly) thought that no ab initio electron diffraction determinations have been carried out for previously unsolved structures. In addition, the very complexity of n-beam dynamical scattering theory compared to ’primary extinction’ corrections has dampened enthusiasm to continue this work.

On the Epicenter Determination of Historical Earthquakes Attested to by Sparse Intensity Data Sets

2017 ◽  
Vol 107 (3) ◽  
pp. 1136-1146 ◽  
Author(s):  
Päivi Mäntyniemi ◽  
Ruben E. Tatevossian ◽  
Roman N. Vakarchuk
Keyword(s):  
Historical Earthquakes ◽  
Data Sets ◽  
Intensity Data

scholarly journals Direct determination of the area function for nanoindentation experiments

2021 ◽  
Author(s):  
Christian Saringer ◽  
Michael Tkadletz ◽  
Markus Kratzer ◽  
Megan J. Cordill
Keyword(s):  
Laser Scanning ◽  
Operation Mode ◽  
Direct Determination ◽  
Fused Silica ◽  
Laser Scanning Microscopy ◽  
Confocal Laser ◽  
Data Sets ◽  
Area Function ◽  
3D Data

Abstract The determination of a suitable correction for tip blunting is crucial in order to obtain useful mechanical properties from nanoindentation experiments. While typically the required area function is acquired from the indentation of a reference material, the direct imaging by suitable methods is an interesting alternative. In this paper, we investigate the applicability of confocal laser scanning microscopy (CLSM), atomic force microscopy (AFM), and self-imaging by scanning a sharp silicon tip using the scanning probe microscopy extension of the nanoindentation system and compare the results to the area function obtained by the indentation of fused silica. The important tip characteristics were determined by various methods based on the analysis of the obtained 3D data sets. It was found that the suitability of CLSM and AFM depend on the resolution and the operation mode, respectively. While for these methods only limited consistency of the determined tip characteristics was found, self-imaging resulted in an excellent overall agreement. Graphic abstract

Enhanced information from biological materials through technological improvements in cryo-electron microscopy

1992 ◽  
Vol 50 (1) ◽  
pp. 788-789
Author(s):  
Marc J.C. de Jong ◽  
Wim M. Busing ◽  
Max T. Otten
Keyword(s):  
Electron Microscopy ◽  
Electron Beam ◽  
Biological Materials ◽  
Electron Crystallography ◽  
Cryo Electron Microscopy ◽  
Transmission Electron ◽  
The Many ◽  
Technological Improvements ◽  
Beam Damage

Biological materials damage rapidly in the electron beam, limiting the amount of information that can be obtained in the transmission electron microscope. The discovery that observation at cryo temperatures strongly reduces beam damage (in addition to making it unnecessaiy to use chemical fixatives, dehydration agents and stains, which introduce artefacts) has given an important step forward to preserving the ‘live’ situation and makes it possible to study the relation between function, chemical composition and morphology.Among the many cryo-applications, the most challenging is perhaps the determination of the atomic structure. Henderson and co-workers were able to determine the structure of the purple membrane by electron crystallography, providing an understanding of the membrane's working as a proton pump. As far as understood at present, the main stumbling block in achieving high resolution appears to be a random movement of atoms or molecules in the specimen within a fraction of a second after exposure to the electron beam, which destroys the highest-resolution detail sought.

Least-square refinement of structure parameters from CBED integrated intensities: application to determination of temperature factors in Y BA2CU3O7

1992 ◽  
Vol 50 (2) ◽  
pp. 1456-1457
Author(s):  
Kjersti Gjønnes ◽  
Jon Gjønnes
Keyword(s):  
Least Square ◽  
Measured Intensity ◽  
Structure Information ◽  
Accurate Temperature ◽  
Least Square Fit ◽  
Case Application ◽  
Integrated Intensities ◽  
Temperature Factors ◽  
Narrow Bands

Electron diffraction intensities can be obtained at large scattering angles (sinθ/λ ≥ 2.0), and thus structure information can be collected in regions of reciprocal space that are not accessable with other diffraction methods. LACBED intensities in this range can be utilized for determination of accurate temperature factors or for refinement of coordinates. Such high index reflections can usually be treated kinematically or as a pertubed two-beam case. Application to Y Ba2Cu3O7 shows that a least square refinememt based on integrated intensities can determine temperature factors or coordinates.LACBED patterns taken in the (00l) systematic row show an easily recognisable pattern of narrow bands from reflections in the range 15 < l < 40 (figure 1). Integrated intensities obtained from measured intensity profiles after subtraction of inelastic background (figure 2) were used in the least square fit for determination of temperature factors and refinement of z-coordinates for the Ba- and Cu-atoms.

Time consumption and quality of an automated fusion tool for SPECT and MRI images of the brain

2003 ◽  
Vol 42 (05) ◽  
pp. 215-219
Author(s):  
G. Platsch ◽  
A. Schwarz ◽  
K. Schmiedehausen ◽  
B. Tomandl ◽  
W. Huk ◽  
...  
Keyword(s):  
Data Sets ◽  
3D Mri ◽  
Clinical Routine ◽  
Fusion Procedure ◽  
3D Data ◽  
Mri Scans ◽  
2D Data ◽  
Time Required ◽  
The Brain ◽  
Manual Correction

Summary: Aim: Although the fusion of images from different modalities may improve diagnostic accuracy, it is rarely used in clinical routine work due to logistic problems. Therefore we evaluated performance and time needed for fusing MRI and SPECT images using a semiautomated dedicated software. Patients, material and Method: In 32 patients regional cerebral blood flow was measured using 99mTc ethylcystein dimer (ECD) and the three-headed SPECT camera MultiSPECT 3. MRI scans of the brain were performed using either a 0,2 T Open or a 1,5 T Sonata. Twelve of the MRI data sets were acquired using a 3D-T1w MPRAGE sequence, 20 with a 2D acquisition technique and different echo sequences. Image fusion was performed on a Syngo workstation using an entropy minimizing algorithm by an experienced user of the software. The fusion results were classified. We measured the time needed for the automated fusion procedure and in case of need that for manual realignment after automated, but insufficient fusion. Results: The mean time of the automated fusion procedure was 123 s. It was for the 2D significantly shorter than for the 3D MRI datasets. For four of the 2D data sets and two of the 3D data sets an optimal fit was reached using the automated approach. The remaining 26 data sets required manual correction. The sum of the time required for automated fusion and that needed for manual correction averaged 320 s (50-886 s). Conclusion: The fusion of 3D MRI data sets lasted significantly longer than that of the 2D MRI data. The automated fusion tool delivered in 20% an optimal fit, in 80% manual correction was necessary. Nevertheless, each of the 32 SPECT data sets could be merged in less than 15 min with the corresponding MRI data, which seems acceptable for clinical routine use.

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