Strategies for data collection on a CCD-diffractometer

2000 ◽  
Vol 215 (9) ◽  
Author(s):  
M. Bolte ◽  
S. Rühl
Keyword(s):  
Crystal Size ◽  
Organic Molecules ◽  
Data Set ◽  
Detector Resolution ◽  
Small Organic Molecules ◽  
X Ray ◽  
Detector Distance ◽  
Complete Set ◽  
Time Scan

The introduction of area detectors has led to a significant reduction of the time needed for measuring a complete set of X-ray reflections. The default parameters suggested by the manufacturer of the instrument lead to good results, but both the software and the hardware provide the possibility of varying numerous parameters in order to optimize the quality of the data set. The influence of parameters (measuring time, scan angle, crystal-to-detector distance, collimator radius, detector resolution, redundancy, crystal size and scan type) is determined and rated with regard to their importance for the quality of the data. The investigations were carried out on a Siemens (now Bruker AXS) CCD diffractometer on three small organic molecules, p-nitrobenzaldehyde diacetate [P2

Quantitative Crystal Structure Analysis In The Electron Microscope

1987 ◽  
Vol 45 ◽  
pp. 434-437
Author(s):  
Douglas L. Dorset
Keyword(s):  
Electron Microscope ◽  
Structure Analysis ◽  
Organic Molecules ◽  
Analytical Techniques ◽  
Crystal Structure Analysis ◽  
Linear Polymers ◽  
X Ray Diffraction ◽  
Electron Crystallography ◽  
Small Organic Molecules ◽  
X Ray

Electron crystallography is a term which has emerged in the past few years to describe the quantitative structure analysis of microcrystalline preparations in the electron microscope. The field represents the confluence of two techniques, i.e. the ultramicroscopic capabilities of the electron microscope coupled with analytical techniques long in use by X-ray crystallographers. In the area of organic materials, the most visible success of the technique to date has been in the structure analysis of thin protein microcrystals typically to ca20 Å resolution but sometimes out to e.g. 7 Å and, in this field, there has been considerable effort by an increasing number of laboratories.Although the electron crystallography of small organic molecules and linear polymers has a much longer history than the application to globular proteins, one cannot cite an overwhelming enthusiasm for this technique, despite its promise as a probe for molecules which are not easily crystallized to sample sizes useful for single crystal X-ray diffraction measurements.

Exploration of a library of triazolothiadiazole and triazolothiadiazine compounds as a highly potent and selective family of cholinesterase and monoamine oxidase inhibitors: design, synthesis, X-ray diffraction analysis and molecular docking studies

RSC Advances ◽  
2015 ◽  
Vol 5 (27) ◽  
pp. 21249-21267 ◽  
Author(s):  
Imtiaz Khan ◽  
Syeda Mahwish Bakht ◽  
Aliya Ibrar ◽  
Saba Abbas ◽  
Shahid Hameed ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Drug Discovery ◽  
Monoamine Oxidase ◽  
Organic Molecules ◽  
Docking Studies ◽  
X Ray Diffraction ◽  
High Demand ◽  
Design Synthesis ◽  
Small Organic Molecules ◽  
X Ray

There is a high demand for the collection of small organic molecules (especially N-heterocycles) with diversity and complexity in the process of drug discovery.

scholarly journals MeshAndCollect: an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines

2015 ◽  
Vol 71 (11) ◽  
pp. 2328-2343 ◽  
Author(s):  
Ulrich Zander ◽  
Gleb Bourenkov ◽  
Alexander N. Popov ◽  
Daniele de Sanctis ◽  
Olof Svensson ◽  
...  
Keyword(s):  
Hierarchical Cluster ◽  
Data Sets ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Partial Data ◽  
Final Data ◽  
Dispersion Technique

Here, an automated procedure is described to identify the positions of many cryocooled crystals mounted on the same sample holder, to rapidly predict and rank their relative diffraction strengths and to collect partial X-ray diffraction data sets from as many of the crystals as desired. Subsequent hierarchical cluster analysis then allows the best combination of partial data sets, optimizing the quality of the final data set obtained. The results of applying the method developed to various systems and scenarios including the compilation of a complete data set from tiny crystals of the membrane protein bacteriorhodopsin and the collection of data sets for successful structure determination using the single-wavelength anomalous dispersion technique are also presented.

X-ray Fluorescence Investigation of Ordered Intermetallic Phases as Electrocatalysts towards the Oxidation of Small Organic Molecules

2010 ◽  
Vol 16 (46) ◽  
pp. 13689-13697 ◽  
Author(s):  
Yi Liu ◽  
Michael A. Lowe ◽  
Ken D. Finkelstein ◽  
Darren S. Dale ◽  
Francis J. DiSalvo ◽  
...  
Keyword(s):  
Organic Molecules ◽  
Intermetallic Phases ◽  
Small Organic Molecules ◽  
X Ray ◽  
Ordered Intermetallic

Highly Sheared Anti-Parallel Dipolar Carbonyl···Carbonyl Interaction in the Crystal Packing of Strapped Crown-3-Pyromellitimide

2012 ◽  
Vol 65 (10) ◽  
pp. 1384 ◽  
Author(s):  
Ethan Nam Wei Howe ◽  
Mohan Bhadbhade ◽  
Pall Thordarson
Keyword(s):  
Molecular Structure ◽  
Torsion Angle ◽  
Organic Molecules ◽  
Crystal Packing ◽  
Dipolar Interactions ◽  
High Dilution ◽  
Small Organic Molecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Structural Architecture

Non-covalent dipolar interactions between pairs of carbonyls have been demonstrated to play a significant role in the crystal packing and formation of supramolecular structural architecture of small organic molecules. Under high dilution, the strapped crown-3-pyromellitimide 4 and macrocyclic crown-6-bispyromellitimide 5 were synthesised in concert and demonstrated selective molecular recognition towards Na+ and K+, respectively. The molecular structure of strapped crown-3-pyromellitimide 4 was solved using X-ray crystallography and an unusual highly sheared anti-parallel dipolar carbonyl···carbonyl interaction was observed in the crystal packing. The intermolecular interaction has a torsion angle of 44.1°, and deviates from the three idealised motifs reported in literature. This finding further highlights the importance and versatility of dipolar carbonyl···carbonyl interaction in the crystal packing of organic molecules.

scholarly journals The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination

2018 ◽  
Author(s):  
Christopher G. Jones ◽  
Michael W. Martynowycz ◽  
Johan Hattne ◽  
Tyler J. Fulton ◽  
Brian M. Stoltz ◽  
...  
Keyword(s):  
Organic Chemistry ◽  
Organic Molecules ◽  
Spectroscopic Techniques ◽  
Small Organic Molecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Minimal Sample ◽  
The Many ◽  
Almost All

<p>In the many scientific endeavors that are driven by organic chemistry, unambiguous identification of small molecules is of paramount importance. Over the past 50 years, NMR and other powerful spectroscopic techniques have been developed to address this challenge. While almost all of these techniques rely on inference of connectivity, the unambiguous determination of a small molecule’s structure requires X-ray and/or neutron diffraction studies. In practice, however, x-ray crystallography is rarely applied in routine organic chemistry due to intrinsic limitations of both the analytes and the technique. Here we report the use of the CryoEM method MicroED to provide routine and unambiguous structural determination of small organic molecules. From simple powders, with minimal sample preparation, we could collect high quality MicroED data from nanocrystals (~100x100x100 nm, ~10<sup>–15</sup>g) resulting in atomic resolution (<1 Å) crystal structures in minutes.</p>

scholarly journals Modeling and Molecular Dyanamics Simulations Study of Enol-carbonates and their Derivatives

2018 ◽  
Vol 19 (2) ◽  
pp. 139-148
Author(s):  
Miljan Bigovic ◽  
Luka Filipovic ◽  
Zarko Zecevic ◽  
Bozo Krstajic
Keyword(s):  
Carbonyl Compounds ◽  
Organic Molecules ◽  
X Ray Diffraction ◽  
Dynamic Simulations ◽  
Small Organic Molecules ◽  
X Ray ◽  
Software Packages ◽  
Vis Spectroscopy ◽  
Barbier Reaction ◽  
Final Confirmation

In view of the fact that the mechanisms of the interaction of organic molecules with the properties of the drug occur in most cases by their binding to the receptors (proteins), we wanted to examine the interactions of small organic molecules that we synthesized and certain proteins. In this paper the comparison between molecules, modeled by different software packages, and experimental results is performed. The series of new molecules are synthesized using Barbier reaction of allylation of carbonyl compounds with 4-(bromomethyl)-1,3-dioxol-2-one as a highly fictionalized allylic synthon. Their structure was determined by spectroscopic methods (NMR-, IR- and UV/VIS-spectroscopy and MS-spectrometry), while for three individual molecules analysis of x-ray diffraction (X-ray analysis) was also performed, which gave the final confirmation of the exact arrangement of all atoms in the space. The molecules are represented in standard chemical format, visualized and prepared for simulations. In order to obtain datasets that further can be used to examine and analyze interactions with well-known proteins, molecular dynamic simulations are performed. The purpose of this research was to present that using powerful computer infrastructure and appropriate software tools, an accurate molecule models can be created.

scholarly journals Predicting the Skin Sensitization Potential of Small Molecules with Machine Learning Models Trained on Biologically Meaningful Descriptors

2021 ◽  
Vol 14 (8) ◽  
pp. 790
Author(s):  
Anke Wilm ◽  
Marina Garcia de Lomana ◽  
Conrad Stork ◽  
Neann Mathai ◽  
Steffen Hirte ◽  
...  
Keyword(s):  
Machine Learning ◽  
Organic Molecules ◽  
Academic Research ◽  
Skin Sensitization ◽  
Learning Models ◽  
Data Set ◽  
Molecular Fingerprints ◽  
Small Organic Molecules ◽  
Significance Level ◽  
Machine Learning Models

In recent years, a number of machine learning models for the prediction of the skin sensitization potential of small organic molecules have been reported and become available. These models generally perform well within their applicability domains but, as a result of the use of molecular fingerprints and other non-intuitive descriptors, the interpretability of the existing models is limited. The aim of this work is to develop a strategy to replace the non-intuitive features by predicted outcomes of bioassays. We show that such replacement is indeed possible and that as few as ten interpretable, predicted bioactivities are sufficient to reach competitive performance. On a holdout data set of 257 compounds, the best model (“Skin Doctor CP:Bio”) obtained an efficiency of 0.82 and an MCC of 0.52 (at the significance level of 0.20). Skin Doctor CP:Bio is available free of charge for academic research. The modeling strategies explored in this work are easily transferable and could be adopted for the development of more interpretable machine learning models for the prediction of the bioactivity and toxicity of small organic compounds.

Global indicators of X-ray data quality

2001 ◽  
Vol 34 (2) ◽  
pp. 130-135 ◽  
Author(s):  
Manfred S. Weiss
Keyword(s):  
Data Quality ◽  
Diffraction Data ◽  
Optical Resolution ◽  
Data Set ◽  
X Ray ◽  
Global Indicators ◽  
Nominal Resolution

Global indicators of the quality of diffraction data are presented and discussed, and are evaluated in terms of their performance with respect to various tasks. Based on the results obtained, it is suggested that some of the conventional indicators still in use in the crystallographic community should be abandoned, such as the nominal resolutiondminor the mergingRfactorRmerge, and replaced by more objective and more meaningful numbers, such as the effective optical resolutiondeff,optand the redundancy-independent mergingRfactorRr.i.m.. Furthermore, it is recommended that the precision-indicating mergingRfactorRp.i.m.should be reported with every diffraction data set published, because it describes the precision of the averaged measurements, which are the quantities normally used in crystallography as observables.

Sign in / Sign up

Export Citation Format

Share Document